RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4665
(673 letters)
>gnl|CDD|223606 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 453 bits (1168), Expect = e-153
Identities = 209/557 (37%), Positives = 296/557 (53%), Gaps = 61/557 (10%)
Query: 114 RPPVVTIMGHVDHGKTTLLDTLRNTSVVKSEFGGITQHIGAFVVTLKSGE--QVTFLDTP 171
RPPVVTIMGHVDHGKTTLLD +R T+V E GGITQHIGA+ V L + +TF+DTP
Sbjct: 4 RPPVVTIMGHVDHGKTTLLDKIRKTNVAAGEAGGITQHIGAYQVPLDVIKIPGITFIDTP 63
Query: 172 GHAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMAREAKVPIIVAINKIDKPAAD 231
GH AF+ MR+RGA TDI +LVVAADDGVM QT+E+I A+ A VPI+VAINKIDKP A+
Sbjct: 64 GHEAFTAMRARGASVTDIAILVVAADDGVMPQTIEAINHAKAAGVPIVVAINKIDKPEAN 123
Query: 232 IERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIERTKNMLLAQGITVEDLG 291
++ K L E G+ E+ G
Sbjct: 124 PDKVKQ------------------------------ELQE-----------YGLVPEEWG 142
Query: 292 GDIQAVPISALTGTNVDNLTEAIVAQAEIMHLKADYGGPVEAMIVESKFDTHRGKLATAL 351
GD+ VP+SA TG +D L E I+ AE++ LKA+ GP ++E K D G +AT +
Sbjct: 143 GDVIFVPVSAKTGEGIDELLELILLLAEVLELKANPEGPARGTVIEVKLDKGLGPVATVI 202
Query: 352 VQRGTLKKGAIVVAGQAWAKVRSISRKTLINTALGTVQRTSGTVKISLGFKINPFCPSGD 411
VQ GTLKKG I+VAG + +VR++ S V+I LG P +GD
Sbjct: 203 VQDGTLKKGDIIVAGGEYGRVRTMVDDLGKPIKEAGP---SKPVEI-LGLSEVPA--AGD 256
Query: 412 VDGSVEALLDVFD--TYTSALCRLDIVHYGVT-STDQWRRYWTCSTPTRESKHGRIYLIG 468
V V+ L R + ++ +E + L
Sbjct: 257 VFIVVKDEKKARAIAELRVVLLREAELASKKKGELEELIAEIKIRGELKELN---VILKA 313
Query: 469 DVDGSVEALLDVFDTYTSALCRLDIVHYGVGQVSATDVELATLFNAIIYTFNTTLHPAAK 528
D GS+EAL ++ I+H GVG ++ +DV LA +A+I FN + P A+
Sbjct: 314 DTQGSLEALKGSLKKLGVDEVKVRIIHAGVGGITESDVMLAAASDAVIIGFNVRVDPEAR 373
Query: 529 TSAEELGVTVKQFNVIYKLVEDVKEEINAMLPHTYAEEVLGEANVLQMFLITDGKKKVP- 587
AE GV ++ ++VIYKL+EDV+ + ML E V+G A V +F + KV
Sbjct: 374 RLAESEGVKIRYYDVIYKLIEDVEAAMKGMLEPEKKERVIGLAEVRAVFKL----PKVGA 429
Query: 588 VAGCRCSKGVLKKNALFKLVRRNEVLFEGKLESMKHLKEEVTSIKKELECGLRLEDPSIE 647
+AGC ++GV+K+ A ++VR V++EG++ES+K K++V ++K ECG+ +E+ +
Sbjct: 430 IAGCMVTEGVIKRGAPVRVVRDGVVIYEGEVESLKRFKDDVKEVRKGQECGIAIENYR-D 488
Query: 648 FEPGDTIVCFVKNKVPQ 664
+ GD + F +V +
Sbjct: 489 IKEGDILEVFEPVEVKR 505
>gnl|CDD|232995 TIGR00487, IF-2, translation initiation factor IF-2. This model
discriminates eubacterial (and mitochondrial)
translation initiation factor 2 (IF-2), encoded by the
infB gene in bacteria, from similar proteins in the
Archaea and Eukaryotes. In the bacteria and in
organelles, the initiator tRNA is charged with
N-formyl-Met instead of Met. This translation factor
acts in delivering the initator tRNA to the ribosome. It
is one of a number of GTP-binding translation factors
recognized by the pfam model GTP_EFTU [Protein
synthesis, Translation factors].
Length = 587
Score = 406 bits (1046), Expect = e-134
Identities = 213/564 (37%), Positives = 310/564 (54%), Gaps = 72/564 (12%)
Query: 109 SVLMKRPPVVTIMGHVDHGKTTLLDTLRNTSVVKSEFGGITQHIGAFVVTLKSGEQVTFL 168
+L++RPPVVTIMGHVDHGKT+LLD++R T V + E GGITQHIGA+ V + G+ +TFL
Sbjct: 81 DLLVERPPVVTIMGHVDHGKTSLLDSIRKTKVAQGEAGGITQHIGAYHVENEDGKMITFL 140
Query: 169 DTPGHAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMAREAKVPIIVAINKIDKP 228
DTPGH AF++MR+RGA TDIVVLVVAADDGVM QT+E+I A+ A VPIIVAINKIDKP
Sbjct: 141 DTPGHEAFTSMRARGAKVTDIVVLVVAADDGVMPQTIEAISHAKAANVPIIVAINKIDKP 200
Query: 229 AADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIERTKNMLLAQGITVE 288
A+ +R K L G+ VP E
Sbjct: 201 EANPDRVKQELSEYGL-----------VP------------------------------E 219
Query: 289 DLGGDIQAVPISALTGTNVDNLTEAIVAQAEIMHLKADYGGPVEAMIVESKFDTHRGKLA 348
D GGD VP+SALTG +D L + I+ Q+E+ LKA+ G +++E++ D RG +A
Sbjct: 220 DWGGDTIFVPVSALTGDGIDELLDMILLQSEVEELKANPNGQASGVVIEAQLDKGRGPVA 279
Query: 349 TALVQRGTLKKGAIVVAGQAWAKVRSISRKTLINTALGTVQRTSGTVKIS-LGFKINPFC 407
T LVQ GTL+ G IVV G A+ +VR +I+ +V+ + + LG P
Sbjct: 280 TVLVQSGTLRVGDIVVVGAAYGRVR-----AMIDENGKSVKEAGPSKPVEILGLSDVP-- 332
Query: 408 PSGDVDGSVEALLDVFDTYTSALCRLDIVHYGVTSTDQWRRYWTCSTP---------TRE 458
+GD VF A RL + Q + E
Sbjct: 333 AAGDE-------FIVFKDEKDA--RL-VAEKRAGKLRQKALSRSVKVTLDNLFEQIKEGE 382
Query: 459 SKHGRIYLIGDVDGSVEALLDVFDTYTSALCRLDIVHYGVGQVSATDVELATLFNAIIYT 518
K I L DV GS+EA+ + + + ++ ++H GVG ++ TD+ LA+ NAII
Sbjct: 383 LKELNIILKADVQGSLEAIKNSLEKLNNEEVKVKVIHSGVGGITETDISLASASNAIIIG 442
Query: 519 FNTTLHPAAKTSAEELGVTVKQFNVIYKLVEDVKEEINAMLPHTYAEEVLGEANVLQMFL 578
FN AK AE V ++ ++VIYKL+++++ + ML Y EE++G+A V Q+F
Sbjct: 443 FNVRPDATAKNVAEAENVDIRYYSVIYKLIDEIRAAMKGMLDPEYEEEIIGQAEVRQVFN 502
Query: 579 ITDGKKKVPVAGCRCSKGVLKKNALFKLVRRNEVLFEGKLESMKHLKEEVTSIKKELECG 638
+ K +AGC ++GV+K+ +++R V+FEG+++S+K K++V + ECG
Sbjct: 503 VP---KIGNIAGCYVTEGVIKRGNPLRVIRDGVVIFEGEIDSLKRFKDDVKEVSNGYECG 559
Query: 639 LRLEDPSIEFEPGDTIVCFVKNKV 662
+ +++ + + + GD I F +V
Sbjct: 560 IGIKNYN-DIKEGDIIEAFEVQEV 582
>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional.
Length = 742
Score = 386 bits (993), Expect = e-124
Identities = 226/637 (35%), Positives = 328/637 (51%), Gaps = 98/637 (15%)
Query: 36 IDIIQKSDHLYEVMMYVDNSVNYDRPSSVIYDFQVIIDIIQKSGMKYMVINPTNSVADDS 95
+II KS L + + V+ ++ S V DF + I +K+ + N N+ A
Sbjct: 180 TEII-KSLFLKGISVTVNQIIDISIISQVADDFGINIISEEKNNINEKTSNLDNTSAFTE 238
Query: 96 NGKDVERRPPADPSVLMKRPPVVTIMGHVDHGKTTLLDTLRNTSVVKSEFGGITQHIGAF 155
N + RPP+VTI+GHVDHGKTTLLD +R T + + E GGITQ IGA+
Sbjct: 239 N--------------SINRPPIVTILGHVDHGKTTLLDKIRKTQIAQKEAGGITQKIGAY 284
Query: 156 VVTLK---SGEQVTFLDTPGHAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMAR 212
V + +++ FLDTPGH AFS+MRSRGA+ TDI +L++AADDGV QT+E+I +
Sbjct: 285 EVEFEYKDENQKIVFLDTPGHEAFSSMRSRGANVTDIAILIIAADDGVKPQTIEAINYIQ 344
Query: 213 EAKVPIIVAINKIDKPAADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEA 272
A VPIIVAINKIDK A+ ER K L + I
Sbjct: 345 AANVPIIVAINKIDKANANTERIKQQLAKYNL-------------IP------------- 378
Query: 273 IERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIVAQAEIMHLKADYGGPVE 332
E GGD +PISA GTN+D L E I+ AEI LKAD +
Sbjct: 379 ---------------EKWGGDTPMIPISASQGTNIDKLLETILLLAEIEDLKADPTQLAQ 423
Query: 333 AMIVESKFDTHRGKLATALVQRGTLKKGAIVVAGQAWAKVRSISRKTLINTALGTVQRTS 392
+I+E+ D +G +AT LVQ GTL G I+V G ++AK+R + IN
Sbjct: 424 GIILEAHLDKTKGPVATILVQNGTLHIGDIIVIGTSYAKIRGM-----IN---------- 468
Query: 393 GTVKISLGFKINPFCPSGDVDGSVEALLDVFDTYTSALC-------RLDIVHYGVTSTDQ 445
SLG KIN PS V+ + L V T +L I+ +
Sbjct: 469 -----SLGNKINLATPSSVVE--IWGLSSVPATGEHFQVFNSEKEAKLKIIKNKENNKKD 521
Query: 446 WRRYWTCSTP---TRESKHGRIYLI--GDVDGSVEALLDVFDTYTSALCRLDIVHYGVGQ 500
+ T ST ++ +I LI D GS+EA+++ +L+I++ +G+
Sbjct: 522 TTKRITLSTTKTINKKDNKKQINLIIKTDTQGSIEAIINSISQIPQKKVQLNILYASLGE 581
Query: 501 VSATDVELATLFNAIIYTFNTTLHPAAKTSAEELGVTVKQFNVIYKLVEDVKEEINAMLP 560
V+ TDVE A+ NA I FNT L P AK +A +L + +K++ VIY L+E ++ + +L
Sbjct: 582 VTETDVEFASTTNAEILAFNTNLAPGAKKAARKLNIIIKEYQVIYDLLEYIEALMEDLLD 641
Query: 561 HTYAEEVLGEANVLQMFLITDGKKKVPVAGCRCSKGVLKKNALFKLVRRNEVLFEGKLES 620
Y + +GEA V +F + VAGCR ++G + KNAL K++R N++++EGK+ S
Sbjct: 642 PEYKKVPIGEAEVKTVFPLAKRF----VAGCRVTEGKITKNALIKVIRENKLIYEGKITS 697
Query: 621 MKHLKEEVTSIKKELECGLRLEDPSIEFEPGDTIVCF 657
+K +KE+V ++ ECG+ +E+ ++ GD I F
Sbjct: 698 LKRVKEDVEEAQEGNECGIFIEEFQ-LWQSGDKIHAF 733
>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated.
Length = 746
Score = 367 bits (944), Expect = e-117
Identities = 140/313 (44%), Positives = 180/313 (57%), Gaps = 52/313 (16%)
Query: 73 DIIQKSGMKYMVINPTNSVADDS-------NGKDVERRPPAD---PSVLMKRPPVVTIMG 122
++I+K ++ S+ ++ G +V+ + L+ RPPVVTIMG
Sbjct: 197 EVIKKLFKLGVMATINQSLDQETAELLAEEFGHEVKLVSLLEDDDEEDLVPRPPVVTIMG 256
Query: 123 HVDHGKTTLLDTLRNTSVVKSEFGGITQHIGAFVVTLKSGEQVTFLDTPGHAAFSNMRSR 182
HVDHGKT+LLD +R T+V E GGITQHIGA+ V G ++TFLDTPGH AF+ MR+R
Sbjct: 257 HVDHGKTSLLDAIRKTNVAAGEAGGITQHIGAYQVETN-GGKITFLDTPGHEAFTAMRAR 315
Query: 183 GAHCTDIVVLVVAADDGVMEQTVESIRMAREAKVPIIVAINKIDKPAADIERTKNMLLAQ 242
GA TDIVVLVVAADDGVM QT+E+I A+ A VPIIVAINKIDKP A+ +R K L
Sbjct: 316 GAQVTDIVVLVVAADDGVMPQTIEAINHAKAAGVPIIVAINKIDKPGANPDRVKQELSEY 375
Query: 243 GITVEDLGGDIQAVPISALTGTNVDNLTEAIERTKNMLLAQGITVEDLGGDIQAVPISAL 302
G+ E+ GGD VP+SA TG +D L EAI LL
Sbjct: 376 GLVPEEWGGDTIFVPVSAKTGEGIDELLEAI------LL--------------------- 408
Query: 303 TGTNVDNLTEAIVAQAEIMHLKADYGGPVEAMIVESKFDTHRGKLATALVQRGTLKKGAI 362
QAE++ LKA+ P ++E+K D RG +AT LVQ GTLK G I
Sbjct: 409 --------------QAEVLELKANPDRPARGTVIEAKLDKGRGPVATVLVQNGTLKVGDI 454
Query: 363 VVAGQAWAKVRSI 375
VVAG + +VR++
Sbjct: 455 VVAGTTYGRVRAM 467
Score = 176 bits (448), Expect = 1e-46
Identities = 72/201 (35%), Positives = 122/201 (60%), Gaps = 12/201 (5%)
Query: 468 GDVDGSVEALLDVFDTYTSALCRLDIVHYGVGQVSATDVELATLFNAIIYTFNTTLHPAA 527
DV GSVEAL D + ++ +++I+H GVG ++ +DV LA NAII FN A
Sbjct: 553 ADVQGSVEALKDSLEKLSTDEVKVNIIHSGVGAITESDVTLAAASNAIIIGFNVRPDAKA 612
Query: 528 KTSAEELGVTVKQFNVIYKLVEDVKEEINAMLPHTYAEEVLGEANVLQMFLITDGKKKVP 587
+ AE+ GV ++ +++IY L++DVK ++ ML Y EE++G+A V ++F KV
Sbjct: 613 RKLAEQEGVDIRYYSIIYDLIDDVKAAMSGMLEPEYEEEIIGQAEVREVF-------KVS 665
Query: 588 ----VAGCRCSKGVLKKNALFKLVRRNEVLFEGKLESMKHLKEEVTSIKKELECGLRLED 643
+AGC ++G +K+NA +++R V++EG+LES+K K++V ++ ECG+ LE+
Sbjct: 666 KVGTIAGCMVTEGKIKRNAKVRVLRDGVVIYEGELESLKRFKDDVKEVRAGYECGIGLEN 725
Query: 644 PSIEFEPGDTIVCFVKNKVPQ 664
+ + + GD I + +V +
Sbjct: 726 YN-DIKEGDIIEAYEMVEVKR 745
Score = 29.8 bits (68), Expect = 5.2
Identities = 15/38 (39%), Positives = 23/38 (60%), Gaps = 3/38 (7%)
Query: 410 GDVDGSVEALLDVFDTYTSALCRLDIVHYGV---TSTD 444
DV GSVEAL D + ++ +++I+H GV T +D
Sbjct: 553 ADVQGSVEALKDSLEKLSTDEVKVNIIHSGVGAITESD 590
>gnl|CDD|206674 cd01887, IF2_eIF5B, Initiation Factor 2 (IF2)/ eukaryotic
Initiation Factor 5B (eIF5B) family. IF2/eIF5B
contribute to ribosomal subunit joining and function as
GTPases that are maximally activated by the presence of
both ribosomal subunits. As seen in other GTPases,
IF2/IF5B undergoes conformational changes between its
GTP- and GDP-bound states. Eukaryotic IF2/eIF5Bs possess
three characteristic segments, including a divergent
N-terminal region followed by conserved central and
C-terminal segments. This core region is conserved among
all known eukaryotic and archaeal IF2/eIF5Bs and
eubacterial IF2s.
Length = 169
Score = 277 bits (711), Expect = 4e-90
Identities = 105/172 (61%), Positives = 125/172 (72%), Gaps = 9/172 (5%)
Query: 116 PVVTIMGHVDHGKTTLLDTLRNTSVVKSEFGGITQHIGAFVVTLK-SGEQVTFLDTPGHA 174
PVVT+MGHVDHGKTTLLD +R T+V E GGITQHIGA+ V + +TF+DTPGH
Sbjct: 1 PVVTVMGHVDHGKTTLLDKIRKTNVAAGEAGGITQHIGAYQVPIDVKIPGITFIDTPGHE 60
Query: 175 AFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMAREAKVPIIVAINKIDKP---AAD 231
AF+NMR+RGA TDI +LVVAADDGVM QT+E+I A+ A VPIIVAINKIDKP AD
Sbjct: 61 AFTNMRARGASVTDIAILVVAADDGVMPQTIEAINHAKAANVPIIVAINKIDKPYGTEAD 120
Query: 232 IERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIERTKNMLLAQ 283
ER KN L G+ E+ GGD+ VPISA TG +D+L EAI +LLA+
Sbjct: 121 PERVKNELSELGLVGEEWGGDVSIVPISAKTGEGIDDLLEAI-----LLLAE 167
>gnl|CDD|215653 pfam00009, GTP_EFTU, Elongation factor Tu GTP binding domain. This
domain contains a P-loop motif, also found in several
other families such as pfam00071, pfam00025 and
pfam00063. Elongation factor Tu consists of three
structural domains, this plus two C-terminal beta barrel
domains.
Length = 184
Score = 173 bits (440), Expect = 2e-50
Identities = 68/181 (37%), Positives = 91/181 (50%), Gaps = 19/181 (10%)
Query: 113 KRPPVVTIMGHVDHGKTTLLDTLRNTSVVKSE----------------FGGITQHIGAFV 156
KR + I+GHVDHGKTTL D L + S+ GIT I A
Sbjct: 1 KRHRNIGIIGHVDHGKTTLTDALLYVTGAISKESAKGARVLDKLKEERERGITIKIAAVS 60
Query: 157 VTLKSGEQVTFLDTPGHAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMAREAKV 216
K + +DTPGH F+ RGA D +LVV A +GVM QT E + +A+ V
Sbjct: 61 FETKKR-LINIIDTPGHVDFTKEMIRGASQADGAILVVDAVEGVMPQTREHLLLAKTLGV 119
Query: 217 PIIVAINKIDKPA-ADIERTKNMLLAQGITVEDLGGD-IQAVPISALTGTNVDNLTEAIE 274
PIIV INKID+ A++E + + + GG+ + VP SALTG +D L EA++
Sbjct: 120 PIIVFINKIDRVDDAELEEVVEEISRELLEKYGFGGETVPVVPGSALTGEGIDELLEALD 179
Query: 275 R 275
Sbjct: 180 L 180
>gnl|CDD|235195 PRK04004, PRK04004, translation initiation factor IF-2; Validated.
Length = 586
Score = 158 bits (401), Expect = 4e-41
Identities = 60/131 (45%), Positives = 80/131 (61%), Gaps = 17/131 (12%)
Query: 114 RPPVVTIMGHVDHGKTTLLDTLRNTSVVKSEFGGITQHIGAFVVTLKSGEQVT------- 166
R P+V ++GHVDHGKTTLLD +R T+V E GGITQHIGA V + E++
Sbjct: 5 RQPIVVVLGHVDHGKTTLLDKIRGTAVAAKEAGGITQHIGATEVPIDVIEKIAGPLKKPL 64
Query: 167 ----------FLDTPGHAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMAREAKV 216
F+DTPGH AF+N+R RG DI +LVV ++G QT+E+I + + K
Sbjct: 65 PIKLKIPGLLFIDTPGHEAFTNLRKRGGALADIAILVVDINEGFQPQTIEAINILKRRKT 124
Query: 217 PIIVAINKIDK 227
P +VA NKID+
Sbjct: 125 PFVVAANKIDR 135
Score = 48.6 bits (117), Expect = 8e-06
Identities = 20/67 (29%), Positives = 33/67 (49%), Gaps = 6/67 (8%)
Query: 498 VGQVSATDVELATL------FNAIIYTFNTTLHPAAKTSAEELGVTVKQFNVIYKLVEDV 551
VG +S DV A+ +I FN + P A+ AE+ V + +VIY+L+ED
Sbjct: 385 VGDISKRDVIEASTVAEKDPLYGVILAFNVKVLPDAEEEAEKSDVKIFTGDVIYQLIEDY 444
Query: 552 KEEINAM 558
++ +
Sbjct: 445 EKWVKEQ 451
Score = 30.9 bits (71), Expect = 2.3
Identities = 27/88 (30%), Positives = 44/88 (50%), Gaps = 11/88 (12%)
Query: 297 VPISALTGTNVDNLTEAIV--AQ---AEIMHLKADYGGPVEAMIVESKFDTHRGKLATAL 351
VP+SA TG + +L + AQ E + + + GP + ++E K + G +
Sbjct: 196 VPVSAKTGEGIPDLLMVLAGLAQRYLEERLKIDVE--GPGKGTVLEVKEERGLGTTIDVI 253
Query: 352 VQRGTLKKG-AIVVAGQ---AWAKVRSI 375
+ GTL+KG IVV G+ KVR++
Sbjct: 254 LYDGTLRKGDTIVVGGKDGPIVTKVRAL 281
>gnl|CDD|129582 TIGR00491, aIF-2, translation initiation factor aIF-2/yIF-2. This
model describes archaeal and eukaryotic orthologs of
bacterial IF-2. Like IF-2, it helps convey the initiator
tRNA to the ribosome, although the initiator is
N-formyl-Met in bacteria and Met here. This protein is
not closely related to the subunits of eIF-2 of
eukaryotes, which is also involved in the initiation of
translation. The aIF-2 of Methanococcus jannaschii
contains a large intein interrupting a region of very
strongly conserved sequence very near the amino end; the
alignment generated by This model does not correctly
align the sequences from Methanococcus jannaschii and
Pyrococcus horikoshii in this region [Protein synthesis,
Translation factors].
Length = 590
Score = 144 bits (364), Expect = 2e-36
Identities = 87/280 (31%), Positives = 128/280 (45%), Gaps = 43/280 (15%)
Query: 114 RPPVVTIMGHVDHGKTTLLDTLRNTSVVKSEFGGITQHIGAFVVTLKSGEQVT------- 166
R P+V+++GHVDHGKTTLLD +R ++V K E GGITQHIGA + + E +
Sbjct: 3 RSPIVSVLGHVDHGKTTLLDKIRGSAVAKREAGGITQHIGATEIPMDVIEGICGDLLKKF 62
Query: 167 ----------FLDTPGHAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMAREAKV 216
F+DTPGH AF+N+R RG D+ +L+V ++G QT E++ + R K
Sbjct: 63 KIRLKIPGLLFIDTPGHEAFTNLRKRGGALADLAILIVDINEGFKPQTQEALNILRMYKT 122
Query: 217 PIIVAINKIDK-PAADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIER 275
P +VA NKID+ P + + + S NL +
Sbjct: 123 PFVVAANKIDRIPGWRSHEGRPFMES----------------FSKQEIQVQQNLDTKVYN 166
Query: 276 TKNMLLAQGITVE------DLGGDIQAVPISALTGTNVDNLTEAIVAQAEIM---HLKAD 326
L +G E D + +PISA+TG + L + A+ LK +
Sbjct: 167 LVIKLHEEGFEAERFDRVTDFTKTVAIIPISAITGEGIPELLTMLAGLAQQYLEEQLKLE 226
Query: 327 YGGPVEAMIVESKFDTHRGKLATALVQRGTLKKGAIVVAG 366
GP I+E K +T G A++ G L+KG +
Sbjct: 227 EEGPARGTILEVKEETGLGMTIDAVIYDGILRKGDTIAMA 266
Score = 35.2 bits (81), Expect = 0.11
Identities = 27/99 (27%), Positives = 48/99 (48%), Gaps = 13/99 (13%)
Query: 464 IYLIGDVDGSVEALLDVFDTYTSALCRLDIVHYGVGQVSATDV-------ELATLFNAII 516
+ + D GS+EAL++ + + DI G VS DV + ++ AII
Sbjct: 354 VVVKADTLGSLEALVNELRDMGVPIKKADI-----GDVSKRDVVEAGIAKQEDRVYGAII 408
Query: 517 YTFNTTLHPAAKTSAEELGVTVKQFNVIYKLVEDVKEEI 555
FN + P A+ ++ + + N+IY+L+E+ +E I
Sbjct: 409 -AFNVKVLPGAEQELKKYDIKLFSDNIIYRLMEEFEEWI 446
>gnl|CDD|206647 cd00881, GTP_translation_factor, GTP translation factor family
primarily contains translation initiation, elongation
and release factors. The GTP translation factor family
consists primarily of translation initiation,
elongation, and release factors, which play specific
roles in protein translation. In addition, the family
includes Snu114p, a component of the U5 small nuclear
riboprotein particle which is a component of the
spliceosome and is involved in excision of introns,
TetM, a tetracycline resistance gene that protects the
ribosome from tetracycline binding, and the unusual
subfamily CysN/ATPS, which has an unrelated function
(ATP sulfurylase) acquired through lateral transfer of
the EF1-alpha gene and development of a new function.
Length = 183
Score = 116 bits (293), Expect = 4e-30
Identities = 64/178 (35%), Positives = 87/178 (48%), Gaps = 23/178 (12%)
Query: 118 VTIMGHVDHGKTTLLDTLRNTSVVKSEFG----------------GITQHIGAFVVTLKS 161
V ++GHVDHGKTTL +L + G GIT G VV +
Sbjct: 2 VGVIGHVDHGKTTLTGSLLYQTGAIDRRGTRKETFLDTLKEERERGITIKTG--VVEFEW 59
Query: 162 GE-QVTFLDTPGHAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMAREAKVPIIV 220
+ ++ F+DTPGH FS RG D +LVV A++GV QT E + +A +PIIV
Sbjct: 60 PKRRINFIDTPGHEDFSKETVRGLAQADGALLVVDANEGVEPQTREHLNIALAGGLPIIV 119
Query: 221 AINKIDK-PAADIERTKNM---LLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIE 274
A+NKID+ D + LL G D+ +PISALTG ++ L +AI
Sbjct: 120 AVNKIDRVGEEDFDEVLREIKELLKLIGFTFLKGKDVPIIPISALTGEGIEELLDAIV 177
>gnl|CDD|239663 cd03692, mtIF2_IVc, mtIF2_IVc: this family represents the C2
subdomain of domain IV of mitochondrial translation
initiation factor 2 (mtIF2) which adopts a beta-barrel
fold displaying a high degree of structural similarity
with domain II of the translation elongation factor
EF-Tu. The C-terminal part of mtIF2 contains the entire
fMet-tRNAfmet binding site of IF-2 and is resistant to
proteolysis. This C-terminal portion consists of two
domains, IF2 C1 and IF2 C2. IF2 C2 been shown to
contain all molecular determinants necessary and
sufficient for the recognition and binding of
fMet-tRNAfMet. Like IF2 from certain prokaryotes such as
Thermus thermophilus, mtIF2lacks domain II which is
thought to be involved in binding of E.coli IF-2 to 30S
subunits.
Length = 84
Score = 100 bits (252), Expect = 9e-26
Identities = 34/88 (38%), Positives = 54/88 (61%), Gaps = 4/88 (4%)
Query: 569 GEANVLQMFLITDGKKKVPVAGCRCSKGVLKKNALFKLVRRNEVLFEGKLESMKHLKEEV 628
GEA V +F I+ K +AGC + G +K+NA +++R EV++EGK+ S+K K++V
Sbjct: 1 GEAEVRAVFKIS---KVGNIAGCYVTDGKIKRNAKVRVLRNGEVIYEGKISSLKRFKDDV 57
Query: 629 TSIKKELECGLRLEDPSIEFEPGDTIVC 656
+KK ECG+ LE+ + + GD I
Sbjct: 58 KEVKKGYECGITLEN-FNDIKVGDIIEA 84
>gnl|CDD|237833 PRK14845, PRK14845, translation initiation factor IF-2;
Provisional.
Length = 1049
Score = 112 bits (282), Expect = 1e-25
Identities = 88/274 (32%), Positives = 128/274 (46%), Gaps = 39/274 (14%)
Query: 129 TTLLDTLRNTSVVKSEFGGITQHIGAFVVTLKSGEQVT-----------------FLDTP 171
TTLLD +R T V K E GGITQHIGA + + +++ F+DTP
Sbjct: 475 TTLLDKIRKTRVAKKEAGGITQHIGATEIPIDVIKKICGPLLKLLKAEIKIPGLLFIDTP 534
Query: 172 GHAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMAREAKVPIIVAINKIDK-PAA 230
GH AF+++R RG D+ VLVV ++G QT+E+I + R+ K P +VA NKID P
Sbjct: 535 GHEAFTSLRKRGGSLADLAVLVVDINEGFKPQTIEAINILRQYKTPFVVAANKIDLIPGW 594
Query: 231 DIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIERTKNMLLAQGI--TVE 288
+I + LL + ALT + L E I + + V+
Sbjct: 595 NISEDEPFLL-----------NFNEQDQHALTELEI-KLYELIGKLYELGFDADRFDRVQ 642
Query: 289 DLGGDIQAVPISALTGTNVDNLTEAIVAQAEIM---HLKADYGGPVEAMIVESKFDTHRG 345
D + VP+SA TG + L + A+ LK + G + I+E K + G
Sbjct: 643 DFTRTVAIVPVSAKTGEGIPELLMMVAGLAQKYLEERLKLNVEGYAKGTILEVKEEKGLG 702
Query: 346 KLATALVQRGTLKKG-AIVVAGQAWA---KVRSI 375
A++ GTL++G IVV G KVR++
Sbjct: 703 TTIDAIIYDGTLRRGDTIVVGGPDDVIVTKVRAL 736
Score = 43.7 bits (103), Expect = 3e-04
Identities = 26/67 (38%), Positives = 35/67 (52%), Gaps = 10/67 (14%)
Query: 498 VGQVSATDV-ELATL-----FNAIIYTFNTTLHPAAKTSAEELGVTVKQFNVIYKLVED- 550
VG ++ DV E + +I FN + P A+ AE+ GV + N+IYKLVED
Sbjct: 841 VGDITKKDVIEALSYKQENPLYGVILGFNVKVLPEAQEEAEKYGVKIFVDNIIYKLVEDY 900
Query: 551 ---VKEE 554
VKEE
Sbjct: 901 TEWVKEE 907
Score = 34.1 bits (78), Expect = 0.29
Identities = 16/36 (44%), Positives = 21/36 (58%), Gaps = 4/36 (11%)
Query: 114 RPPVVTIMGHVDHGKTTLLDTLRNTSVVKSEFGGIT 149
R P+V ++GHVDHGK L + V+ E G IT
Sbjct: 9 RCPIVAVLGHVDHGKCLLPE----EKVILPEHGLIT 40
>gnl|CDD|232886 TIGR00231, small_GTP, small GTP-binding protein domain. Proteins
with a small GTP-binding domain recognized by this model
include Ras, RhoA, Rab11, translation elongation factor
G, translation initiation factor IF-2, tetratcycline
resistance protein TetM, CDC42, Era, ADP-ribosylation
factors, tdhF, and many others. In some proteins the
domain occurs more than once.This model recognizes a
large number of small GTP-binding proteins and related
domains in larger proteins. Note that the alpha chains
of heterotrimeric G proteins are larger proteins in
which the NKXD motif is separated from the GxxxxGK[ST]
motif (P-loop) by a long insert and are not easily
detected by this model [Unknown function, General].
Length = 162
Score = 102 bits (255), Expect = 4e-25
Identities = 50/171 (29%), Positives = 82/171 (47%), Gaps = 19/171 (11%)
Query: 115 PPVVTIMGHVDHGKTTLLDTLRNTSVVKSEFG-GITQHIGAFVVTLKSGEQVTF--LDTP 171
+ I+G + GK+TLL+ L + +E+ G T++ V+ G+ F LDT
Sbjct: 1 EIKIVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEED-GKTYKFNLLDTA 59
Query: 172 GHAAFSNMR-------SRGAHCTDIVVLVVAADDGVMEQTVESIRMAREAKVPIIVAINK 224
G + +R DIV+LV+ ++ + +QT E I E+ VPII+ NK
Sbjct: 60 GQEDYDAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIH-HAESGVPIILVGNK 118
Query: 225 IDKPAADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIER 275
ID A ++ L A+ L G+ +P+SA TG N+D+ + +E
Sbjct: 119 IDLRDAKLKTHVAFLFAK------LNGEPI-IPLSAETGKNIDSAFKIVEA 162
>gnl|CDD|206677 cd01890, LepA, LepA also known as Elongation Factor 4 (EF4). LepA
(also known as elongation factor 4, EF4) belongs to the
GTPase family and exhibits significant homology to the
translation factors EF-G and EF-Tu, indicating its
possible involvement in translation and association with
the ribosome. LepA is ubiquitous in bacteria and
eukaryota (e.g. yeast GUF1p), but is missing from
archaea. This pattern of phyletic distribution suggests
that LepA evolved through a duplication of the EF-G gene
in bacteria, followed by early transfer into the
eukaryotic lineage, most likely from the
promitochondrial endosymbiont. Yeast GUF1p is not
essential and mutant cells did not reveal any marked
phenotype.
Length = 179
Score = 100 bits (251), Expect = 2e-24
Identities = 67/176 (38%), Positives = 86/176 (48%), Gaps = 30/176 (17%)
Query: 120 IMGHVDHGKTTLLDT-LRNTSVVKSEFG--------------GITQHIGAFVVTL----K 160
I+ H+DHGK+TL D L T V GIT I A V L K
Sbjct: 5 IIAHIDHGKSTLADRLLELTGTVSEREMKEQVLDSMDLERERGIT--IKAQAVRLFYKAK 62
Query: 161 SGE--QVTFLDTPGHAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMAREAKVPI 218
GE + +DTPGH FS SR + +LVV A GV QT+ + +A E + I
Sbjct: 63 DGEEYLLNLIDTPGHVDFSYEVSRSLAACEGALLVVDATQGVEAQTLANFYLALENNLEI 122
Query: 219 IVAINKIDKPAADIERTKNMLLAQGITVEDLGGDI-QAVPISALTGTNVDNLTEAI 273
I INKID PAAD +R K + + LG D +A+ +SA TG V++L EAI
Sbjct: 123 IPVINKIDLPAADPDRVKQEI------EDVLGLDASEAILVSAKTGLGVEDLLEAI 172
>gnl|CDD|206734 cd04171, SelB, SelB, the dedicated elongation factor for delivery
of selenocysteinyl-tRNA to the ribosome. SelB is an
elongation factor needed for the co-translational
incorporation of selenocysteine. Selenocysteine is coded
by a UGA stop codon in combination with a specific
downstream mRNA hairpin. In bacteria, the C-terminal
part of SelB recognizes this hairpin, while the
N-terminal part binds GTP and tRNA in analogy with
elongation factor Tu (EF-Tu). It specifically recognizes
the selenocysteine charged tRNAsec, which has a UCA
anticodon, in an EF-Tu like manner. This allows
insertion of selenocysteine at in-frame UGA stop codons.
In E. coli SelB binds GTP, selenocysteyl-tRNAsec, and a
stem-loop structure immediately downstream of the UGA
codon (the SECIS sequence). The absence of active SelB
prevents the participation of selenocysteyl-tRNAsec in
translation. Archaeal and animal mechanisms of
selenocysteine incorporation are more complex. Although
the SECIS elements have different secondary structures
and conserved elements between archaea and eukaryotes,
they do share a common feature. Unlike in E. coli, these
SECIS elements are located in the 3' UTRs. This group
contains bacterial SelBs, as well as, one from archaea.
Length = 170
Score = 97.7 bits (244), Expect = 1e-23
Identities = 52/159 (32%), Positives = 82/159 (51%), Gaps = 11/159 (6%)
Query: 122 GHVDHGKTTLLDTL--RNTSVVKSEFG-GITQHIGAFVVTLKSGEQVTFLDTPGHAAF-S 177
GH+DHGKTTL+ L T + E GIT +G + L G+++ F+D PGH F
Sbjct: 6 GHIDHGKTTLIKALTGIETDRLPEEKKRGITIDLGFAYLDLPDGKRLGFIDVPGHEKFVK 65
Query: 178 NMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMAREAKVP-IIVAINKIDKPAADIERTK 236
NM + GA D V+LVVAAD+G+M QT E + + + +V + K D D +R
Sbjct: 66 NMLA-GAGGIDAVLLVVAADEGIMPQTREHLEILELLGIKKGLVVLTKADL--VDEDR-L 121
Query: 237 NMLLAQGITV--EDLGGDIQAVPISALTGTNVDNLTEAI 273
++ + + + D P+S++TG ++ L +
Sbjct: 122 ELVEEEILELLAGTFLADAPIFPVSSVTGEGIEELKNYL 160
>gnl|CDD|223556 COG0480, FusA, Translation elongation factors (GTPases)
[Translation, ribosomal structure and biogenesis].
Length = 697
Score = 103 bits (259), Expect = 7e-23
Identities = 74/329 (22%), Positives = 115/329 (34%), Gaps = 82/329 (24%)
Query: 118 VTIMGHVDHGKTTLLDTLRNTSVVKSEFG------------------GITQHIGAFVVTL 159
+ I+ H+D GKTTL + + + + S+ G GIT A +
Sbjct: 13 IGIVAHIDAGKTTLTERILFYTGIISKIGEVHDGAATMDWMEQEQERGITITSAATTLFW 72
Query: 160 KSGEQVTFLDTPGHAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMAREAKVPII 219
K ++ +DTPGH F+ R D V+VV A +GV QT R A + VP I
Sbjct: 73 KGDYRINLIDTPGHVDFTIEVERSLRVLDGAVVVVDAVEGVEPQTETVWRQADKYGVPRI 132
Query: 220 VAINKIDKPAADIERTKNM---------------------------LLAQGITVEDLGGD 252
+ +NK+D+ AD L+ G
Sbjct: 133 LFVNKMDRLGADFYLVVEQLKERLGANPVPVQLPIGAEEEFEGVIDLVEMKAVAFGDGAK 192
Query: 253 IQAVPI-SALTGTN-------VDNLTEAIERTKNMLLA-QGITVEDLGGDIQAVPI---- 299
+ + I + L ++ L E E L + T E++ ++ I
Sbjct: 193 YEWIEIPADLKEIAEEAREKLLEALAEFDEELMEKYLEGEEPTEEEIKKALRKGTIAGKI 252
Query: 300 ------SALTGTNVDNLTEAIV------------------AQAEIMHLKADYGGPVEAMI 335
SA V L +A+V + + KA GP+ A++
Sbjct: 253 VPVLCGSAFKNKGVQPLLDAVVDYLPSPLDVPPIKGDLDDEIEKAVLRKASDEGPLSALV 312
Query: 336 VESKFDTHRGKLATALVQRGTLKKGAIVV 364
+ D GKL V GTLK G+ V+
Sbjct: 313 FKIMTDPFVGKLTFVRVYSGTLKSGSEVL 341
>gnl|CDD|130460 TIGR01393, lepA, GTP-binding protein LepA. LepA (GUF1 in
Saccaromyces) is a GTP-binding membrane protein related
to EF-G and EF-Tu. Two types of phylogenetic tree,
rooted by other GTP-binding proteins, suggest that
eukaryotic homologs (including GUF1 of yeast) originated
within the bacterial LepA family. The function is
unknown [Unknown function, General].
Length = 595
Score = 102 bits (257), Expect = 9e-23
Identities = 81/263 (30%), Positives = 114/263 (43%), Gaps = 73/263 (27%)
Query: 120 IMGHVDHGKTTLLDTLRNTSVVKSEFG---------------GITQHIGAFVVTL----K 160
I+ H+DHGK+TL D L + SE GIT I A V L K
Sbjct: 8 IIAHIDHGKSTLADRLLEYTGAISEREMREQVLDSMDLERERGIT--IKAQAVRLNYKAK 65
Query: 161 SGE--QVTFLDTPGHAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMAREAKVPI 218
GE + +DTPGH FS SR + +L+V A G+ QT+ ++ +A E + I
Sbjct: 66 DGETYVLNLIDTPGHVDFSYEVSRSLAACEGALLLVDAAQGIEAQTLANVYLALENDLEI 125
Query: 219 IVAINKIDKPAADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIERTKN 278
I INKID P+AD ER K + IE
Sbjct: 126 IPVINKIDLPSADPERVK----------------------------------KEIE---- 147
Query: 279 MLLAQGITVEDLGGDI-QAVPISALTGTNVDNLTEAIVAQAEIMHLKADYGGPVEAMIVE 337
E +G D +A+ SA TG ++ + EAIV + + K D P++A+I +
Sbjct: 148 ---------EVIGLDASEAILASAKTGIGIEEILEAIVKR--VPPPKGDPDAPLKALIFD 196
Query: 338 SKFDTHRGKLATALVQRGTLKKG 360
S +D +RG +A V GT+K G
Sbjct: 197 SHYDNYRGVVALVRVFEGTIKPG 219
>gnl|CDD|235462 PRK05433, PRK05433, GTP-binding protein LepA; Provisional.
Length = 600
Score = 102 bits (256), Expect = 2e-22
Identities = 89/268 (33%), Positives = 116/268 (43%), Gaps = 83/268 (30%)
Query: 120 IMGHVDHGKTTLLDTL-RNTSVV-KSEFG-------------GITQHIGAFVVTL----K 160
I+ H+DHGK+TL D L T + + E GIT I A V L K
Sbjct: 12 IIAHIDHGKSTLADRLIELTGTLSEREMKAQVLDSMDLERERGIT--IKAQAVRLNYKAK 69
Query: 161 SGEQVTF--LDTPGHAAFSNMRSR------GAHCTDIVVLVVAADDGVMEQTVESIRMAR 212
GE +DTPGH FS SR GA +LVV A GV QT+ ++ +A
Sbjct: 70 DGETYILNLIDTPGHVDFSYEVSRSLAACEGA------LLVVDASQGVEAQTLANVYLAL 123
Query: 213 EAKVPIIVAINKIDKPAADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEA 272
E + II +NKID PAAD ER K + ED+ I
Sbjct: 124 ENDLEIIPVLNKIDLPAADPERVKQEI-------EDV---I------------------- 154
Query: 273 IERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIVAQAEIMHLKADYGGPVE 332
GI D AV +SA TG ++ + EAIV + I K D P++
Sbjct: 155 -----------GIDASD------AVLVSAKTGIGIEEVLEAIVER--IPPPKGDPDAPLK 195
Query: 333 AMIVESKFDTHRGKLATALVQRGTLKKG 360
A+I +S +D +RG + V GTLKKG
Sbjct: 196 ALIFDSWYDNYRGVVVLVRVVDGTLKKG 223
>gnl|CDD|223557 COG0481, LepA, Membrane GTPase LepA [Cell envelope biogenesis,
outer membrane].
Length = 603
Score = 101 bits (253), Expect = 3e-22
Identities = 86/263 (32%), Positives = 118/263 (44%), Gaps = 73/263 (27%)
Query: 120 IMGHVDHGKTTLLD-TLRNTSVV-KSEFG-------------GITQHIGAFVVTL----K 160
I+ H+DHGK+TL D L T + + E GIT I A V L K
Sbjct: 14 IIAHIDHGKSTLADRLLELTGGLSEREMRAQVLDSMDIERERGIT--IKAQAVRLNYKAK 71
Query: 161 SGE--QVTFLDTPGHAAFSNMRSRG-AHCTDIVVLVVAADDGVMEQTVESIRMAREAKVP 217
GE + +DTPGH FS SR A C +LVV A GV QT+ ++ +A E +
Sbjct: 72 DGETYVLNLIDTPGHVDFSYEVSRSLAACEG-ALLVVDASQGVEAQTLANVYLALENNLE 130
Query: 218 IIVAINKIDKPAADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIERTK 277
II +NKID PAAD ER K + IE
Sbjct: 131 IIPVLNKIDLPAADPERVK----------------------------------QEIE--- 153
Query: 278 NMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIVAQAEIMHLKADYGGPVEAMIVE 337
+++ GI D AV +SA TG ++++ EAIV + I K D P++A+I +
Sbjct: 154 DII---GIDASD------AVLVSAKTGIGIEDVLEAIVEK--IPPPKGDPDAPLKALIFD 202
Query: 338 SKFDTHRGKLATALVQRGTLKKG 360
S +D + G + + GTLKKG
Sbjct: 203 SWYDNYLGVVVLVRIFDGTLKKG 225
>gnl|CDD|206678 cd01891, TypA_BipA, Tyrosine phosphorylated protein A (TypA)/BipA
family belongs to ribosome-binding GTPases. BipA is a
protein belonging to the ribosome-binding family of
GTPases and is widely distributed in bacteria and
plants. BipA was originally described as a protein that
is induced in Salmonella typhimurium after exposure to
bactericidal/permeability-inducing protein (a cationic
antimicrobial protein produced by neutrophils), and has
since been identified in E. coli as well. The properties
thus far described for BipA are related to its role in
the process of pathogenesis by enteropathogenic E. coli.
It appears to be involved in the regulation of several
processes important for infection, including
rearrangements of the cytoskeleton of the host,
bacterial resistance to host defense peptides,
flagellum-mediated cell motility, and expression of K5
capsular genes. It has been proposed that BipA may
utilize a novel mechanism to regulate the expression of
target genes. In addition, BipA from enteropathogenic E.
coli has been shown to be phosphorylated on a tyrosine
residue, while BipA from Salmonella and from E. coli K12
strains is not phosphorylated under the conditions
assayed. The phosphorylation apparently modifies the
rate of nucleotide hydrolysis, with the phosphorylated
form showing greatly increased GTPase activity.
Length = 194
Score = 90.7 bits (226), Expect = 5e-21
Identities = 61/178 (34%), Positives = 77/178 (43%), Gaps = 25/178 (14%)
Query: 118 VTIMGHVDHGKTTLLDTLRNTSVVKSEFG----------------GITQHIGAFVVTLK- 160
+ I+ HVDHGKTTL+D L S E GIT I A +
Sbjct: 5 IAIIAHVDHGKTTLVDALLKQSGTFRENEEVGERVMDSNDLERERGIT--ILAKNTAITY 62
Query: 161 SGEQVTFLDTPGHAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMAREAKVPIIV 220
++ +DTPGHA F R D V+L+V A +G M QT ++ A EA + IV
Sbjct: 63 KDTKINIIDTPGHADFGGEVERVLSMVDGVLLLVDASEGPMPQTRFVLKKALEAGLKPIV 122
Query: 221 AINKIDKPAADIERTKNM----LLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIE 274
INKID+P A E + L T E L D V SA G NL + E
Sbjct: 123 VINKIDRPDARPEEVVDEVFDLFLELNATDEQL--DFPIVYASAKNGWASLNLDDPSE 178
>gnl|CDD|233394 TIGR01394, TypA_BipA, GTP-binding protein TypA/BipA. This
bacterial (and Arabidopsis) protein, termed TypA or
BipA, a GTP-binding protein, is phosphorylated on a
tyrosine residue under some cellular conditions. Mutants
show altered regulation of some pathways, but the
precise function is unknown [Regulatory functions,
Other, Cellular processes, Adaptations to atypical
conditions, Protein synthesis, Translation factors].
Length = 594
Score = 96.6 bits (241), Expect = 8e-21
Identities = 74/267 (27%), Positives = 107/267 (40%), Gaps = 58/267 (21%)
Query: 118 VTIMGHVDHGKTTLLDTLRNTSVVKSEFG----------------GITQHIGAFVVTLK- 160
+ I+ HVDHGKTTL+D L S GIT I A ++
Sbjct: 4 IAIIAHVDHGKTTLVDALLKQSGTFRANEAVAERVMDSNDLERERGIT--ILAKNTAIRY 61
Query: 161 SGEQVTFLDTPGHAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMAREAKVPIIV 220
+G ++ +DTPGHA F R D V+L+V A +G M QT ++ A E + IV
Sbjct: 62 NGTKINIVDTPGHADFGGEVERVLGMVDGVLLLVDASEGPMPQTRFVLKKALELGLKPIV 121
Query: 221 AINKIDKPAADIERTKNM----LLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIERT 276
INKID+P+A + + G E L D V S G +L +
Sbjct: 122 VINKIDRPSARPDEVVDEVFDLFAELGADDEQL--DFPIVYASGRAGWASLDLDD----- 174
Query: 277 KNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIVAQAEIMHLKADYGGPVEAMIV 336
N+ L +AIV + K D P++ ++
Sbjct: 175 --------------------------PSDNMAPLFDAIVRH--VPAPKGDLDEPLQMLVT 206
Query: 337 ESKFDTHRGKLATALVQRGTLKKGAIV 363
+D + G++A V RGT+KKG V
Sbjct: 207 NLDYDEYLGRIAIGRVHRGTVKKGQQV 233
>gnl|CDD|221359 pfam11987, IF-2, Translation-initiation factor 2. IF-2 is a
translation initiator in each of the three main
phylogenetic domains (Eukaryotes, Bacteria and Archaea).
IF2 interacts with formylmethionine-tRNA, GTP, IF1, IF3
and both ribosomal subunits. Through these interactions,
IF2 promotes the binding of the initiator tRNA to the A
site in the smaller ribosomal subunit and catalyzes the
hydrolysis of GTP following initiation-complex
formation.
Length = 109
Score = 87.5 bits (218), Expect = 9e-21
Identities = 34/90 (37%), Positives = 57/90 (63%)
Query: 464 IYLIGDVDGSVEALLDVFDTYTSALCRLDIVHYGVGQVSATDVELATLFNAIIYTFNTTL 523
+ L DV GS+EA+ D + ++ +++I+H GVG ++ +DV LA+ NAII FN
Sbjct: 20 LILKADVQGSLEAIKDSLEKLSTDEVKVNIIHAGVGAITESDVMLASASNAIIIGFNVRP 79
Query: 524 HPAAKTSAEELGVTVKQFNVIYKLVEDVKE 553
A+ AE+ GV ++ +++IY L++DVK
Sbjct: 80 DAKARKLAEQEGVDIRYYSIIYDLIDDVKA 109
Score = 28.6 bits (65), Expect = 4.4
Identities = 13/38 (34%), Positives = 23/38 (60%), Gaps = 3/38 (7%)
Query: 410 GDVDGSVEALLDVFDTYTSALCRLDIVHYGV---TSTD 444
DV GS+EA+ D + ++ +++I+H GV T +D
Sbjct: 24 ADVQGSLEAIKDSLEKLSTDEVKVNIIHAGVGAITESD 61
>gnl|CDD|206648 cd00882, Ras_like_GTPase, Rat sarcoma (Ras)-like superfamily of
small guanosine triphosphatases (GTPases). Ras-like
GTPase superfamily. The Ras-like superfamily of small
GTPases consists of several families with an extremely
high degree of structural and functional similarity. The
Ras superfamily is divided into at least four families
in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families.
This superfamily also includes proteins like the GTP
translation factors, Era-like GTPases, and G-alpha chain
of the heterotrimeric G proteins. Members of the Ras
superfamily regulate a wide variety of cellular
functions: the Ras family regulates gene expression, the
Rho family regulates cytoskeletal reorganization and
gene expression, the Rab and Sar1/Arf families regulate
vesicle trafficking, and the Ran family regulates
nucleocytoplasmic transport and microtubule
organization. The GTP translation factor family
regulates initiation, elongation, termination, and
release in translation, and the Era-like GTPase family
regulates cell division, sporulation, and DNA
replication. Members of the Ras superfamily are
identified by the GTP binding site, which is made up of
five characteristic sequence motifs, and the switch I
and switch II regions.
Length = 161
Score = 84.8 bits (210), Expect = 3e-19
Identities = 42/163 (25%), Positives = 67/163 (41%), Gaps = 14/163 (8%)
Query: 120 IMGHVDHGKTTLLDTLRNTSV-VKSEFGGITQHIGAFVVTL-KSGEQVTFLDTPGHAAFS 177
++G GK++LL+ L V S+ G T+ +V L K ++ +DTPG F
Sbjct: 2 VVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKVKLVLVDTPGLDEFG 61
Query: 178 NMRSRG-----AHCTDIVVLVVAADDGVMEQTVE--SIRMAREAKVPIIVAINKIDKPAA 230
+ D+++LVV + D E+ + +R R+ +PII+ NKID
Sbjct: 62 GLGREELARLLLRGADLILLVVDSTDRESEEDAKLLILRRLRKEGIPIILVGNKIDLLEE 121
Query: 231 DIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAI 273
L + +SA TG VD L E +
Sbjct: 122 REVEELLRLE-----ELAKILGVPVFEVSAKTGEGVDELFEKL 159
>gnl|CDD|206646 cd00880, Era_like, E. coli Ras-like protein (Era)-like GTPase. The
Era (E. coli Ras-like protein)-like family includes
several distinct subfamilies (TrmE/ThdF, FeoB, YihA
(EngB), Era, and EngA/YfgK) that generally show sequence
conservation in the region between the Walker A and B
motifs (G1 and G3 box motifs), to the exclusion of other
GTPases. TrmE is ubiquitous in bacteria and is a
widespread mitochondrial protein in eukaryotes, but is
absent from archaea. The yeast member of TrmE family,
MSS1, is involved in mitochondrial translation;
bacterial members are often present in
translation-related operons. FeoB represents an unusual
adaptation of GTPases for high-affinity iron (II)
transport. YihA (EngB) family of GTPases is typified by
the E. coli YihA, which is an essential protein involved
in cell division control. Era is characterized by a
distinct derivative of the KH domain (the pseudo-KH
domain) which is located C-terminal to the GTPase
domain. EngA and its orthologs are composed of two
GTPase domains and, since the sequences of the two
domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family.
Length = 161
Score = 82.3 bits (204), Expect = 2e-18
Identities = 44/166 (26%), Positives = 69/166 (41%), Gaps = 16/166 (9%)
Query: 120 IMGHVDHGKTTLLDTL--RNTSVVKSEFGGITQHIGAFVVTLKSGEQVTFLDTPG---HA 174
I G + GK++LL+ L +N +V S G T+ L V +DTPG
Sbjct: 2 IFGRPNVGKSSLLNALLGQNVGIV-SPIPGTTRDPVRKEWELLPLGPVVLIDTPGLDEEG 60
Query: 175 AFSNMRSRGAHC----TDIVVLVVAADDGVMEQTVESIRMAREAKVPIIVAINKIDKPAA 230
R A D+V+LVV +D +E+ + + RE P+++ +NKID
Sbjct: 61 GLGRERVEEARQVADRADLVLLVVDSDLTPVEE-EAKLGLLRERGKPVLLVLNKIDLVPE 119
Query: 231 DIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIERT 276
E +L D+ + +SAL G +D L + I
Sbjct: 120 SEEEELLRER-----KLELLPDLPVIAVSALPGEGIDELRKKIAEL 160
>gnl|CDD|224138 COG1217, TypA, Predicted membrane GTPase involved in stress
response [Signal transduction mechanisms].
Length = 603
Score = 88.8 bits (221), Expect = 2e-18
Identities = 71/277 (25%), Positives = 108/277 (38%), Gaps = 76/277 (27%)
Query: 118 VTIMGHVDHGKTTLLDTLRNTSVVKSEFG----------------GITQHIGAFVVTLK- 160
+ I+ HVDHGKTTL+D L S E GIT I A +
Sbjct: 8 IAIIAHVDHGKTTLVDALLKQSGTFREREEVAERVMDSNDLEKERGIT--ILAKNTAVNY 65
Query: 161 SGEQVTFLDTPGHAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMAREAKVPIIV 220
+G ++ +DTPGHA F R D V+L+V A +G M QT ++ A + IV
Sbjct: 66 NGTRINIVDTPGHADFGGEVERVLSMVDGVLLLVDASEGPMPQTRFVLKKALALGLKPIV 125
Query: 221 AINKIDKPAADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIERTKNML 280
INKID+P A + E ++ ++
Sbjct: 126 VINKIDRPDARPD-------------------------------------EVVDEVFDLF 148
Query: 281 LAQGITVEDLGGDIQAVPISALTGT----------NVDNLTEAIVAQAEIMHL---KADY 327
+ G T E L D V SA GT ++ L E I + H+ K D
Sbjct: 149 VELGATDEQL--DFPIVYASARNGTASLDPEDEADDMAPLFETI-----LDHVPAPKGDL 201
Query: 328 GGPVEAMIVESKFDTHRGKLATALVQRGTLKKGAIVV 364
P++ + + ++++ G++ + RGT+K V
Sbjct: 202 DEPLQMQVTQLDYNSYVGRIGIGRIFRGTVKPNQQVA 238
>gnl|CDD|129567 TIGR00475, selB, selenocysteine-specific elongation factor SelB.
In prokaryotes, the incorporation of selenocysteine as
the 21st amino acid, encoded by TGA, requires several
elements: SelC is the tRNA itself, SelD acts as a donor
of reduced selenium, SelA modifies a serine residue on
SelC into selenocysteine, and SelB is a
selenocysteine-specific translation elongation factor.
3-prime or 5-prime non-coding elements of mRNA have been
found as probable structures for directing
selenocysteine incorporation. This model describes the
elongation factor SelB, a close homolog rf EF-Tu. It may
function by replacing EF-Tu. A C-terminal domain not
found in EF-Tu is in all SelB sequences in the seed
alignment except that from Methanococcus jannaschii.
This model does not find an equivalent protein for
eukaryotes [Protein synthesis, Translation factors].
Length = 581
Score = 84.5 bits (209), Expect = 4e-17
Identities = 55/171 (32%), Positives = 81/171 (47%), Gaps = 14/171 (8%)
Query: 117 VVTIMGHVDHGKTTLLDTLRNTSVV---KSEFGGITQHIGAFVVTLKSGEQVTFLDTPGH 173
++ GHVDHGKTTLL L + + + G+T +G L ++ F+D PGH
Sbjct: 2 IIATAGHVDHGKTTLLKALTGIAADRLPEEKKRGMTIDLGFAYFPLPD-YRLGFIDVPGH 60
Query: 174 AAF-SNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMAREAKVP-IIVAINKIDKPAAD 231
F SN + G D +LVV AD+GVM QT E + + +P IV I K D+ +
Sbjct: 61 EKFISNAIA-GGGGIDAALLVVDADEGVMTQTGEHLAVLDLLGIPHTIVVITKADR--VN 117
Query: 232 IERTK--NMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIERTKNML 280
E K M + Q + + + SA TG + L + + KN+L
Sbjct: 118 EEEIKRTEMFMKQILNSYIFLKNAKIFKTSAKTGQGIGELKKEL---KNLL 165
>gnl|CDD|206676 cd01889, SelB_euk, SelB, the dedicated elongation factor for
delivery of selenocysteinyl-tRNA to the ribosome. SelB
is an elongation factor needed for the co-translational
incorporation of selenocysteine. Selenocysteine is coded
by a UGA stop codon in combination with a specific
downstream mRNA hairpin. In bacteria, the C-terminal
part of SelB recognizes this hairpin, while the
N-terminal part binds GTP and tRNA in analogy with
elongation factor Tu (EF-Tu). It specifically recognizes
the selenocysteine charged tRNAsec, which has a UCA
anticodon, in an EF-Tu like manner. This allows
insertion of selenocysteine at in-frame UGA stop codons.
In E. coli SelB binds GTP, selenocysteyl-tRNAsec and a
stem-loop structure immediately downstream of the UGA
codon (the SECIS sequence). The absence of active SelB
prevents the participation of selenocysteyl-tRNAsec in
translation. Archaeal and animal mechanisms of
selenocysteine incorporation are more complex. Although
the SECIS elements have different secondary structures
and conserved elements between archaea and eukaryotes,
they do share a common feature. Unlike in E. coli, these
SECIS elements are located in the 3' UTRs. This group
contains eukaryotic SelBs and some from archaea.
Length = 192
Score = 78.9 bits (195), Expect = 6e-17
Identities = 51/170 (30%), Positives = 78/170 (45%), Gaps = 23/170 (13%)
Query: 118 VTIMGHVDHGKTTL---LDTLRNTSVV----KSEFGGITQHIG--AFVVTLKSGE----- 163
V ++GHVD GKT+L L + +T+ +S+ GIT +G +F V
Sbjct: 3 VGLLGHVDSGKTSLAKALSEIASTAAFDKNPQSQERGITLDLGFSSFEVDKPKHLEDNEN 62
Query: 164 ------QVTFLDTPGHAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMAREAKVP 217
Q+T +D PGHA+ GA D+++LVV A G+ QT E + + P
Sbjct: 63 PQIENYQITLVDCPGHASLIRTIIGGAQIIDLMLLVVDAKKGIQTQTAECLVIGELLCKP 122
Query: 218 IIVAINKIDK-PAADIERTKNMLLA--QGITVEDLGGDIQAVPISALTGT 264
+IV +NKID P + +R + Q + D +P+SA G
Sbjct: 123 LIVVLNKIDLIPEEERKRKIEKMKKRLQKTLEKTRLKDSPIIPVSAKPGE 172
>gnl|CDD|237186 PRK12740, PRK12740, elongation factor G; Reviewed.
Length = 668
Score = 82.5 bits (205), Expect = 2e-16
Identities = 81/347 (23%), Positives = 123/347 (35%), Gaps = 103/347 (29%)
Query: 121 MGHVDHGKTTLLDTLRNTSVVKSEFG------------------GITQHIGAFVVTLK-S 161
+GH GKTTL + + + G GI+ I + T +
Sbjct: 1 VGHSGAGKTTLTEAILFYTGAIHRIGEVEDGTTTMDFMPEERERGIS--ITSAATTCEWK 58
Query: 162 GEQVTFLDTPGHAAFS-NMRS--RGAHCTDIVVLVVAADDGVMEQTVESIRMAREAKVPI 218
G ++ +DTPGH F+ + R D V+VV A GV QT R A + VP
Sbjct: 59 GHKINLIDTPGHVDFTGEVERALRVL---DGAVVVVCAVGGVEPQTETVWRQAEKYGVPR 115
Query: 219 IVAINKIDKPAADIERT---------KNMLLAQ----------GIT--------VEDLGG 251
I+ +NK+D+ AD R ++ Q G+ D GG
Sbjct: 116 IIFVNKMDRAGADFFRVLAQLQEKLGAPVVPLQLPIGEGDDFTGVVDLLSMKAYRYDEGG 175
Query: 252 DIQAVPISALTGTNVDNLTEAIERTKNML---------------LAQG-ITVEDLGGDI- 294
+ + I A L + E + L L ++ E++ +
Sbjct: 176 PSEEIEIPA-------ELLDRAEEAREELLEALAEFDDELMEKYLEGEELSEEEIKAGLR 228
Query: 295 ------QAVPI---SALTGTNVDNLTEAIVA---------------QAEIMHLKADYGGP 330
+ VP+ SAL V L +A+V E L D GP
Sbjct: 229 KATLAGEIVPVFCGSALKNKGVQRLLDAVVDYLPSPLEVPPVDGEDGEEGAELAPDPDGP 288
Query: 331 VEAMIVESKFDTHRGKLATALVQRGTLKKGAIVVAGQAWAKVRSISR 377
+ A++ ++ D GKL+ V GTLKKG + K R + R
Sbjct: 289 LVALVFKTMDDPFVGKLSLVRVYSGTLKKGDTLYNSGTGKKER-VGR 334
>gnl|CDD|182508 PRK10512, PRK10512, selenocysteinyl-tRNA-specific translation
factor; Provisional.
Length = 614
Score = 79.3 bits (196), Expect = 3e-15
Identities = 54/160 (33%), Positives = 74/160 (46%), Gaps = 17/160 (10%)
Query: 122 GHVDHGKTTLLDTLR--NTSVVKSEFG-GITQHIGAFVVTLKSGEQVTFLDTPGHAAF-S 177
GHVDHGKTTLL + N + E G+T +G G + F+D PGH F S
Sbjct: 7 GHVDHGKTTLLQAITGVNADRLPEEKKRGMTIDLGYAYWPQPDGRVLGFIDVPGHEKFLS 66
Query: 178 NMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMAREAKVP-IIVAINKIDK-PAADIERT 235
NM + G D +LVVA DDGVM QT E + + + P + VA+ K D+ A I
Sbjct: 67 NMLA-GVGGIDHALLVVACDDGVMAQTREHLAILQLTGNPMLTVALTKADRVDEARIAEV 125
Query: 236 KN----MLLAQGITVEDLGGDIQAVPISALTGTNVDNLTE 271
+ +L G + + +A G +D L E
Sbjct: 126 RRQVKAVLREYGFA------EAKLFVTAATEGRGIDALRE 159
>gnl|CDD|239673 cd03702, IF2_mtIF2_II, This family represents the domain II of
bacterial Initiation Factor 2 (IF2) and its eukaryotic
mitochondrial homologue mtIF2. IF2, the largest
initiation factor is an essential GTP binding protein.
In E. coli three natural forms of IF2 exist in the cell,
IF2alpha, IF2beta1, and IF2beta2. Bacterial IF-2 is
structurally and functionally related to eukaryotic
mitochondrial mtIF-2.
Length = 95
Score = 70.6 bits (174), Expect = 5e-15
Identities = 33/85 (38%), Positives = 45/85 (52%), Gaps = 12/85 (14%)
Query: 331 VEAMIVESKFDTHRGKLATALVQRGTLKKGAIVVAGQAWAKVRSI--SRKTLINTAL-GT 387
E +++ESK D RG +AT LVQ GTLK G ++VAG + KVR++ + A T
Sbjct: 1 AEGVVIESKLDKGRGPVATVLVQNGTLKVGDVLVAGTTYGKVRAMFDENGKRVKEAGPST 60
Query: 388 VQRTSGTVKISLGFKINPFCPSGDV 412
V+I LG K P +GD
Sbjct: 61 P------VEI-LGLKGVP--QAGDK 76
>gnl|CDD|225815 COG3276, SelB, Selenocysteine-specific translation elongation
factor [Translation, ribosomal structure and
biogenesis].
Length = 447
Score = 75.5 bits (186), Expect = 2e-14
Identities = 51/162 (31%), Positives = 80/162 (49%), Gaps = 11/162 (6%)
Query: 117 VVTIMGHVDHGKTTLLDTLRN--TSVVKSEFG-GITQHIGAFVVTLKSGEQVTFLDTPGH 173
++ GH+DHGKTTLL L T + E GIT +G + L+ G + F+D PGH
Sbjct: 2 IIGTAGHIDHGKTTLLKALTGGVTDRLPEEKKRGITIDLGFYYRKLEDG-VMGFIDVPGH 60
Query: 174 AAF-SNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMAREAKVP-IIVAINKIDKPAAD 231
F SN+ + G D +LVVAAD+G+M QT E + + + I+ + K D+ D
Sbjct: 61 PDFISNLLA-GLGGIDYALLVVAADEGLMAQTGEHLLILDLLGIKNGIIVLTKADR--VD 117
Query: 232 IERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAI 273
R + + + I + + + SA TG ++ L +
Sbjct: 118 EARIEQKI--KQILADLSLANAKIFKTSAKTGRGIEELKNEL 157
>gnl|CDD|237055 PRK12317, PRK12317, elongation factor 1-alpha; Reviewed.
Length = 425
Score = 75.3 bits (186), Expect = 2e-14
Identities = 69/209 (33%), Positives = 96/209 (45%), Gaps = 64/209 (30%)
Query: 118 VTIMGHVDHGKTTLLDTLRNTSVVKSEFGGITQHI-----------G------AFV---- 156
+ ++GHVDHGK+TL+ L E G I +HI G A+V
Sbjct: 9 LAVIGHVDHGKSTLVGRL------LYETGAIDEHIIEELREEAKEKGKESFKFAWVMDRL 62
Query: 157 -------VTLKSGEQ--------VTFLDTPGHAAF-SNMRSRGAHCTDIVVLVVAADD-- 198
VT+ + T +D PGH F NM + GA D VLVVAADD
Sbjct: 63 KEERERGVTIDLAHKKFETDKYYFTIVDCPGHRDFVKNMIT-GASQADAAVLVVAADDAG 121
Query: 199 GVMEQTVESIRMAREAKVP-IIVAINKIDKPAADIERTKNM------LLAQ-GITVEDLG 250
GVM QT E + +AR + +IVAINK+D D +R + + LL G +D
Sbjct: 122 GVMPQTREHVFLARTLGINQLIVAINKMDAVNYDEKRYEEVKEEVSKLLKMVGYKPDD-- 179
Query: 251 GDIQAVPISALTGTNVDNLTEAIERTKNM 279
I +P+SA G NV +++++NM
Sbjct: 180 --IPFIPVSAFEGDNV------VKKSENM 200
>gnl|CDD|206670 cd01883, EF1_alpha, Elongation Factor 1-alpha (EF1-alpha) protein
family. EF1 is responsible for the GTP-dependent
binding of aminoacyl-tRNAs to the ribosomes. EF1 is
composed of four subunits: the alpha chain which binds
GTP and aminoacyl-tRNAs, the gamma chain that probably
plays a role in anchoring the complex to other cellular
components and the beta and delta (or beta') chains.
This subfamily is the alpha subunit, and represents the
counterpart of bacterial EF-Tu for the archaea
(aEF1-alpha) and eukaryotes (eEF1-alpha). eEF1-alpha
interacts with the actin of the eukaryotic cytoskeleton
and may thereby play a role in cellular transformation
and apoptosis. EF-Tu can have no such role in bacteria.
In humans, the isoform eEF1A2 is overexpressed in 2/3 of
breast cancers and has been identified as a putative
oncogene. This subfamily also includes Hbs1, a G protein
known to be important for efficient growth and protein
synthesis under conditions of limiting translation
initiation in yeast, and to associate with Dom34. It has
been speculated that yeast Hbs1 and Dom34 proteins may
function as part of a complex with a role in gene
expression.
Length = 219
Score = 71.0 bits (175), Expect = 6e-14
Identities = 59/214 (27%), Positives = 86/214 (40%), Gaps = 71/214 (33%)
Query: 120 IMGHVDHGKTTLLDTLRNTSVVKSEFGGITQH-----------IG------AFV------ 156
++GHVD GK+TL L + GG+ + +G A+V
Sbjct: 4 VIGHVDAGKSTLTGHL------LYKLGGVDKRTIEKYEKEAKEMGKESFKYAWVLDKLKE 57
Query: 157 ---------VTLKSGE----QVTFLDTPGHAAF-SNMRSRGAHCTDIVVLVVAADDG--- 199
V L E + T +D PGH F NM + GA D+ VLVV+A G
Sbjct: 58 ERERGVTIDVGLAKFETEKYRFTIIDAPGHRDFVKNMIT-GASQADVAVLVVSARKGEFE 116
Query: 200 ----VMEQTVESIRMAREAKVP-IIVAINKIDKPAAD---------IERTKNMLLAQGIT 245
QT E +AR V +IVA+NK+D + ++ L G
Sbjct: 117 AGFEKGGQTREHALLARTLGVKQLIVAVNKMDDVTVNWSQERYDEIKKKVSPFLKKVGYN 176
Query: 246 VEDLGGDIQAVPISALTGTNVDNLTEAIERTKNM 279
+D + +PIS TG N+ IE+++NM
Sbjct: 177 PKD----VPFIPISGFTGDNL------IEKSENM 200
>gnl|CDD|227581 COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 428
Score = 73.5 bits (181), Expect = 9e-14
Identities = 58/217 (26%), Positives = 86/217 (39%), Gaps = 61/217 (28%)
Query: 112 MKRPPVVTI--MGHVDHGKTTLL------------DTLRNTSVVKSEFG----------- 146
P + + +GHVD GK+TL+ T+ E G
Sbjct: 2 ASEKPHLNLVFIGHVDAGKSTLVGRLLYDLGEIDKRTMEKLEKEAKELGKESFKFAWVLD 61
Query: 147 --------GITQHIGAFVVTLKSGE----QVTFLDTPGHAAF-SNMRSRGAHCTDIVVLV 193
G+T V E T +D PGH F NM GA D+ VLV
Sbjct: 62 KTKEERERGVT-----IDVAHSKFETDKYNFTIIDAPGHRDFVKNM-ITGASQADVAVLV 115
Query: 194 VAADDG-------VMEQTVESIRMAREAKVP-IIVAINKIDKPAADIERTKNMLLAQGIT 245
V A DG V QT E +AR + +IVA+NK+D + D ER + ++
Sbjct: 116 VDARDGEFEAGFGVGGQTREHAFLARTLGIKQLIVAVNKMDLVSWDEERFEEIVSEVSKL 175
Query: 246 VEDLG---GDIQAVPISALTGTNVDNLTEAIERTKNM 279
++ +G D+ +PIS G N+ ++++NM
Sbjct: 176 LKMVGYNPKDVPFIPISGFKGDNL------TKKSENM 206
>gnl|CDD|223128 COG0050, TufB, GTPases - translation elongation factors
[Translation, ribosomal structure and biogenesis].
Length = 394
Score = 73.1 bits (180), Expect = 1e-13
Identities = 79/277 (28%), Positives = 109/277 (39%), Gaps = 76/277 (27%)
Query: 117 VVTIMGHVDHGKTTLLDTLRNTSVVKSEFG------------------GITQHIGAFVVT 158
V TI GHVDHGKTTL + T+V+ + G GIT I V
Sbjct: 15 VGTI-GHVDHGKTTLTAAI--TTVLAKKGGAEAKAYDQIDNAPEEKARGIT--INTAHVE 69
Query: 159 LKSGEQ-VTFLDTPGHAAF-SNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMAREAKV 216
++ + +D PGHA + NM + GA D +LVVAA DG M QT E I +AR+ V
Sbjct: 70 YETANRHYAHVDCPGHADYVKNMIT-GAAQMDGAILVVAATDGPMPQTREHILLARQVGV 128
Query: 217 P-IIVAINKIDKPAADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIER 275
P I+V +NK+D V+D + L E +E
Sbjct: 129 PYIVVFLNKVD------------------MVDD------------------EELLELVEM 152
Query: 276 TKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIVAQAEIMHLKADYGGPVEA-- 333
LL++ GD + + ++ + E+M Y E
Sbjct: 153 EVRELLSE----YGFPGDDTPIIRGSALKA-LEGDAKWEAKIEELMDAVDSYIPTPERDI 207
Query: 334 -----MIVESKFD-THRGKLATALVQRGTLKKGAIVV 364
M VE F + RG + T V+RG LK G V
Sbjct: 208 DKPFLMPVEDVFSISGRGTVVTGRVERGILKVGEEVE 244
>gnl|CDD|206671 cd01884, EF_Tu, Elongation Factor Tu (EF-Tu) GTP-binding proteins.
EF-Tu subfamily. This subfamily includes orthologs of
translation elongation factor EF-Tu in bacteria,
mitochondria, and chloroplasts. It is one of several
GTP-binding translation factors found in the larger
family of GTP-binding elongation factors. The eukaryotic
counterpart, eukaryotic translation elongation factor 1
(eEF-1 alpha), is excluded from this family. EF-Tu is
one of the most abundant proteins in bacteria, as well
as, one of the most highly conserved, and in a number of
species the gene is duplicated with identical function.
When bound to GTP, EF-Tu can form a complex with any
(correctly) aminoacylated tRNA except those for
initiation and for selenocysteine, in which case EF-Tu
is replaced by other factors. Transfer RNA is carried to
the ribosome in these complexes for protein translation.
Length = 195
Score = 69.5 bits (171), Expect = 1e-13
Identities = 49/129 (37%), Positives = 65/129 (50%), Gaps = 27/129 (20%)
Query: 119 TIMGHVDHGKTTLLDTLRNTSVVKSEFG------------------GITQHIGAFVVTLK 160
TI GHVDHGKTTL + T V+ + G GIT I V +
Sbjct: 7 TI-GHVDHGKTTLTAAI--TKVLAKKGGAKAKKYDEIDKAPEEKARGIT--INTAHVEYE 61
Query: 161 SGEQV-TFLDTPGHAAF-SNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMAREAKVP- 217
+ + +D PGHA + NM + GA D +LVV+A DG M QT E + +AR+ VP
Sbjct: 62 TANRHYAHVDCPGHADYIKNMIT-GAAQMDGAILVVSATDGPMPQTREHLLLARQVGVPY 120
Query: 218 IIVAINKID 226
I+V +NK D
Sbjct: 121 IVVFLNKAD 129
>gnl|CDD|206726 cd04163, Era, E. coli Ras-like protein (Era) is a multifunctional
GTPase. Era (E. coli Ras-like protein) is a
multifunctional GTPase found in all bacteria except some
eubacteria. It binds to the 16S ribosomal RNA (rRNA) of
the 30S subunit and appears to play a role in the
assembly of the 30S subunit, possibly by chaperoning the
16S rRNA. It also contacts several assembly elements of
the 30S subunit. Era couples cell growth with
cytokinesis and plays a role in cell division and energy
metabolism. Homologs have also been found in eukaryotes.
Era contains two domains: the N-terminal GTPase domain
and a C-terminal domain KH domain that is critical for
RNA binding. Both domains are important for Era
function. Era is functionally able to compensate for
deletion of RbfA, a cold-shock adaptation protein that
is required for efficient processing of the 16S rRNA.
Length = 168
Score = 68.6 bits (169), Expect = 1e-13
Identities = 36/118 (30%), Positives = 56/118 (47%), Gaps = 13/118 (11%)
Query: 164 QVTFLDTPG----HAAFSNMRSRGAHCT----DIVVLVVAADDGVMEQTVESIRMAREAK 215
Q+ F+DTPG + A D+V+ VV A + + E + + +++K
Sbjct: 52 QIIFVDTPGIHKPKKKLGERMVKAAWSALKDVDLVLFVVDASEWIGEGDEFILELLKKSK 111
Query: 216 VPIIVAINKIDKPAADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAI 273
P+I+ +NKID + K LL +++L + PISAL G NVD L E I
Sbjct: 112 TPVILVLNKIDL-----VKDKEDLLPLLEKLKELHPFAEIFPISALKGENVDELLEYI 164
>gnl|CDD|206730 cd04167, Snu114p, Snu114p, a spliceosome protein, is a GTPase.
Snu114p subfamily. Snu114p is one of several proteins
that make up the U5 small nuclear ribonucleoprotein
(snRNP) particle. U5 is a component of the spliceosome,
which catalyzes the splicing of pre-mRNA to remove
introns. Snu114p is homologous to EF-2, but typically
contains an additional N-terminal domain not found in
Ef-2. This protein is part of the GTP translation factor
family and the Ras superfamily, characterized by five
G-box motifs.
Length = 213
Score = 69.2 bits (170), Expect = 3e-13
Identities = 37/133 (27%), Positives = 59/133 (44%), Gaps = 23/133 (17%)
Query: 118 VTIMGHVDHGKTTLLDTLRNTSVVKSEFGGITQHIGAFV----------VTLKSG----- 162
V I GH+ HGKT+LLD L + ++ + + +++KS
Sbjct: 3 VCIAGHLHHGKTSLLDMLIEQTHKRTPSVKLGWKPLRYTDTRKDEQERGISIKSNPISLV 62
Query: 163 --------EQVTFLDTPGHAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMAREA 214
+ +DTPGH F + + D VVLVV +G+ T IR A +
Sbjct: 63 LEDSKGKSYLINIIDTPGHVNFMDEVAAALRLCDGVVLVVDVVEGLTSVTERLIRHAIQE 122
Query: 215 KVPIIVAINKIDK 227
+P+++ INKID+
Sbjct: 123 GLPMVLVINKIDR 135
>gnl|CDD|129581 TIGR00490, aEF-2, translation elongation factor aEF-2. This model
represents archaeal elongation factor 2, a protein more
similar to eukaryotic EF-2 than to bacterial EF-G, both
in sequence similarity and in sharing with eukaryotes
the property of having a diphthamide (modified His)
residue at a conserved position. The diphthamide can be
ADP-ribosylated by diphtheria toxin in the presence of
NAD [Protein synthesis, Translation factors].
Length = 720
Score = 71.5 bits (175), Expect = 6e-13
Identities = 76/337 (22%), Positives = 127/337 (37%), Gaps = 82/337 (24%)
Query: 111 LMKRPPVVT---IMGHVDHGKTTLLDTL-RNTSVVKSEFGGITQHI-------------- 152
LM +P + I+ H+DHGKTTL D L ++ E G ++
Sbjct: 12 LMWKPKFIRNIGIVAHIDHGKTTLSDNLLAGAGMISEELAGQQLYLDFDEQEQERGITIN 71
Query: 153 GAFVVTLKSGEQ----VTFLDTPGHAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESI 208
A V + E + +DTPGH F +R D ++VV A +GVM QT +
Sbjct: 72 AANVSMVHEYEGNEYLINLIDTPGHVDFGGDVTRAMRAVDGAIVVVCAVEGVMPQTETVL 131
Query: 209 RMAREAKVPIIVAINKIDKPAADIERTKNMLLAQGITV-EDLGGDIQA------------ 255
R A + V ++ INK+D+ +++ T L + I + ++ I+A
Sbjct: 132 RQALKENVKPVLFINKVDRLINELKLTPQELQERFIKIITEVNKLIKAMAPEEFRDKWKV 191
Query: 256 -------------------VPISALTGTNVDNLTEAIERTKNMLLAQGITVEDLGGDIQA 296
VP TG ++ + + K LA+ + +
Sbjct: 192 RVEDGSVAFGSAYYNWAISVPSMKKTGIGFKDIYKYCKEDKQKELAKKSPLHQV------ 245
Query: 297 VPISALTGTNVDNLTEAIVAQAE-IMH--------------LKADYGGPVEAMIVESKFD 341
+ + +L I AQ I L D GP+ MI + D
Sbjct: 246 -----VLDMVIRHLPSPIEAQKYRIPVIWKGDLNSEVGKAMLNCDPKGPLALMITKIVVD 300
Query: 342 THRGKLATALVQRGTLKKGAIV--VAGQAWAKVRSIS 376
H G++A + GT++ G V V +A A+++ +
Sbjct: 301 KHAGEVAVGRLYSGTIRPGMEVYIVDRKAKARIQQVG 337
>gnl|CDD|237358 PRK13351, PRK13351, elongation factor G; Reviewed.
Length = 687
Score = 70.0 bits (172), Expect = 2e-12
Identities = 37/137 (27%), Positives = 58/137 (42%), Gaps = 21/137 (15%)
Query: 118 VTIMGHVDHGKTTLLDTLRNTSVVKSEFG------------------GITQHIGAFVVTL 159
+ I+ H+D GKTTL + + + + G GIT I + +
Sbjct: 11 IGILAHIDAGKTTLTERILFYTGKIHKMGEVEDGTTVTDWMPQEQERGIT--IESAATSC 68
Query: 160 KSGE-QVTFLDTPGHAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMAREAKVPI 218
++ +DTPGH F+ R D V+V A GV QT R A +P
Sbjct: 69 DWDNHRINLIDTPGHIDFTGEVERSLRVLDGAVVVFDAVTGVQPQTETVWRQADRYGIPR 128
Query: 219 IVAINKIDKPAADIERT 235
++ INK+D+ AD+ +
Sbjct: 129 LIFINKMDRVGADLFKV 145
>gnl|CDD|206672 cd01885, EF2, Elongation Factor 2 (EF2) in archaea and eukarya.
Translocation requires hydrolysis of a molecule of GTP
and is mediated by EF-G in bacteria and by eEF2 in
eukaryotes. The eukaryotic elongation factor eEF2 is a
GTPase involved in the translocation of the
peptidyl-tRNA from the A site to the P site on the
ribosome. The 95-kDa protein is highly conserved, with
60% amino acid sequence identity between the human and
yeast proteins. Two major mechanisms are known to
regulate protein elongation and both involve eEF2.
First, eEF2 can be modulated by reversible
phosphorylation. Increased levels of phosphorylated eEF2
reduce elongation rates presumably because
phosphorylated eEF2 fails to bind the ribosomes.
Treatment of mammalian cells with agents that raise the
cytoplasmic Ca2+ and cAMP levels reduce elongation rates
by activating the kinase responsible for phosphorylating
eEF2. In contrast, treatment of cells with insulin
increases elongation rates by promoting eEF2
dephosphorylation. Second, the protein can be
post-translationally modified by ADP-ribosylation.
Various bacterial toxins perform this reaction after
modification of a specific histidine residue to
diphthamide, but there is evidence for endogenous ADP
ribosylase activity. Similar to the bacterial toxins, it
is presumed that modification by the endogenous enzyme
also inhibits eEF2 activity.
Length = 218
Score = 66.1 bits (162), Expect = 3e-12
Identities = 43/134 (32%), Positives = 62/134 (46%), Gaps = 24/134 (17%)
Query: 118 VTIMGHVDHGKTTLLDTL--RNTSVVKSEFG--------------GITQHIGA----FVV 157
+ I+ HVDHGKTTL D+L + + G GIT A F
Sbjct: 3 ICIIAHVDHGKTTLSDSLLASAGIISEKLAGKARYLDTREDEQERGITIKSSAISLYFEY 62
Query: 158 TLKSGEQVTFL----DTPGHAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMARE 213
+ + +L D+PGH FS+ + TD ++VV A +GV QT +R A E
Sbjct: 63 EEEKMDGNDYLINLIDSPGHVDFSSEVTAALRLTDGALVVVDAVEGVCVQTETVLRQALE 122
Query: 214 AKVPIIVAINKIDK 227
+V ++ INKID+
Sbjct: 123 ERVKPVLVINKIDR 136
>gnl|CDD|206731 cd04168, TetM_like, Tet(M)-like family includes Tet(M), Tet(O),
Tet(W), and OtrA, containing tetracycline resistant
proteins. Tet(M), Tet(O), Tet(W), and OtrA are
tetracycline resistance genes found in Gram-positive and
Gram-negative bacteria. Tetracyclines inhibit protein
synthesis by preventing aminoacyl-tRNA from binding to
the ribosomal acceptor site. This subfamily contains
tetracycline resistance proteins that function through
ribosomal protection and are typically found on mobile
genetic elements, such as transposons or plasmids, and
are often conjugative. Ribosomal protection proteins are
homologous to the elongation factors EF-Tu and EF-G.
EF-G and Tet(M) compete for binding on the ribosomes.
Tet(M) has a higher affinity than EF-G, suggesting these
two proteins may have overlapping binding sites and that
Tet(M) must be released before EF-G can bind. Tet(M) and
Tet(O) have been shown to have ribosome-dependent GTPase
activity. These proteins are part of the GTP translation
factor family, which includes EF-G, EF-Tu, EF2, LepA,
and SelB.
Length = 237
Score = 66.1 bits (162), Expect = 4e-12
Identities = 63/229 (27%), Positives = 99/229 (43%), Gaps = 36/229 (15%)
Query: 120 IMGHVDHGKTTLLDTLRNTSVVKSEFG------------------GITQHIGAFVVTLKS 161
I+ HVD GKTTL ++L TS E G GIT I + V + +
Sbjct: 4 ILAHVDAGKTTLTESLLYTSGAIRELGSVDKGTTRTDSMELERQRGIT--IFSAVASFQW 61
Query: 162 GEQ-VTFLDTPGHAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMAREAKVPIIV 220
+ V +DTPGH F R D +LV++A +GV QT R+ R+ +P I+
Sbjct: 62 EDTKVNIIDTPGHMDFIAEVERSLSVLDGAILVISAVEGVQAQTRILFRLLRKLNIPTII 121
Query: 221 AINKIDKPAADIERT-KNM--LLAQGITVEDLGGDIQAVPISALTGTN-VDNLTEAIERT 276
+NKID+ AD+E+ + + L+ I G + + ++ + E +
Sbjct: 122 FVNKIDRAGADLEKVYQEIKEKLSPDIVPMQKVGLYPNICDTNNIDDEQIETVAEGNDEL 181
Query: 277 KNMLLAQG-ITVEDLGGDIQAV-------PI---SALTGTNVDNLTEAI 314
L+ G + +L ++ A P+ SAL G +D L E I
Sbjct: 182 LEKYLSGGPLEELELDNELSARIQKASLFPVYHGSALKGIGIDELLEGI 230
>gnl|CDD|234596 PRK00049, PRK00049, elongation factor Tu; Reviewed.
Length = 396
Score = 68.3 bits (168), Expect = 4e-12
Identities = 52/139 (37%), Positives = 63/139 (45%), Gaps = 47/139 (33%)
Query: 119 TIMGHVDHGKTTLLDTLRNTSVVKSEFG------------------GIT---QHIG---- 153
TI GHVDHGKTTL T T V+ + G GIT H+
Sbjct: 17 TI-GHVDHGKTTL--TAAITKVLAKKGGAEAKAYDQIDKAPEEKARGITINTAHVEYETE 73
Query: 154 ----AFVVTLKSGEQVTFLDTPGHAAF-SNMRSRGAHCTDIVVLVVAADDGVMEQTVESI 208
A V D PGHA + NM + GA D +LVV+A DG M QT E I
Sbjct: 74 KRHYAHV------------DCPGHADYVKNMIT-GAAQMDGAILVVSAADGPMPQTREHI 120
Query: 209 RMAREAKVP-IIVAINKID 226
+AR+ VP I+V +NK D
Sbjct: 121 LLARQVGVPYIVVFLNKCD 139
>gnl|CDD|239672 cd03701, IF2_IF5B_II, IF2_IF5B_II: This family represents the
domain II of prokaryotic Initiation Factor 2 (IF2) and
its archeal and eukaryotic homologue aeIF5B. IF2, the
largest initiation factor is an essential GTP binding
protein. In E. coli three natural forms of IF2 exist in
the cell, IF2alpha, IF2beta1, and IF2beta2. Disruption
of the eIF5B gene (FUN12) in yeast causes a severe
slow-growth phenotype, associated with a defect in
translation. eIF5B has a function analogous to
prokaryotic IF2 in mediating the joining of the 60S
ribosomal subunit. The eIF5B consists of three
N-terminal domains (I, II, II) connected by a long
helix to domain IV. Domain I is a G domain, domain II
and IV are beta-barrels and domain III has a novel
alpha-beta-alpha sandwich fold. The G domain and the
beta-barrel domain II display a similar structure and
arrangement to the homologous domains in EF1A, eEF1A and
aeIF2gamma.
Length = 95
Score = 62.1 bits (152), Expect = 4e-12
Identities = 22/47 (46%), Positives = 32/47 (68%)
Query: 331 VEAMIVESKFDTHRGKLATALVQRGTLKKGAIVVAGQAWAKVRSISR 377
E ++ESK D RG +AT +VQ GTLKKG ++VAG + K+R++
Sbjct: 1 AEGTVIESKLDKGRGPVATVIVQNGTLKKGDVIVAGGTYGKIRTMVD 47
>gnl|CDD|206733 cd04170, EF-G_bact, Elongation factor G (EF-G) family.
Translocation is mediated by EF-G (also called
translocase). The structure of EF-G closely resembles
that of the complex between EF-Tu and tRNA. This is an
example of molecular mimicry; a protein domain evolved
so that it mimics the shape of a tRNA molecule. EF-G in
the GTP form binds to the ribosome, primarily through
the interaction of its EF-Tu-like domain with the 50S
subunit. The binding of EF-G to the ribosome in this
manner stimulates the GTPase activity of EF-G. On GTP
hydrolysis, EF-G undergoes a conformational change that
forces its arm deeper into the A site on the 30S
subunit. To accommodate this domain, the peptidyl-tRNA
in the A site moves to the P site, carrying the mRNA and
the deacylated tRNA with it. The ribosome may be
prepared for these rearrangements by the initial binding
of EF-G as well. The dissociation of EF-G leaves the
ribosome ready to accept the next aminoacyl-tRNA into
the A site. This group contains only bacterial members.
Length = 268
Score = 66.1 bits (162), Expect = 6e-12
Identities = 38/140 (27%), Positives = 62/140 (44%), Gaps = 19/140 (13%)
Query: 118 VTIMGHVDHGKTTLLDTLRNTSVVKSEFG----GIT----------QHIG---AFVVTLK 160
+ ++GH GKTTL + L + G G T + + +
Sbjct: 2 IALVGHSGSGKTTLAEALLYATGAIDRLGRVEDGNTVSDYDPEEKKRKMSIETSVAPLEW 61
Query: 161 SGEQVTFLDTPGHAAFSNMRSRGA-HCTDIVVLVVAADDGVMEQTVESIRMAREAKVPII 219
+G ++ +DTPG+A F + A D ++VV A GV T + +AK+P I
Sbjct: 62 NGHKINLIDTPGYADFVG-ETLSALRAVDAALIVVEAQSGVEVGTEKVWEFLDDAKLPRI 120
Query: 220 VAINKIDKPAADIERTKNML 239
+ INK+D+ AD ++T L
Sbjct: 121 IFINKMDRARADFDKTLAAL 140
>gnl|CDD|237184 PRK12736, PRK12736, elongation factor Tu; Reviewed.
Length = 394
Score = 67.3 bits (165), Expect = 7e-12
Identities = 53/134 (39%), Positives = 67/134 (50%), Gaps = 28/134 (20%)
Query: 116 PVVTI--MGHVDHGKTTLLDTLRNTSVVKSEFG-------------------GITQHIGA 154
P V I +GHVDHGKTTL T T V+ +E G GIT + A
Sbjct: 11 PHVNIGTIGHVDHGKTTL--TAAITKVL-AERGLNQAKDYDSIDAAPEEKERGITINT-A 66
Query: 155 FVVTLKSGEQVTFLDTPGHAAF-SNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMARE 213
V +D PGHA + NM + GA D +LVVAA DG M QT E I +AR+
Sbjct: 67 HVEYETEKRHYAHVDCPGHADYVKNMIT-GAAQMDGAILVVAATDGPMPQTREHILLARQ 125
Query: 214 AKVP-IIVAINKID 226
VP ++V +NK+D
Sbjct: 126 VGVPYLVVFLNKVD 139
>gnl|CDD|183708 PRK12735, PRK12735, elongation factor Tu; Reviewed.
Length = 396
Score = 66.8 bits (164), Expect = 1e-11
Identities = 53/139 (38%), Positives = 65/139 (46%), Gaps = 43/139 (30%)
Query: 117 VVTIMGHVDHGKTTLLDTLRNTSVVKSEFG------------------GIT---QHIGAF 155
V TI GHVDHGKTTL T T V+ + G GIT H+
Sbjct: 15 VGTI-GHVDHGKTTL--TAAITKVLAKKGGGEAKAYDQIDNAPEEKARGITINTSHV--- 68
Query: 156 VVTLKSGEQVT------FLDTPGHAAF-SNMRSRGAHCTDIVVLVVAADDGVMEQTVESI 208
E T +D PGHA + NM + GA D +LVV+A DG M QT E I
Sbjct: 69 -------EYETANRHYAHVDCPGHADYVKNMIT-GAAQMDGAILVVSAADGPMPQTREHI 120
Query: 209 RMAREAKVP-IIVAINKID 226
+AR+ VP I+V +NK D
Sbjct: 121 LLARQVGVPYIVVFLNKCD 139
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 64.7 bits (159), Expect = 2e-11
Identities = 39/123 (31%), Positives = 59/123 (47%), Gaps = 23/123 (18%)
Query: 164 QVTFLDTPG-------------HAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRM 210
Q+ F+DTPG AA+S+++ D+V+ VV AD+ + +
Sbjct: 54 QIIFVDTPGIHKPKRALNRAMNKAAWSSLKD-----VDLVLFVVDADEKIGPGDEFILEK 108
Query: 211 AREAKVPIIVAINKIDKPAADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLT 270
++ K P+I+ +NKID D E LL + +L + VPISAL G NVD L
Sbjct: 109 LKKVKTPVILVLNKIDL-VKDKEE----LLPLLEELSELMDFAEIVPISALKGDNVDELL 163
Query: 271 EAI 273
+ I
Sbjct: 164 DVI 166
>gnl|CDD|129574 TIGR00483, EF-1_alpha, translation elongation factor EF-1 alpha.
This model represents the counterpart of bacterial EF-Tu
for the Archaea (aEF-1 alpha) and Eukaryotes (eEF-1
alpha). The trusted cutoff is set fairly high so that
incomplete sequences will score between suggested and
trusted cutoff levels [Protein synthesis, Translation
factors].
Length = 426
Score = 66.0 bits (161), Expect = 2e-11
Identities = 59/222 (26%), Positives = 87/222 (39%), Gaps = 55/222 (24%)
Query: 118 VTIMGHVDHGKTTLLDTLRNTSVVKSEFGGITQHI-----------------GAFVVTLK 160
V +GHVDHGK+T + L G I + A+V+
Sbjct: 10 VAFIGHVDHGKSTTVGHLLYKC------GAIDEQTIEKFEKEAQEKGKASFEFAWVMDRL 63
Query: 161 SGE-------------------QVTFLDTPGHAAFSNMRSRGAHCTDIVVLVVAADDG-- 199
E +VT +D PGH F GA D VLVVA DG
Sbjct: 64 KEERERGVTIDVAHWKFETDKYEVTIVDCPGHRDFIKNMITGASQADAAVLVVAVGDGEF 123
Query: 200 -VMEQTVESIRMAREAKV-PIIVAINKIDKPAADIERTKNMLLAQGITVEDLG---GDIQ 254
V QT E +AR + +IVAINK+D D E + + ++ +G +
Sbjct: 124 EVQPQTREHAFLARTLGINQLIVAINKMDSVNYDEEEFEAIKKEVSNLIKKVGYNPDTVP 183
Query: 255 AVPISALTGTNVDNLTEAIERTKNMLLAQGITVEDLGGDIQA 296
+PISA G NV I++++N +G T+ + ++
Sbjct: 184 FIPISAWNGDNV------IKKSENTPWYKGKTLLEALDALEP 219
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 63.7 bits (156), Expect = 5e-11
Identities = 55/172 (31%), Positives = 84/172 (48%), Gaps = 27/172 (15%)
Query: 118 VTIMGHVDHGKTTLLDTLRNT--SVVKSEFGGITQHIGAFVVTLKSGEQVTFLDTPG--- 172
V I+G + GK+TLL+ L S+V S T++ +VT + Q+ F+DTPG
Sbjct: 9 VAIIGRPNVGKSTLLNALVGQKISIV-SPKPQTTRNRIRGIVTTDN-AQIIFVDTPGIHK 66
Query: 173 ----------HAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMAREAKVPIIVAI 222
AA S ++ D+++ VV AD+G + ++ K P+I+ +
Sbjct: 67 PKHALGELMNKAARSALKD-----VDLILFVVDADEGWGPGDEFILEQLKKTKTPVILVV 121
Query: 223 NKIDKPAADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIE 274
NKIDK + K +LL ++ L + VPISAL G NVD L E I+
Sbjct: 122 NKIDK-----VKPKTVLLKLIAFLKKLLPFKEIVPISALKGDNVDTLLEIIK 168
>gnl|CDD|211860 TIGR03680, eif2g_arch, translation initiation factor 2 subunit
gamma. This model represents the archaeal translation
initiation factor 2 subunit gamma and is found in all
known archaea. eIF-2 functions in the early steps of
protein synthesis by forming a ternary complex with GTP
and initiator tRNA.
Length = 406
Score = 63.9 bits (156), Expect = 1e-10
Identities = 62/200 (31%), Positives = 84/200 (42%), Gaps = 47/200 (23%)
Query: 114 RPPVVTI--MGHVDHGKTTLLDTLRN--TSVVKSEFG-GITQHIG--------------- 153
R P V I +GHVDHGKTTL L T E GI+ +G
Sbjct: 1 RQPEVNIGMVGHVDHGKTTLTKALTGVWTDTHSEELKRGISIRLGYADAEIYKCPECDGP 60
Query: 154 -AFVVTLKSGE---------QVTFLDTPGHAAF-SNMRSRGAHCTDIVVLVVAADDGV-M 201
+ +V+F+D PGH + M S GA D +LV+AA++
Sbjct: 61 ECYTTEPVCPNCGSETELLRRVSFVDAPGHETLMATMLS-GAALMDGALLVIAANEPCPQ 119
Query: 202 EQTVESIRMAREA--KVPIIVAINKID-----KPAADIERTKNMLLAQGITVEDLGGDIQ 254
QT E + MA E I++ NKID K + E K + +G E+
Sbjct: 120 PQTREHL-MALEIIGIKNIVIVQNKIDLVSKEKALENYEEIKEFV--KGTIAEN----AP 172
Query: 255 AVPISALTGTNVDNLTEAIE 274
+P+SAL N+D L EAIE
Sbjct: 173 IIPVSALHNANIDALLEAIE 192
>gnl|CDD|178673 PLN03127, PLN03127, Elongation factor Tu; Provisional.
Length = 447
Score = 63.3 bits (154), Expect = 2e-10
Identities = 91/326 (27%), Positives = 133/326 (40%), Gaps = 87/326 (26%)
Query: 74 IIQKSGMKYMVINPTNSVADDSNGKDVERRPPADPSVLM-----KRPPV-VTIMGHVDHG 127
++ S Y + S +R+ P+ M +P V V +GHVDHG
Sbjct: 14 LLPFSSQIYCACRGSAPSTSASISAADDRQSPSPWWRSMATFTRTKPHVNVGTIGHVDHG 73
Query: 128 KTTLLDTLRNTSVVKSEFG------------------GITQHIGAFVVTLKSGEQ-VTFL 168
KTTL T T V+ E GIT I V ++ ++ +
Sbjct: 74 KTTL--TAAITKVLAEEGKAKAVAFDEIDKAPEEKARGIT--IATAHVEYETAKRHYAHV 129
Query: 169 DTPGHAAF-SNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMAREAKVP-IIVAINKID 226
D PGHA + NM + GA D +LVV+A DG M QT E I +AR+ VP ++V +NK+D
Sbjct: 130 DCPGHADYVKNMIT-GAAQMDGGILVVSAPDGPMPQTKEHILLARQVGVPSLVVFLNKVD 188
Query: 227 KPAADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIERTKNMLLAQGIT 286
V+D + L E +E M L + ++
Sbjct: 189 ------------------VVDD------------------EELLELVE----MELRELLS 208
Query: 287 VEDLGGD----IQAVPISALTGTNVDNLTEAIVAQAEIMHLKADY-GGPVEA------MI 335
GD I+ +SAL GTN + AI+ ++M +Y PV M
Sbjct: 209 FYKFPGDEIPIIRGSALSALQGTNDEIGKNAIL---KLMDAVDEYIPEPVRVLDKPFLMP 265
Query: 336 VESKFDTH-RGKLATALVQRGTLKKG 360
+E F RG +AT V++GT+K G
Sbjct: 266 IEDVFSIQGRGTVATGRVEQGTIKVG 291
>gnl|CDD|129576 TIGR00485, EF-Tu, translation elongation factor TU. This model
models orthologs of translation elongation factor EF-Tu
in bacteria, mitochondria, and chloroplasts, one of
several GTP-binding translation factors found by the
more general pfam model GTP_EFTU. The eukaryotic
conterpart, eukaryotic translation elongation factor 1
(eEF-1 alpha), is excluded from this model. EF-Tu is one
of the most abundant proteins in bacteria, as well as
one of the most highly conserved, and in a number of
species the gene is duplicated with identical function.
When bound to GTP, EF-Tu can form a complex with any
(correctly) aminoacylated tRNA except those for
initiation and for selenocysteine, in which case EF-Tu
is replaced by other factors. Transfer RNA is carried to
the ribosome in these complexes for protein translation
[Protein synthesis, Translation factors].
Length = 394
Score = 62.9 bits (153), Expect = 2e-10
Identities = 50/130 (38%), Positives = 66/130 (50%), Gaps = 26/130 (20%)
Query: 118 VTIMGHVDHGKTTLLDTLRNTSVVKSEFG------------------GITQHIGAFVVTL 159
+ +GHVDHGKTTL T T+V+ E G GIT I V
Sbjct: 15 IGTIGHVDHGKTTL--TAAITTVLAKEGGAAARAYDQIDNAPEEKARGIT--INTAHVEY 70
Query: 160 KSGEQ-VTFLDTPGHAAF-SNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMAREAKVP 217
++ + +D PGHA + NM + GA D +LVV+A DG M QT E I +AR+ VP
Sbjct: 71 ETENRHYAHVDCPGHADYVKNMIT-GAAQMDGAILVVSATDGPMPQTREHILLARQVGVP 129
Query: 218 -IIVAINKID 226
I+V +NK D
Sbjct: 130 YIVVFLNKCD 139
>gnl|CDD|104396 PRK10218, PRK10218, GTP-binding protein; Provisional.
Length = 607
Score = 63.2 bits (153), Expect = 3e-10
Identities = 77/281 (27%), Positives = 116/281 (41%), Gaps = 64/281 (22%)
Query: 118 VTIMGHVDHGKTTLLDTLRNTS------------VVKS----EFGGITQHIGAFVVTLKS 161
+ I+ HVDHGKTTL+D L S V+ S + GIT I A +K
Sbjct: 8 IAIIAHVDHGKTTLVDKLLQQSGTFDSRAETQERVMDSNDLEKERGIT--ILAKNTAIKW 65
Query: 162 GE-QVTFLDTPGHAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMAREAKVPIIV 220
+ ++ +DTPGHA F R D V+LVV A DG M QT + A + IV
Sbjct: 66 NDYRINIVDTPGHADFGGEVERVMSMVDSVLLVVDAFDGPMPQTRFVTKKAFAYGLKPIV 125
Query: 221 AINKIDKPAAD----IERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIERT 276
INK+D+P A +++ ++ + T E L D V SAL G
Sbjct: 126 VINKVDRPGARPDWVVDQVFDLFVNLDATDEQL--DFPIVYASALNGI------------ 171
Query: 277 KNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIVAQAEIMHLKA---DYGGPVEA 333
G+ ED+ D+ + QA + H+ A D GP +
Sbjct: 172 ------AGLDHEDMAEDMTP------------------LYQAIVDHVPAPDVDLDGPFQM 207
Query: 334 MIVESKFDTHRGKLATALVQRGTLKKGAIVVAGQAWAKVRS 374
I + ++++ G + ++RG +K V + K R+
Sbjct: 208 QISQLDYNSYVGVIGIGRIKRGKVKPNQQVTIIDSEGKTRN 248
>gnl|CDD|206682 cd01895, EngA2, EngA2 GTPase contains the second domain of EngA.
This EngA2 subfamily CD represents the second GTPase
domain of EngA and its orthologs, which are composed of
two adjacent GTPase domains. Since the sequences of the
two domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family. Although the exact function of
these proteins has not been elucidated, studies have
revealed that the E. coli EngA homolog, Der, and
Neisseria gonorrhoeae EngA are essential for cell
viability. A recent report suggests that E. coli Der
functions in ribosome assembly and stability.
Length = 174
Score = 59.4 bits (145), Expect = 3e-10
Identities = 46/176 (26%), Positives = 79/176 (44%), Gaps = 24/176 (13%)
Query: 118 VTIMGHVDHGKTTLLDTL-RNTSVVKSEFGGITQHIGAFVVTLKSGEQVTFLDTPG---- 172
+ I+G + GK++LL+ L V+ S+ G T+ G++ T +DT G
Sbjct: 5 IAIIGRPNVGKSSLLNALLGEERVIVSDIAGTTRDSIDVPFEYD-GQKYTLIDTAGIRKK 63
Query: 173 ------HAAFSNMRSRGA-HCTDIVVLVVAADDGVMEQTVESIRMAREAKVPIIVAINK- 224
+S +R+ A D+V+LV+ A +G+ EQ + + E +I+ +NK
Sbjct: 64 GKVTEGIEKYSVLRTLKAIERADVVLLVLDASEGITEQDLRIAGLILEEGKALIIVVNKW 123
Query: 225 --IDKPAADIERTKNMLLAQGITVEDLG--GDIQAVPISALTGTNVDNLTEAIERT 276
++K ++ + L + L V ISALTG VD L +AI+
Sbjct: 124 DLVEKDEKTMKEFEKELRRK------LPFLDYAPIVFISALTGQGVDKLFDAIKEV 173
>gnl|CDD|215592 PLN03126, PLN03126, Elongation factor Tu; Provisional.
Length = 478
Score = 62.7 bits (152), Expect = 3e-10
Identities = 77/276 (27%), Positives = 112/276 (40%), Gaps = 56/276 (20%)
Query: 113 KRPPV-VTIMGHVDHGKTTLLDTLRNTSVVKSEFGGITQH----------------IGAF 155
K+P V + +GHVDHGKTTL L T + S G + I
Sbjct: 78 KKPHVNIGTIGHVDHGKTTLTAAL--TMALASMGGSAPKKYDEIDAAPEERARGITINTA 135
Query: 156 VVTLKSGEQ-VTFLDTPGHAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMAREA 214
V ++ + +D PGHA + GA D +LVV+ DG M QT E I +A++
Sbjct: 136 TVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQV 195
Query: 215 KVP-IIVAINKIDKPAAD-----IERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDN 268
VP ++V +NK D+ + +E LL+ + E G DI + SAL
Sbjct: 196 GVPNMVVFLNKQDQVDDEELLELVELEVRELLS---SYEFPGDDIPIISGSALLALEALM 252
Query: 269 LTEAIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIVAQAEIMHLKADYG 328
I+R N + + + D VD+ Q ++ L
Sbjct: 253 ENPNIKRGDNKWVDKIYELMD----------------AVDSYIPIPQRQTDLPFL----- 291
Query: 329 GPVEAMIVESKFD-THRGKLATALVQRGTLKKGAIV 363
+ VE F T RG +AT V+RGT+K G V
Sbjct: 292 -----LAVEDVFSITGRGTVATGRVERGTVKVGETV 322
>gnl|CDD|206729 cd04166, CysN_ATPS, CysN, together with protein CysD, forms the ATP
sulfurylase (ATPS) complex. CysN_ATPS subfamily. CysN,
together with protein CysD, form the ATP sulfurylase
(ATPS) complex in some bacteria and lower eukaryotes.
ATPS catalyzes the production of ATP sulfurylase (APS)
and pyrophosphate (PPi) from ATP and sulfate. CysD,
which catalyzes ATP hydrolysis, is a member of the ATP
pyrophosphatase (ATP PPase) family. CysN hydrolysis of
GTP is required for CysD hydrolysis of ATP; however,
CysN hydrolysis of GTP is not dependent on CysD
hydrolysis of ATP. CysN is an example of lateral gene
transfer followed by acquisition of new function. In
many organisms, an ATPS exists which is not
GTP-dependent and shares no sequence or structural
similarity to CysN.
Length = 209
Score = 59.9 bits (146), Expect = 4e-10
Identities = 58/212 (27%), Positives = 89/212 (41%), Gaps = 65/212 (30%)
Query: 122 GHVDHGKTTL---------------LDTLRNTSVVKSEFGGITQHIGAFVV-TLKSG-EQ 164
G VD GK+TL L L + ++ + A +V L++ EQ
Sbjct: 6 GSVDDGKSTLIGRLLYDSKSIFEDQLAALERSKSSGTQGEKLDL---ALLVDGLQAEREQ 62
Query: 165 -----VTF------------LDTPGHAAFS-NMRSRGAHCTDIVVLVVAADDGVMEQTVE 206
V + DTPGH ++ NM + GA D+ +L+V A GV+EQT
Sbjct: 63 GITIDVAYRYFSTPKRKFIIADTPGHEQYTRNMVT-GASTADLAILLVDARKGVLEQTRR 121
Query: 207 SIRMAREAKVP-IIVAINKID----------KPAADIERTKNMLLAQGITVEDLGGDIQA 255
+A + ++VA+NK+D + AD A + +ED I
Sbjct: 122 HSYIASLLGIRHVVVAVNKMDLVDYDEEVFEEIKADYLA-----FAASLGIED----ITF 172
Query: 256 VPISALTGTNVDNLTEAIERTKNMLLAQGITV 287
+PISAL G NV + R++NM +G T+
Sbjct: 173 IPISALEGDNV------VSRSENMPWYKGPTL 198
>gnl|CDD|236047 PRK07560, PRK07560, elongation factor EF-2; Reviewed.
Length = 731
Score = 62.6 bits (153), Expect = 5e-10
Identities = 47/141 (33%), Positives = 68/141 (48%), Gaps = 26/141 (18%)
Query: 111 LMKRPPVVTIMG---HVDHGKTTLLDTLRNTSVVKSEFG----------------GITQH 151
LMK P + +G H+DHGKTTL D L + + SE GIT
Sbjct: 13 LMKNPEQIRNIGIIAHIDHGKTTLSDNLLAGAGMISEELAGEQLALDFDEEEQARGIT-- 70
Query: 152 IGAFVVTL---KSGEQ--VTFLDTPGHAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVE 206
I A V++ G++ + +DTPGH F +R D ++VV A +GVM QT
Sbjct: 71 IKAANVSMVHEYEGKEYLINLIDTPGHVDFGGDVTRAMRAVDGAIVVVDAVEGVMPQTET 130
Query: 207 SIRMAREAKVPIIVAINKIDK 227
+R A +V ++ INK+D+
Sbjct: 131 VLRQALRERVKPVLFINKVDR 151
>gnl|CDD|225448 COG2895, CysN, GTPases - Sulfate adenylate transferase subunit 1
[Inorganic ion transport and metabolism].
Length = 431
Score = 61.5 bits (150), Expect = 6e-10
Identities = 59/206 (28%), Positives = 89/206 (43%), Gaps = 52/206 (25%)
Query: 122 GHVDHGKTTL---------------LDTLRNTSVVKSEFG------------------GI 148
G VD GK+TL L +L S K G GI
Sbjct: 13 GSVDDGKSTLIGRLLYDTKAIYEDQLASLERDSKRKGTQGEKIDLALLVDGLEAEREQGI 72
Query: 149 TQHIGAFVVTLK--SGEQVTFL--DTPGHAAFS-NMRSRGAHCTDIVVLVVAADDGVMEQ 203
T V + S E+ F+ DTPGH ++ NM + GA D+ +L+V A GV+EQ
Sbjct: 73 T-----IDVAYRYFSTEKRKFIIADTPGHEQYTRNMAT-GASTADLAILLVDARKGVLEQ 126
Query: 204 TVESIRMAREAKVP-IIVAINKIDKPAADIERTKNMLLAQGITVEDLGG-DIQAVPISAL 261
T +A + ++VA+NK+D E + ++ LG D++ +PISAL
Sbjct: 127 TRRHSFIASLLGIRHVVVAVNKMDLVDYSEEVFEAIVADYLAFAAQLGLKDVRFIPISAL 186
Query: 262 TGTNVDNLTEAIERTKNMLLAQGITV 287
G NV + +++NM +G T+
Sbjct: 187 LGDNV------VSKSENMPWYKGPTL 206
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 60.3 bits (147), Expect = 1e-09
Identities = 46/177 (25%), Positives = 80/177 (45%), Gaps = 22/177 (12%)
Query: 118 VTIMGHVDHGKTTLLDT-LRNTSVVKSEFGGITQHIGAFVVTLKSGEQV-TFLDTPG--- 172
+ I+G + GK++L++ L V+ S+ G T + + + + +DT G
Sbjct: 181 IAIIGRPNVGKSSLINAILGEERVIVSDIAGTT--RDSIDIEFERDGRKYVLIDTAGIRR 238
Query: 173 -------HAAFSNMRSRGA-HCTDIVVLVVAADDGVMEQTVESIRMAREAKVPIIVAINK 224
+S R+ A D+V+LV+ A +G+ EQ + + EA I++ +NK
Sbjct: 239 KGKITESVEKYSVARTLKAIERADVVLLVIDATEGISEQDLRIAGLIEEAGRGIVIVVNK 298
Query: 225 ---IDKPAADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIERTKN 278
+++ A +E K L + + L V ISALTG +D L EAI+
Sbjct: 299 WDLVEEDEATMEEFKKKLRRK---LPFLDF-APIVFISALTGQGLDKLFEAIKEIYE 351
Score = 54.9 bits (133), Expect = 8e-08
Identities = 44/174 (25%), Positives = 74/174 (42%), Gaps = 31/174 (17%)
Query: 115 PPVVTIMGHVDHGKTTLLDTL--RNTSVVKSEFGGIT----QHIGAFVVTLKSGEQVTFL 168
PVV I+G + GK+TL + L R ++V S+ G+T + G + +
Sbjct: 3 TPVVAIVGRPNVGKSTLFNRLTGRRIAIV-SDTPGVTRDRIYGDAEW-----LGREFILI 56
Query: 169 DTPGHAAFSN------MR---SRGAHCTDIVVLVVAADDGVMEQTVESIRMAREAKVPII 219
DT G +R D+++ VV +G+ E ++ R +K P+I
Sbjct: 57 DTGGLDDGDEDELQELIREQALIAIEEADVILFVVDGREGITPADEEIAKILRRSKKPVI 116
Query: 220 VAINKIDKPAADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAI 273
+ +NKID A+ + G G+ VPISA G + +L +A+
Sbjct: 117 LVVNKIDNLKAEEL--AYEFYSLGF------GEP--VPISAEHGRGIGDLLDAV 160
>gnl|CDD|235194 PRK04000, PRK04000, translation initiation factor IF-2 subunit
gamma; Validated.
Length = 411
Score = 59.9 bits (146), Expect = 2e-09
Identities = 69/208 (33%), Positives = 93/208 (44%), Gaps = 55/208 (26%)
Query: 112 MKRPPVVTI--MGHVDHGKTTLLDTLRNTSV---VKSE--FGGITQHIG----------- 153
K P V I +GHVDHGKTTL+ L T V SE GIT +G
Sbjct: 4 EKVQPEVNIGMVGHVDHGKTTLVQAL--TGVWTDRHSEELKRGITIRLGYADATIRKCPD 61
Query: 154 -----AFVVTLK---SGEQ------VTFLDTPGHAAF-SNMRSRGAHCTDIVVLVVAADD 198
A+ K G + V+F+D PGH + M S GA D +LV+AA++
Sbjct: 62 CEEPEAYTTEPKCPNCGSETELLRRVSFVDAPGHETLMATMLS-GAALMDGAILVIAANE 120
Query: 199 GV-MEQTVESIRMAREA---KVPIIVAINKID---KPAADIERTKNML-LAQGITVEDLG 250
QT E + MA + K I++ NKID K A +E + + +G E+
Sbjct: 121 PCPQPQTKEHL-MALDIIGIK-NIVIVQNKIDLVSKERA-LENYEQIKEFVKGTVAEN-- 175
Query: 251 GDIQA--VPISALTGTNVDNLTEAIERT 276
A +P+SAL N+D L EAIE
Sbjct: 176 ----APIIPVSALHKVNIDALIEAIEEE 199
>gnl|CDD|177010 CHL00071, tufA, elongation factor Tu.
Length = 409
Score = 59.2 bits (144), Expect = 3e-09
Identities = 81/276 (29%), Positives = 110/276 (39%), Gaps = 70/276 (25%)
Query: 119 TIMGHVDHGKTTLLDTLRNTSVVKSEFG------------------GI---TQHIGAFVV 157
TI GHVDHGKTTL T T + ++ G GI T H+ +
Sbjct: 17 TI-GHVDHGKTTL--TAAITMTLAAKGGAKAKKYDEIDSAPEEKARGITINTAHV-EYET 72
Query: 158 TLKSGEQVTFLDTPGHAAF-SNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMAREAKV 216
+ V D PGHA + NM + GA D +LVV+A DG M QT E I +A++ V
Sbjct: 73 ENRHYAHV---DCPGHADYVKNMIT-GAAQMDGAILVVSAADGPMPQTKEHILLAKQVGV 128
Query: 217 P-IIVAINKIDKPAADIE-------RTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDN 268
P I+V +NK D+ D E + +L G DI V SAL
Sbjct: 129 PNIVVFLNKEDQ-VDDEELLELVELEVRELLSKYDFP----GDDIPIVSGSALLA----- 178
Query: 269 LTEAIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIVAQAEIMHLKADYG 328
EA+ + + V+ I L VD+ + L
Sbjct: 179 -LEALTENPKIKRGENKWVDK---------IYNLM-DAVDSYIPTPERDTDKPFL----- 222
Query: 329 GPVEAMIVESKFD-THRGKLATALVQRGTLKKGAIV 363
M +E F T RG +AT ++RGT+K G V
Sbjct: 223 -----MAIEDVFSITGRGTVATGRIERGTVKVGDTV 253
>gnl|CDD|227583 COG5258, GTPBP1, GTPase [General function prediction only].
Length = 527
Score = 59.4 bits (144), Expect = 4e-09
Identities = 61/213 (28%), Positives = 86/213 (40%), Gaps = 59/213 (27%)
Query: 118 VTIMGHVDHGKTTLLDTLRN-------------TSVVKSEF-GGITQHI--------GAF 155
V + GHVDHGK+TL+ L V K E G++ I
Sbjct: 120 VGVAGHVDHGKSTLVGVLVTGRLDDGDGATRSYLDVQKHEVERGLSADISLRVYGFDDGK 179
Query: 156 VVTLK--------------SGEQVTFLDTPGHAAFSNMRSRG--AHCTDIVVLVVAADDG 199
VV LK + + V+F+DT GH + RG D +LVVAADDG
Sbjct: 180 VVRLKNPLDEAEKAAVVKRADKLVSFVDTVGHEPWLRTTIRGLLGQKVDYGLLVVAADDG 239
Query: 200 VMEQTVESIRMAREAKVPIIVAINKIDKPAAD--------IERTKNMLLAQGITVEDLGG 251
V + T E + +A ++P+IV + KID D I + + V+D
Sbjct: 240 VTKMTKEHLGIALAMELPVIVVVTKIDMVPDDRFQGVVEEISALLKRVGRIPLIVKDTDD 299
Query: 252 DIQA----------VPI---SALTGTNVDNLTE 271
+ A VPI S++TG +D L E
Sbjct: 300 VVLAAKAMKAGRGVVPIFYTSSVTGEGLDLLDE 332
>gnl|CDD|206675 cd01888, eIF2_gamma, Gamma subunit of initiation factor 2 (eIF2
gamma). eIF2 is a heterotrimeric translation initiation
factor that consists of alpha, beta, and gamma subunits.
The GTP-bound gamma subunit also binds initiator
methionyl-tRNA and delivers it to the 40S ribosomal
subunit. Following hydrolysis of GTP to GDP, eIF2:GDP is
released from the ribosome. The gamma subunit has no
intrinsic GTPase activity, but is stimulated by the
GTPase activating protein (GAP) eIF5, and GDP/GTP
exchange is stimulated by the guanine nucleotide
exchange factor (GEF) eIF2B. eIF2B is a heteropentamer,
and the epsilon chain binds eIF2. Both eIF5 and
eIF2B-epsilon are known to bind strongly to eIF2-beta,
but have also been shown to bind directly to eIF2-gamma.
It is possible that eIF2-beta serves simply as a
high-affinity docking site for eIF5 and eIF2B-epsilon,
or that eIF2-beta serves a regulatory role. eIF2-gamma
is found only in eukaryotes and archaea. It is closely
related to SelB, the selenocysteine-specific elongation
factor from eubacteria. The translational factor
components of the ternary complex, IF2 in eubacteria and
eIF2 in eukaryotes are not the same protein (despite
their unfortunately similar names). Both factors are
GTPases; however, eubacterial IF-2 is a single
polypeptide, while eIF2 is heterotrimeric. eIF2-gamma is
a member of the same family as eubacterial IF2, but the
two proteins are only distantly related. This family
includes translation initiation, elongation, and release
factors.
Length = 197
Score = 56.1 bits (136), Expect = 5e-09
Identities = 56/191 (29%), Positives = 77/191 (40%), Gaps = 42/191 (21%)
Query: 122 GHVDHGKTTLLDTLRNTSVV--KSEFG-GITQHIG-AFVVTLKSGEQ------------- 164
GHV HGKTTL+ L V K E IT +G A K
Sbjct: 7 GHVAHGKTTLVKALSGVWTVRHKEELKRNITIKLGYANAKIYKCPNCGCPRPYDTPECEC 66
Query: 165 ------------VTFLDTPGHAAF-SNMRSRGAHCTDIVVLVVAADDGVME-QTVESIRM 210
V+F+D PGH + M S GA D +L++AA++ + QT E +
Sbjct: 67 PGCGGETKLVRHVSFVDCPGHEILMATMLS-GAAVMDGALLLIAANEPCPQPQTSEHL-A 124
Query: 211 AREAKVP--IIVAINKID--KPAADIERTKNML-LAQGITVEDLGGDIQAVPISALTGTN 265
A E II+ NKID K +E + + +G E+ +PISA N
Sbjct: 125 ALEIMGLKHIIILQNKIDLVKEEQALENYEQIKEFVKGTIAEN----APIIPISAQLKYN 180
Query: 266 VDNLTEAIERT 276
+D L E I +
Sbjct: 181 IDVLCEYIVKK 191
>gnl|CDD|129575 TIGR00484, EF-G, translation elongation factor EF-G. After peptide
bond formation, this elongation factor of bacteria and
organelles catalyzes the translocation of the tRNA-mRNA
complex, with its attached nascent polypeptide chain,
from the A-site to the P-site of the ribosome. Every
completed bacterial genome has at least one copy, but
some species have additional EF-G-like proteins. The
closest homolog to canonical (e.g. E. coli) EF-G in the
spirochetes clusters as if it is derived from
mitochondrial forms, while a more distant second copy is
also present. Synechocystis PCC6803 has a few proteins
more closely related to EF-G than to any other
characterized protein. Two of these resemble E. coli
EF-G more closely than does the best match from the
spirochetes; it may be that both function as authentic
EF-G [Protein synthesis, Translation factors].
Length = 689
Score = 58.7 bits (142), Expect = 6e-09
Identities = 44/138 (31%), Positives = 58/138 (42%), Gaps = 19/138 (13%)
Query: 120 IMGHVDHGKTT-----LLDTLRNTSVVKSEFG-------------GITQHIGAFVVTLKS 161
I H+D GKTT L T R + + G GIT A V K
Sbjct: 15 ISAHIDAGKTTTTERILFYTGRIHKIGEVHDGAATMDWMEQEKERGITITSAATTVFWK- 73
Query: 162 GEQVTFLDTPGHAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMAREAKVPIIVA 221
G ++ +DTPGH F+ R D V V+ A GV Q+ R A +VP I
Sbjct: 74 GHRINIIDTPGHVDFTVEVERSLRVLDGAVAVLDAVGGVQPQSETVWRQANRYEVPRIAF 133
Query: 222 INKIDKPAADIERTKNML 239
+NK+DK A+ R N +
Sbjct: 134 VNKMDKTGANFLRVVNQI 151
>gnl|CDD|234395 TIGR03918, GTP_HydF, [FeFe] hydrogenase H-cluster maturation GTPase
HydF. This model describes the family of the [Fe]
hydrogenase maturation protein HypF as characterized in
Chlamydomonas reinhardtii and found, in an operon with
radical SAM proteins HydE and HydG, in numerous
bacteria. It has GTPase activity, can bind an 4Fe-4S
cluster, and is essential for hydrogenase activity
[Protein fate, Protein modification and repair].
Length = 391
Score = 57.9 bits (141), Expect = 7e-09
Identities = 51/186 (27%), Positives = 74/186 (39%), Gaps = 42/186 (22%)
Query: 127 GKTTLLDTLRNTSV-VKSEFGGIT----------QHIGAFVVTLKSGEQVTFLDTPG--- 172
GK++L++ L + + S+ G T +G V +DT G
Sbjct: 18 GKSSLINALTGQDIAIVSDVPGTTTDPVYKAMELLPLGP----------VVLIDTAGLDD 67
Query: 173 HAAFSNMR---SRGA-HCTDIVVLVVAADDGVMEQTVESIRMAREAKVPIIVAINKIDKP 228
+R +R TD+ +LVV A G E +E I +E K+P IV INKID
Sbjct: 68 EGELGELRVEKTREVLDKTDLALLVVDAGVGPGEYELELIEELKERKIPYIVVINKIDLG 127
Query: 229 AADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIERTKNMLLAQGITVE 288
E K G+ + +SALTG +D L EAI LL +
Sbjct: 128 EESAELEKLE-KKFGLPP---------IFVSALTGEGIDELKEAIIE----LLPEDFEEP 173
Query: 289 DLGGDI 294
+ GD+
Sbjct: 174 TIVGDL 179
>gnl|CDD|206728 cd04165, GTPBP1_like, GTP binding protein 1 (GTPBP1)-like family
includes GTPBP2. Mammalian GTP binding protein 1
(GTPBP1), GTPBP2, and nematode homologs AGP-1 and CGP-1
are GTPases whose specific functions remain unknown. In
mouse, GTPBP1 is expressed in macrophages, in smooth
muscle cells of various tissues and in some neurons of
the cerebral cortex; GTPBP2 tissue distribution appears
to overlap that of GTPBP1. In human leukemia and
macrophage cell lines, expression of both GTPBP1 and
GTPBP2 is enhanced by interferon-gamma (IFN-gamma). The
chromosomal location of both genes has been identified
in humans, with GTPBP1 located in chromosome 22q12-13.1
and GTPBP2 located in chromosome 6p21-12. Human
glioblastoma multiforme (GBM), a highly-malignant
astrocytic glioma and the most common cancer in the
central nervous system, has been linked to chromosomal
deletions and a translocation on chromosome 6. The GBM
translocation results in a fusion of GTPBP2 and PTPRZ1,
a protein involved in oligodendrocyte differentiation,
recovery, and survival. This fusion product may
contribute to the onset of GBM.
Length = 224
Score = 56.1 bits (136), Expect = 7e-09
Identities = 54/215 (25%), Positives = 84/215 (39%), Gaps = 63/215 (29%)
Query: 118 VTIMGHVDHGKTTLLDTLRN-------------------------TSVVKSEFGG----- 147
V ++G+VD GK+TLL L TS V ++ G
Sbjct: 2 VAVVGNVDAGKSTLLGVLTQGELDNGRGKARLNLFRHKHEVESGRTSSVSNDILGFDSDG 61
Query: 148 --------ITQHIGAFVVTLKSGEQVTFLDTPGHAAFSNMRSRG--AHCTDIVVLVVAAD 197
+ + KS + VTF+D GH + G + D +LVV A+
Sbjct: 62 EVVNYPDNHLGELDVEICE-KSSKVVTFIDLAGHERYLKTTVFGMTGYAPDYAMLVVGAN 120
Query: 198 DGVMEQTVESIRMAREAKVPIIVAINKIDK-PAADIERT----KNMLLAQGI-----TVE 247
G++ T E + +A KVP+ V + KID PA ++ T K +L + G+ V+
Sbjct: 121 AGIIGMTKEHLGLALALKVPVFVVVTKIDMTPANVLQETLKDLKRLLKSPGVRKLPVPVK 180
Query: 248 DLGGDIQA---------VPI---SALTGTNVDNLT 270
+ + VPI S +TG +D L
Sbjct: 181 SKDDVVLSASNLSSGRVVPIFQVSNVTGEGLDLLR 215
>gnl|CDD|234274 TIGR03594, GTPase_EngA, ribosome-associated GTPase EngA. EngA
(YfgK, Der) is a ribosome-associated essential GTPase
with a duplication of its GTP-binding domain. It is
broadly to universally distributed among bacteria. It
appears to function in ribosome biogenesis or stability
[Protein synthesis, Other].
Length = 429
Score = 57.8 bits (141), Expect = 9e-09
Identities = 39/131 (29%), Positives = 59/131 (45%), Gaps = 21/131 (16%)
Query: 162 GEQVTFLDTPG----------HAAFSNMRSRGA-HCTDIVVLVVAADDGVMEQTVESIRM 210
G++ T +DT G +S +R+ A D+V+LV+ A +G+ EQ + +
Sbjct: 219 GKKYTLIDTAGIRRKGKVTEGVEKYSVLRTLKAIERADVVLLVLDATEGITEQDLRIAGL 278
Query: 211 AREAKVPIIVAINKID--KPAADIERTKNMLLAQGITVEDLG--GDIQAVPISALTGTNV 266
A EA +++ +NK D K E K L + L V ISALTG V
Sbjct: 279 ALEAGKALVIVVNKWDLVKDEKTREEFKKELRRK------LPFLDFAPIVFISALTGQGV 332
Query: 267 DNLTEAIERTK 277
D L +AI+
Sbjct: 333 DKLLDAIDEVY 343
Score = 51.7 bits (125), Expect = 7e-07
Identities = 24/86 (27%), Positives = 41/86 (47%), Gaps = 10/86 (11%)
Query: 188 DIVVLVVAADDGVMEQTVESIRMAREAKVPIIVAINKIDKPAADIERTKNMLLAQGITVE 247
D+++ VV +G+ + E + R++ P+I+ NKID D + L G
Sbjct: 80 DVILFVVDGREGLTPEDEEIAKWLRKSGKPVILVANKIDGKKEDAVAAEFYSL--GF--- 134
Query: 248 DLGGDIQAVPISALTGTNVDNLTEAI 273
G+ +PISA G + +L +AI
Sbjct: 135 ---GEP--IPISAEHGRGIGDLLDAI 155
>gnl|CDD|227582 COG5257, GCD11, Translation initiation factor 2, gamma subunit
(eIF-2gamma; GTPase) [Translation, ribosomal structure
and biogenesis].
Length = 415
Score = 57.4 bits (139), Expect = 1e-08
Identities = 60/192 (31%), Positives = 83/192 (43%), Gaps = 45/192 (23%)
Query: 122 GHVDHGKTTLLDTLRNTSVVK-SE--FGGITQHIG----------------AFVVTLKSG 162
GHVDHGKTTL L + SE GIT +G + K
Sbjct: 17 GHVDHGKTTLTKALSGVWTDRHSEELKRGITIKLGYADAKIYKCPECYRPECYTTEPKCP 76
Query: 163 E---------QVTFLDTPGHAAF-SNMRSRGAHCTDIVVLVVAADDGVME-QTVESIRMA 211
+V+F+D PGH + M S GA D +LV+AA++ + QT E + MA
Sbjct: 77 NCGAETELVRRVSFVDAPGHETLMATMLS-GAALMDGALLVIAANEPCPQPQTREHL-MA 134
Query: 212 RE--AKVPIIVAINKID-----KPAADIERTKNMLLAQGITVEDLGGDIQAVPISALTGT 264
E II+ NKID + + E+ K + +G E+ +PISA
Sbjct: 135 LEIIGIKNIIIVQNKIDLVSRERALENYEQIKEFV--KGTVAEN----APIIPISAQHKA 188
Query: 265 NVDNLTEAIERT 276
N+D L EAIE+
Sbjct: 189 NIDALIEAIEKY 200
>gnl|CDD|129528 TIGR00436, era, GTP-binding protein Era. Era is an essential
GTPase in Escherichia coli and many other bacteria. It
plays a role in ribosome biogenesis. Few bacteria lack
this protein [Protein synthesis, Other].
Length = 270
Score = 55.9 bits (135), Expect = 2e-08
Identities = 66/282 (23%), Positives = 115/282 (40%), Gaps = 44/282 (15%)
Query: 118 VTIMGHVDHGKTTLLDTLRN-TSVVKSEFGGITQHIGAFVVTLKSGEQVTFLDTPG---- 172
V I+G + GK+TLL+ L + S T++ + + T + Q+ F+DTPG
Sbjct: 3 VAILGRPNVGKSTLLNQLHGQKISITSPKAQTTRNRISGIHTTGAS-QIIFIDTPGFHEK 61
Query: 173 HAAFSNMRSRGAHCT----DIVVLVVAADD--GVMEQTVESIRMAREAKVPIIVAINKID 226
+ + + + A D+++ VV +D G E + ++ K P+++ NK+D
Sbjct: 62 KHSLNRLMMKEARSAIGGVDLILFVVDSDQWNGDGEFVLTKLQ---NLKRPVVLTRNKLD 118
Query: 227 KPAADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIERTKNMLLAQGIT 286
D L+ + +ED VPISALTG N L IE
Sbjct: 119 NKFKDKLLP---LIDKYAILEDFK---DIVPISALTGDNTSFLAAFIE------------ 160
Query: 287 VEDLGGDIQAVPISALTGTNVDNLTEAIVAQAEIMHLKADYGGPVEAMIVESKFDTHRGK 346
L P +T I+ + I + K + V I F+ +G
Sbjct: 161 -VHLPEGPFRYPEDYVTDQPDRFKISEIIREKIIRYTKEEIPHSVRVEIERKSFNE-KGL 218
Query: 347 L---ATALVQRGTLKKGAIVVAGQAWAKVRSI---SRKTLIN 382
L A V+R + KK ++ G+ + +++I +RK ++
Sbjct: 219 LKIHALISVERESQKK---IIIGKNGSMIKAIGIAARKDILE 257
>gnl|CDD|213679 TIGR02034, CysN, sulfate adenylyltransferase, large subunit.
Metabolic assimilation of sulfur from inorganic sulfate,
requires sulfate activation by coupling to a nucleoside,
for the production of high-energy nucleoside
phosphosulfates. This pathway appears to be similar in
all prokaryotic organisms. Activation is first achieved
through sulfation of sulfate with ATP by sulfate
adenylyltransferase (ATP sulfurylase) to produce
5'-phosphosulfate (APS), coupled by GTP hydrolysis.
Subsequently, APS is phosphorylated by an APS kinase to
produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS). In
Escherichia coli, ATP sulfurylase is a heterodimer
composed of two subunits encoded by cysD and cysN, with
APS kinase encoded by cysC. These genes are located in a
unidirectionally transcribed gene cluster, and have been
shown to be required for the synthesis of
sulfur-containing amino acids. Homologous to this E.coli
activation pathway are nodPQH gene products found among
members of the Rhizobiaceae family. These gene products
have been shown to exhibit ATP sulfurase and APS kinase
activity, yet are involved in Nod factor sulfation, and
sulfation of other macromolecules. With members of the
Rhizobiaceae family, nodQ often appears as a fusion of
cysN (large subunit of ATP sulfurase) and cysC (APS
kinase) [Central intermediary metabolism, Sulfur
metabolism].
Length = 406
Score = 56.6 bits (137), Expect = 2e-08
Identities = 38/112 (33%), Positives = 60/112 (53%), Gaps = 10/112 (8%)
Query: 169 DTPGHAAFSNMRSRGAHCTDIVVLVVAADDGVMEQT-----VESIRMAREAKVPIIVAIN 223
DTPGH ++ + GA D+ VL+V A GV+EQT + S+ R +++A+N
Sbjct: 86 DTPGHEQYTRNMATGASTADLAVLLVDARKGVLEQTRRHSYIASLLGIRH----VVLAVN 141
Query: 224 KIDKPAADIERTKNMLLAQGITVEDLG-GDIQAVPISALTGTNVDNLTEAIE 274
K+D D E +N+ E LG D+ +P+SAL G NV + +E++
Sbjct: 142 KMDLVDYDEEVFENIKKDYLAFAEQLGFRDVTFIPLSALKGDNVVSRSESMP 193
>gnl|CDD|206732 cd04169, RF3, Release Factor 3 (RF3) protein involved in the
terminal step of translocation in bacteria. Peptide
chain release factor 3 (RF3) is a protein involved in
the termination step of translation in bacteria.
Termination occurs when class I release factors (RF1 or
RF2) recognize the stop codon at the A-site of the
ribosome and activate the release of the nascent
polypeptide. The class II release factor RF3 then
initiates the release of the class I RF from the
ribosome. RF3 binds to the RF/ribosome complex in the
inactive (GDP-bound) state. GDP/GTP exchange occurs,
followed by the release of the class I RF. Subsequent
hydrolysis of GTP to GDP triggers the release of RF3
from the ribosome. RF3 also enhances the efficiency of
class I RFs at less preferred stop codons and at stop
codons in weak contexts.
Length = 268
Score = 54.5 bits (132), Expect = 4e-08
Identities = 41/135 (30%), Positives = 57/135 (42%), Gaps = 25/135 (18%)
Query: 120 IMGHVDHGKTTLLDTL----------------RNTSVVKSEFGGITQHIGAFVVTLKSGE 163
I+ H D GKTTL + L ++ S++ I + G V + S
Sbjct: 7 IISHPDAGKTTLTEKLLLFGGAIQEAGAVKARKSRKHATSDWMEIEKQRGISVTS--SVM 64
Query: 164 QVTF-------LDTPGHAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMAREAKV 216
Q + LDTPGH FS R D V+V+ A GV QT + + R +
Sbjct: 65 QFEYKGCVINLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKGVEPQTRKLFEVCRLRGI 124
Query: 217 PIIVAINKIDKPAAD 231
PII INK+D+ D
Sbjct: 125 PIITFINKLDREGRD 139
>gnl|CDD|206666 cd01878, HflX, HflX GTPase family. HflX subfamily. A distinct
conserved domain with a glycine-rich segment N-terminal
of the GTPase domain characterizes the HflX subfamily.
The E. coli HflX has been implicated in the control of
the lambda cII repressor proteolysis, but the actual
biological functions of these GTPases remain unclear.
HflX is widespread, but not universally represented in
all three superkingdoms.
Length = 204
Score = 53.2 bits (129), Expect = 6e-08
Identities = 54/187 (28%), Positives = 74/187 (39%), Gaps = 53/187 (28%)
Query: 116 PVVTIMGHVDHGKTTLLDTLRNTSV-VKSEFGGITQHIGAFV--------VTLKSGEQVT 166
P V ++G+ + GK+TL + L V + + F + L G +V
Sbjct: 42 PTVALVGYTNAGKSTLFNALTGADVLAEDQL---------FATLDPTTRRIKLPGGREVL 92
Query: 167 FLDTPG------H---AAFSNMRS-----RGAHCTDIVVLVV-AADDGVMEQ--TVESIR 209
DT G H AF RS A D+++ VV A+D EQ TVE +
Sbjct: 93 LTDTVGFIRDLPHQLVEAF---RSTLEEVAEA---DLLLHVVDASDPDREEQIETVEEVL 146
Query: 210 MAREAK-VPIIVAINKIDKPAADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDN 268
A +PII+ +NKID + G AV ISA TG +D
Sbjct: 147 KELGADDIPIILVLNKIDLLDDEELEE-----------RLRAGRPDAVFISAKTGEGLDL 195
Query: 269 LTEAIER 275
L EAIE
Sbjct: 196 LKEAIEE 202
>gnl|CDD|234125 TIGR03156, GTP_HflX, GTP-binding protein HflX. This protein family
is one of a number of homologous small, well-conserved
GTP-binding proteins with pleiotropic effects. Bacterial
members are designated HflX, following the naming
convention in Escherichia coli where HflX is encoded
immediately downstream of the RNA chaperone Hfq, and
immediately upstream of HflKC, a membrane-associated
protease pair with an important housekeeping function.
Over large numbers of other bacterial genomes, the
pairing with hfq is more significant than with hflK and
hlfC. The gene from Homo sapiens in this family has been
named PGPL (pseudoautosomal GTP-binding protein-like)
[Unknown function, General].
Length = 351
Score = 54.4 bits (132), Expect = 9e-08
Identities = 52/194 (26%), Positives = 74/194 (38%), Gaps = 66/194 (34%)
Query: 116 PVVTIMGHVDHGKTTLLDTLRNTSVVKSEFGGITQHIGAFV--------------VTLKS 161
P V ++G+ + GK+TL + L V + + L
Sbjct: 190 PTVALVGYTNAGKSTLFNALTGADV--------------YAADQLFATLDPTTRRLDLPD 235
Query: 162 GEQVTFLDTPG------H---AAFSNMRS-----RGAHCTDIVVLVV-AADDGVMEQ--T 204
G +V DT G H AAF R+ R A D+++ VV A+D EQ
Sbjct: 236 GGEVLLTDTVGFIRDLPHELVAAF---RATLEEVREA---DLLLHVVDASDPDREEQIEA 289
Query: 205 VESIRMAREAK-VPIIVAINKIDK-PAADIERTKNMLLAQGITVEDLGGDIQAVPISALT 262
VE + A+ +P ++ NKID IER G +AV +SA T
Sbjct: 290 VEKVLEELGAEDIPQLLVYNKIDLLDEPRIER-------------LEEGYPEAVFVSAKT 336
Query: 263 GTNVDNLTEAIERT 276
G +D L EAI
Sbjct: 337 GEGLDLLLEAIAER 350
>gnl|CDD|206665 cd01876, YihA_EngB, YihA (EngB) GTPase family. The YihA (EngB)
subfamily of GTPases is typified by the E. coli YihA, an
essential protein involved in cell division control.
YihA and its orthologs are small proteins that typically
contain less than 200 amino acid residues and consists
of the GTPase domain only (some of the eukaryotic
homologs contain an N-terminal extension of about 120
residues that might be involved in organellar
targeting). Homologs of yihA are found in most
Gram-positive and Gram-negative pathogenic bacteria,
with the exception of Mycobacterium tuberculosis. The
broad-spectrum nature of YihA and its essentiality for
cell viability in bacteria make it an attractive
antibacterial target.
Length = 170
Score = 52.1 bits (126), Expect = 9e-08
Identities = 35/165 (21%), Positives = 62/165 (37%), Gaps = 25/165 (15%)
Query: 127 GKTTLLDTL-RNTSVVK-SEFGGITQHIGAFVVTLKSGEQVTFLDTPG----------HA 174
GK++L++ L + + S+ G TQ I F V G++ +D PG
Sbjct: 11 GKSSLINALTNRKKLARTSKTPGRTQLINFFNV----GDKFRLVDLPGYGYAKVSKEVRE 66
Query: 175 AFSNM-----RSRGAHCTDIVVLVVAADDGVMEQTVESIRMAREAKVPIIVAINKIDKPA 229
+ + +R VVL++ A G +E + E +P ++ + K DK
Sbjct: 67 KWGKLIEEYLENR--ENLKGVVLLIDARHGPTPIDLEMLEFLEELGIPFLIVLTKADK-L 123
Query: 230 ADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIE 274
E K + + + + S+ GT +D L I
Sbjct: 124 KKSELAKVLKKIK-EELNLFNILPPVILFSSKKGTGIDELRALIA 167
>gnl|CDD|206681 cd01894, EngA1, EngA1 GTPase contains the first domain of EngA.
This EngA1 subfamily CD represents the first GTPase
domain of EngA and its orthologs, which are composed of
two adjacent GTPase domains. Since the sequences of the
two domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family. Although the exact function of
these proteins has not been elucidated, studies have
revealed that the E. coli EngA homolog, Der, and
Neisseria gonorrhoeae EngA are essential for cell
viability. A recent report suggests that E. coli Der
functions in ribosome assembly and stability.
Length = 157
Score = 51.7 bits (125), Expect = 9e-08
Identities = 24/90 (26%), Positives = 42/90 (46%), Gaps = 10/90 (11%)
Query: 185 HCTDIVVLVVAADDGVMEQTVESIRMAREAKVPIIVAINKIDKPAADIERTKNMLLAQGI 244
D+++ VV +G+ E + R++K P+I+ +NKID + E + L
Sbjct: 75 EEADVILFVVDGREGLTPADEEIAKYLRKSKKPVILVVNKIDNIKEEEEAAEFYSL---- 130
Query: 245 TVEDLGGDIQAVPISALTGTNVDNLTEAIE 274
G + +PISA G + +L +AI
Sbjct: 131 ------GFGEPIPISAEHGRGIGDLLDAIL 154
>gnl|CDD|235349 PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional.
Length = 474
Score = 53.8 bits (130), Expect = 2e-07
Identities = 37/115 (32%), Positives = 59/115 (51%), Gaps = 19/115 (16%)
Query: 169 DTPGHAAFS-NMRSRGAHCTDIVVLVVAADDGVMEQT--------VESIRMAREAKVPII 219
DTPGH ++ NM + GA D+ +L++ A GV++QT + I+ ++
Sbjct: 113 DTPGHEQYTRNMAT-GASTCDLAILLIDARKGVLDQTRRHSFIATLLGIKH-------LV 164
Query: 220 VAINKIDKPAADIERTKNMLLAQGITVEDLGG--DIQAVPISALTGTNVDNLTEA 272
VA+NK+D E + + E L G DI+ VP+SAL G NV + +E+
Sbjct: 165 VAVNKMDLVDYSEEVFERIREDYLTFAEQLPGNLDIRFVPLSALEGDNVVSQSES 219
>gnl|CDD|129594 TIGR00503, prfC, peptide chain release factor 3. This translation
releasing factor, RF-3 (prfC) was originally described
as stop codon-independent, in contrast to peptide chain
release factor 1 (RF-1, prfA) and RF-2 (prfB). RF-1 and
RF-2 are closely related to each other, while RF-3 is
similar to elongation factors EF-Tu and EF-G; RF-1 is
active at UAA and UAG and RF-2 is active at UAA and UGA.
More recently, RF-3 was shown to be active primarily at
UGA stop codons in E. coli. All bacteria and organelles
have RF-1. The Mycoplasmas and organelles, which
translate UGA as Trp rather than as a stop codon, lack
RF-2. RF-3, in contrast, seems to be rare among bacteria
and is found so far only in Escherichia coli and some
other gamma subdivision Proteobacteria, in Synechocystis
PCC6803, and in Staphylococcus aureus [Protein
synthesis, Translation factors].
Length = 527
Score = 54.1 bits (130), Expect = 2e-07
Identities = 34/133 (25%), Positives = 54/133 (40%), Gaps = 21/133 (15%)
Query: 120 IMGHVDHGKTTLLDTL----------------RNTSVVKSEFGGITQHIGAFVVTL---- 159
I+ H D GKTT+ + + + KS++ + + G + T
Sbjct: 16 IISHPDAGKTTITEKVLLYGGAIQTAGAVKGRGSQRHAKSDWMEMEKQRGISITTSVMQF 75
Query: 160 -KSGEQVTFLDTPGHAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMAREAKVPI 218
V LDTPGH FS R D ++V+ A GV +T + + + R PI
Sbjct: 76 PYRDCLVNLLDTPGHEDFSEDTYRTLTAVDNCLMVIDAAKGVETRTRKLMEVTRLRDTPI 135
Query: 219 IVAINKIDKPAAD 231
+NK+D+ D
Sbjct: 136 FTFMNKLDRDIRD 148
>gnl|CDD|206673 cd01886, EF-G, Elongation factor G (EF-G) family involved in both
the elongation and ribosome recycling phases of protein
synthesis. Translocation is mediated by EF-G (also
called translocase). The structure of EF-G closely
resembles that of the complex between EF-Tu and tRNA.
This is an example of molecular mimicry; a protein
domain evolved so that it mimics the shape of a tRNA
molecule. EF-G in the GTP form binds to the ribosome,
primarily through the interaction of its EF-Tu-like
domain with the 50S subunit. The binding of EF-G to the
ribosome in this manner stimulates the GTPase activity
of EF-G. On GTP hydrolysis, EF-G undergoes a
conformational change that forces its arm deeper into
the A site on the 30S subunit. To accommodate this
domain, the peptidyl-tRNA in the A site moves to the P
site, carrying the mRNA and the deacylated tRNA with it.
The ribosome may be prepared for these rearrangements by
the initial binding of EF-G as well. The dissociation of
EF-G leaves the ribosome ready to accept the next
aminoacyl-tRNA into the A site. This group contains both
eukaryotic and bacterial members.
Length = 270
Score = 52.9 bits (128), Expect = 2e-07
Identities = 38/148 (25%), Positives = 50/148 (33%), Gaps = 39/148 (26%)
Query: 120 IMGHVDHGKTTLLDTLRNTSVVKSE----FGGITQHIG---------------------- 153
I+ H+D GKTT +E + G IG
Sbjct: 4 IIAHIDAGKTTT-----------TERILYYTGRIHKIGEVHGGGATMDWMEQERERGITI 52
Query: 154 --AFVVTLKSGEQVTFLDTPGHAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMA 211
A ++ +DTPGH F+ R D V V A GV QT R A
Sbjct: 53 QSAATTCFWKDHRINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVAGVQPQTETVWRQA 112
Query: 212 REAKVPIIVAINKIDKPAADIERTKNML 239
VP I +NK+D+ AD R +
Sbjct: 113 DRYGVPRIAFVNKMDRTGADFYRVVEQI 140
>gnl|CDD|223296 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 51.1 bits (123), Expect = 3e-07
Identities = 38/167 (22%), Positives = 62/167 (37%), Gaps = 20/167 (11%)
Query: 127 GKTTLLDTLRNTSVV--KSEFGGITQHIGAFVVTLKSGEQVTFLDTPGH---AAFSNMRS 181
GK++L++ L N + S+ G TQ I F V +++ +D PG+ ++
Sbjct: 36 GKSSLINALTNQKNLARTSKTPGRTQLINFFEV----DDELRLVDLPGYGYAKVPKEVKE 91
Query: 182 R----------GAHCTDIVVLVVAADDGVMEQTVESIRMAREAKVPIIVAINKIDKPAAD 231
+ VVL++ A + E I E +P+IV + K DK
Sbjct: 92 KWKKLIEEYLEKRANLKGVVLLIDARHPPKDLDREMIEFLLELGIPVIVVLTKADK-LKK 150
Query: 232 IERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIERTKN 278
ER K + + D V S+L +D L I
Sbjct: 151 SERNKQLNKVAEELKKPPPDDQWVVLFSSLKKKGIDELKAKILEWLK 197
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 52.0 bits (126), Expect = 5e-07
Identities = 40/130 (30%), Positives = 59/130 (45%), Gaps = 24/130 (18%)
Query: 162 GEQVTFLDTPG-------HAA---FSNMRSRGA--HCTDIVVLVVAADDGVMEQTVESIR 209
G++ T +DT G +S +R+ A D+V+LV+ A +G+ EQ +
Sbjct: 220 GQKYTLIDTAGIRRKGKVTEGVEKYSVIRTLKAIERA-DVVLLVIDATEGITEQDLRIAG 278
Query: 210 MAREAKVPIIVAINKIDK-PAADIERTKNML---LAQGITVEDLGGDIQAVPISALTGTN 265
+A EA +++ +NK D +E K L L L V ISALTG
Sbjct: 279 LALEAGRALVIVVNKWDLVDEKTMEEFKKELRRRLPF------LDY-APIVFISALTGQG 331
Query: 266 VDNLTEAIER 275
VD L EAI+
Sbjct: 332 VDKLLEAIDE 341
Score = 47.0 bits (113), Expect = 2e-05
Identities = 23/90 (25%), Positives = 42/90 (46%), Gaps = 18/90 (20%)
Query: 188 DIVVLVVAADDGVMEQTVESIRMAREAKVPIIVAINKIDKPAADIERTKNMLLAQGITVE 247
D+++ VV G+ E ++ R++ P+I+ +NK+D P + +
Sbjct: 82 DVILFVVDGRAGLTPADEEIAKILRKSNKPVILVVNKVDGPDEEAD------------AY 129
Query: 248 D---LG-GDIQAVPISALTGTNVDNLTEAI 273
+ LG G+ PISA G + +L +AI
Sbjct: 130 EFYSLGLGEP--YPISAEHGRGIGDLLDAI 157
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 51.9 bits (125), Expect = 6e-07
Identities = 51/180 (28%), Positives = 80/180 (44%), Gaps = 39/180 (21%)
Query: 116 PVVTIMGHVDHGKTTLLDTLRNTSV-VKSE----FGGITQHIGAFVVTLKSGEQVTFLDT 170
P+V ++G+ + GK+TL + L V V + T+ I L G +V DT
Sbjct: 193 PLVALVGYTNAGKSTLFNALTGADVYVADQLFATLDPTTRRI-----ELGDGRKVLLTDT 247
Query: 171 PG------H---AAF-SNMR-SRGAHCTDIVVLVV-AADDGVMEQ--TVESIRMAREA-K 215
G H AF S + + A D+++ VV A+D ++E+ VE + A +
Sbjct: 248 VGFIRDLPHPLVEAFKSTLEEVKEA---DLLLHVVDASDPEILEKLEAVEDVLAEIGADE 304
Query: 216 VPIIVAINKIDKPAADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIER 275
+PII+ +NKID +E + + + G V ISA TG +D L E I
Sbjct: 305 IPIILVLNKIDL----LEDEEILAELER-------GSPNPVFISAKTGEGLDLLRERIIE 353
>gnl|CDD|216791 pfam01926, MMR_HSR1, 50S ribosome-binding GTPase. The full-length
GTPase protein is required for the complete activity of
the protein of interacting with the 50S ribosome and
binding of both adenine and guanine nucleotides, with a
preference for guanine nucleotide.
Length = 117
Score = 47.3 bits (113), Expect = 1e-06
Identities = 33/118 (27%), Positives = 55/118 (46%), Gaps = 13/118 (11%)
Query: 118 VTIMGHVDHGKTTLLDTLRNTSVVK-SEFGGITQHIGAFVVTLKSGEQVTFLDTPG---- 172
V ++G + GK+TL++ L V S++ G T+ + L G Q+ +DTPG
Sbjct: 2 VALVGRPNVGKSTLINALTGAKVAIVSDYPGTTRDP--ILGVLGLGRQIILVDTPGLIEG 59
Query: 173 --HAAFSNMRSR---GAHCTDIVVLVVAADDGVMEQTVESIRMAREA-KVPIIVAINK 224
+R D+++LVV A +G+ E E + + K PII+ +NK
Sbjct: 60 ASEGKGVEGFNRFLEAIREADLILLVVDASEGLTEDDEEILEELEKLPKKPIILVLNK 117
>gnl|CDD|206644 cd00878, Arf_Arl, ADP-ribosylation factor(Arf)/Arf-like (Arl) small
GTPases. Arf (ADP-ribosylation factor)/Arl (Arf-like)
small GTPases. Arf proteins are activators of
phospholipase D isoforms. Unlike Ras proteins they lack
cysteine residues at their C-termini and therefore are
unlikely to be prenylated. Arfs are N-terminally
myristoylated. Members of the Arf family are regulators
of vesicle formation in intracellular traffic that
interact reversibly with membranes of the secretory and
endocytic compartments in a GTP-dependent manner. They
depart from other small GTP-binding proteins by a unique
structural device, interswitch toggle, that implements
front-back communication from N-terminus to the
nucleotide binding site. Arf-like (Arl) proteins are
close relatives of the Arf, but only Arl1 has been shown
to function in membrane traffic like the Arf proteins.
Arl2 has an unrelated function in the folding of native
tubulin, and Arl4 may function in the nucleus. Most
other Arf family proteins are so far relatively poorly
characterized. Thus, despite their significant sequence
homologies, Arf family proteins may regulate unrelated
functions.
Length = 158
Score = 47.6 bits (114), Expect = 2e-06
Identities = 42/158 (26%), Positives = 63/158 (39%), Gaps = 23/158 (14%)
Query: 127 GKTTLLDTLRNTSVVKSEFGGITQHIGAFVVTLKSGE-QVTFLDTPGHAAFSNMRSRGAH 185
GKTT+L L+ VV IG V T++ + T D G +
Sbjct: 11 GKTTILYKLKLGEVVT-----TIPTIGFNVETVEYKNVKFTVWDVGGQDKIRPLWKHYYE 65
Query: 186 CTDIVVLVVAADDGVMEQTVESIR------MAREAK-VPIIVAINKIDKPAADIERTKNM 238
TD ++ VV + D E+ E+ E K P+++ NK D P A E
Sbjct: 66 NTDGLIFVVDSSD--RERIEEAKNELHKLLNEEELKGAPLLILANKQDLPGALTESE--- 120
Query: 239 LLAQGITVEDLGG-DIQAVPISALTGTNVDNLTEAIER 275
L + + +E + G P SA+TG D L E ++
Sbjct: 121 -LIELLGLESIKGRRWHIQPCSAVTG---DGLDEGLDW 154
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 47.3 bits (112), Expect = 7e-06
Identities = 39/164 (23%), Positives = 63/164 (38%), Gaps = 17/164 (10%)
Query: 127 GKTTLLDTLRNTSVVKSEFGGITQHIGAFVVTLKSGE-QVTFLDTPGHAAFSNMRS---R 182
GKTTLL+ L + I A + ++ DT G + ++R R
Sbjct: 17 GKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTAGQEEYRSLRPEYYR 76
Query: 183 GAHCTDIVVLVVAAD--DGVMEQTVESIRMAREAKVPIIVAINKIDKPAADIERTKNM-- 238
GA+ IV + D + E+ +E +R VPI++ NKID + +
Sbjct: 77 GANGILIVYDSTLRESSDELTEEWLEELRELAPDDVPILLVGNKIDLFDEQSSSEEILNQ 136
Query: 239 -------LLAQGITVEDLGGDIQAVPISA--LTGTNVDNLTEAI 273
L+ V + + SA LTG NV+ L + +
Sbjct: 137 LNREVVLLVLAPKAVLPEVANPALLETSAKSLTGPNVNELFKEL 180
>gnl|CDD|206668 cd01881, Obg_like, Obg-like family of GTPases consist of five
subfamilies: Obg, DRG, YyaF/YchF, Ygr210, and NOG1. The
Obg-like subfamily consists of five well-delimited,
ancient subfamilies, namely Obg, DRG, YyaF/YchF, Ygr210,
and NOG1. Four of these groups (Obg, DRG, YyaF/YchF, and
Ygr210) are characterized by a distinct glycine-rich
motif immediately following the Walker B motif (G3 box).
Obg/CgtA is an essential gene that is involved in the
initiation of sporulation and DNA replication in the
bacteria Caulobacter and Bacillus, but its exact
molecular role is unknown. Furthermore, several OBG
family members possess a C-terminal RNA-binding domain,
the TGS domain, which is also present in threonyl-tRNA
synthetase and in bacterial guanosine polyphosphatase
SpoT. Nog1 is a nucleolar protein that might function in
ribosome assembly. The DRG and Nog1 subfamilies are
ubiquitous in archaea and eukaryotes, the Ygr210
subfamily is present in archaea and fungi, and the Obg
and YyaF/YchF subfamilies are ubiquitous in bacteria and
eukaryotes. The Obg/Nog1 and DRG subfamilies appear to
form one major branch of the Obg family and the Ygr210
and YchF subfamilies form another branch. No GEFs, GAPs,
or GDIs for Obg have been identified.
Length = 167
Score = 46.2 bits (110), Expect = 8e-06
Identities = 40/173 (23%), Positives = 70/173 (40%), Gaps = 30/173 (17%)
Query: 120 IMGHVDHGKTTLLD--TLRNTSVVKSEFGGITQHIGAFVVTLKSGEQVTFLDTPG--HAA 175
++G + GK+TLL T + F + ++G V G + +D PG A
Sbjct: 2 LVGLPNVGKSTLLSALTSAKVEIASYPFTTLEPNVG--VFEFGDGVDIQIIDLPGLLDGA 59
Query: 176 FSNMR-----SRGAHCTDIVVLVV-AADDGVMEQTVESIRMAREAKV--------PIIVA 221
+ +D+++ V+ A++D V + + + E P ++
Sbjct: 60 SEGRGLGEQILAHLYRSDLILHVIDASEDCVGDPLEDQKTLNEEVSGSFLFLKNKPEMIV 119
Query: 222 INKIDKPAAD-IERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAI 273
NKID + + ++R K L +GI V VP SALT +D + I
Sbjct: 120 ANKIDMASENNLKRLKLDKLKRGIPV---------VPTSALTRLGLDRVIRTI 163
>gnl|CDD|180120 PRK05506, PRK05506, bifunctional sulfate adenylyltransferase
subunit 1/adenylylsulfate kinase protein; Provisional.
Length = 632
Score = 48.8 bits (117), Expect = 9e-06
Identities = 35/122 (28%), Positives = 54/122 (44%), Gaps = 29/122 (23%)
Query: 169 DTPGHAAFS-NMRSRGAHCTDIVVLVVAADDGVMEQT--------VESIRMAREAKVPII 219
DTPGH ++ NM + GA D+ +++V A GV+ QT + IR ++
Sbjct: 110 DTPGHEQYTRNMVT-GASTADLAIILVDARKGVLTQTRRHSFIASLLGIRH-------VV 161
Query: 220 VAINKIDKPAADIERTKN-----MLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIE 274
+A+NK+D D E A + + D + +PISAL G DN+
Sbjct: 162 LAVNKMDLVDYDQEVFDEIVADYRAFAAKLGLHD----VTFIPISALKG---DNVVTRSA 214
Query: 275 RT 276
R
Sbjct: 215 RM 216
>gnl|CDD|226593 COG4108, PrfC, Peptide chain release factor RF-3 [Translation,
ribosomal structure and biogenesis].
Length = 528
Score = 48.4 bits (116), Expect = 9e-06
Identities = 43/141 (30%), Positives = 55/141 (39%), Gaps = 37/141 (26%)
Query: 120 IMGHVDHGKTTLLDTLRNTSVVKSEFGGITQHIGAFVVTLKSGEQ--------------- 164
I+ H D GKTTL + L FGG Q G V KSG+
Sbjct: 17 IISHPDAGKTTLTEKL-------LLFGGAIQEAGT-VKGRKSGKHAKSDWMEIEKQRGIS 68
Query: 165 --------------VTFLDTPGHAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRM 210
V LDTPGH FS R D V+V+ A G+ QT++ +
Sbjct: 69 VTSSVMQFDYADCLVNLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKGIEPQTLKLFEV 128
Query: 211 AREAKVPIIVAINKIDKPAAD 231
R +PI INK+D+ D
Sbjct: 129 CRLRDIPIFTFINKLDREGRD 149
>gnl|CDD|240409 PTZ00416, PTZ00416, elongation factor 2; Provisional.
Length = 836
Score = 48.5 bits (116), Expect = 1e-05
Identities = 38/139 (27%), Positives = 65/139 (46%), Gaps = 35/139 (25%)
Query: 119 TIMGHVDHGKTTLLDTL---------------RNTS----------VVKSEFGGITQHIG 153
+++ HVDHGK+TL D+L R T +KS GI+ +
Sbjct: 23 SVIAHVDHGKSTLTDSLVCKAGIISSKNAGDARFTDTRADEQERGITIKST--GISLY-- 78
Query: 154 AFVVTLKSGEQ-----VTFLDTPGHAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESI 208
+ L+ G+ + +D+PGH FS+ + TD ++VV +GV QT +
Sbjct: 79 -YEHDLEDGDDKQPFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCVEGVCVQTETVL 137
Query: 209 RMAREAKVPIIVAINKIDK 227
R A + ++ ++ INK+D+
Sbjct: 138 RQALQERIRPVLFINKVDR 156
>gnl|CDD|179525 PRK03003, PRK03003, GTP-binding protein Der; Reviewed.
Length = 472
Score = 48.0 bits (115), Expect = 1e-05
Identities = 45/169 (26%), Positives = 78/169 (46%), Gaps = 22/169 (13%)
Query: 115 PPVVTIMGHVDHGKTTLLDTL--RNTSVVKSEFGGITQHIGAFVVTLKSGEQVTFLDTPG 172
PVV ++G + GK+TL++ + R +VV+ + G+T+ ++ +G + T +DT G
Sbjct: 38 LPVVAVVGRPNVGKSTLVNRILGRREAVVE-DVPGVTRDRVSYDAEW-NGRRFTVVDTGG 95
Query: 173 --------HAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMAREAKVPIIVAINK 224
A+ + D V+ VV A G R+ R + P+I+A NK
Sbjct: 96 WEPDAKGLQASVAEQAEVAMRTADAVLFVVDATVGATATDEAVARVLRRSGKPVILAANK 155
Query: 225 IDKPAADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAI 273
+D + + L + G LG + P+SAL G V +L +A+
Sbjct: 156 VDDERGEADAA--ALWSLG-----LG---EPHPVSALHGRGVGDLLDAV 194
Score = 45.0 bits (107), Expect = 1e-04
Identities = 49/177 (27%), Positives = 81/177 (45%), Gaps = 24/177 (13%)
Query: 115 PPVVTIMGHVDHGKTTLLDTL--RNTSVVKSEFGGITQHIGAFVVTLKSGEQVTFLDTPG 172
P V ++G + GK++LL+ L SVV + G T ++ L G+ F+DT G
Sbjct: 211 PRRVALVGKPNVGKSSLLNKLAGEERSVV-DDVAGTTVDPVDSLIELG-GKTWRFVDTAG 268
Query: 173 ----------HAAFSNMRSRGA-HCTDIVVLVVAADDGVMEQTVESIRMAREAKVPIIVA 221
H ++++R+ A ++ V+++ A + + EQ + M EA +++A
Sbjct: 269 LRRRVKQASGHEYYASLRTHAAIEAAEVAVVLIDASEPISEQDQRVLSMVIEAGRALVLA 328
Query: 222 INKIDKPAADIERTKNMLLAQGITVEDLGGDIQAVP---ISALTGTNVDNLTEAIER 275
NK D D +R L + I +L + P ISA TG VD L A+E
Sbjct: 329 FNKWD--LVDEDR--RYYLEREI-DREL-AQVPWAPRVNISAKTGRAVDKLVPALET 379
>gnl|CDD|185474 PTZ00141, PTZ00141, elongation factor 1- alpha; Provisional.
Length = 446
Score = 47.4 bits (113), Expect = 2e-05
Identities = 41/134 (30%), Positives = 63/134 (47%), Gaps = 15/134 (11%)
Query: 165 VTFLDTPGHAAF-SNMRSRGAHCTDIVVLVVAADDGVME-------QTVESIRMAREAKV 216
T +D PGH F NM + G D+ +LVVA+ G E QT E +A V
Sbjct: 87 FTIIDAPGHRDFIKNMIT-GTSQADVAILVVASTAGEFEAGISKDGQTREHALLAFTLGV 145
Query: 217 P-IIVAINKIDKPAADI--ERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAI 273
+IV INK+D + ER + ++ +G + + VP ++G DN+ I
Sbjct: 146 KQMIVCINKMDDKTVNYSQERYDEIKKEVSAYLKKVGYNPEKVPFIPISGWQGDNM---I 202
Query: 274 ERTKNMLLAQGITV 287
E++ NM +G T+
Sbjct: 203 EKSDNMPWYKGPTL 216
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 45.1 bits (107), Expect = 2e-05
Identities = 32/150 (21%), Positives = 57/150 (38%), Gaps = 16/150 (10%)
Query: 118 VTIMGHVDHGKTTLLDTLRNTSVVKSEFGG------------ITQHIGAFVVTLKSGEQV 165
+ ++G V GKTT + L + +V +E + G+ + L V
Sbjct: 13 IVVIGPVGAGKTTFVRALSDKPLVITEADASSVSGKGKRPTTVAMDFGS--IELDEDTGV 70
Query: 166 TFLDTPGHAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMAR-EAKVPIIVAINK 224
TPG F M + +++V + + E I +P++VAINK
Sbjct: 71 HLFGTPGQERFKFMWEILSRGAVGAIVLVDSSRPITFHAEEIIDFLTSRNPIPVVVAINK 130
Query: 225 IDKPAAD-IERTKNMLLAQGITVEDLGGDI 253
D A E+ + L + ++V + D
Sbjct: 131 QDLFDALPPEKIREALKLELLSVPVIEIDA 160
>gnl|CDD|236546 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 47.1 bits (112), Expect = 2e-05
Identities = 30/125 (24%), Positives = 62/125 (49%), Gaps = 15/125 (12%)
Query: 115 PPVVTIMGHVDHGKTTLLDTLRNT--SVVKSEFGGITQHIGAFVVTLKSGEQVTFLDTPG 172
V ++G + GK++LL+ L + +VV ++ G T+ +V + GE F+DT G
Sbjct: 450 LRRVALVGRPNVGKSSLLNQLTHEERAVV-NDLAGTTRDPVDEIVEI-DGEDWLFIDTAG 507
Query: 173 ----------HAAFSNMRSRGA-HCTDIVVLVVAADDGVMEQTVESIRMAREAKVPIIVA 221
+S++R++ A +++ + + A + EQ ++ + MA +A +++
Sbjct: 508 IKRRQHKLTGAEYYSSLRTQAAIERSELALFLFDASQPISEQDLKVMSMAVDAGRALVLV 567
Query: 222 INKID 226
NK D
Sbjct: 568 FNKWD 572
Score = 46.7 bits (111), Expect = 4e-05
Identities = 49/174 (28%), Positives = 79/174 (45%), Gaps = 27/174 (15%)
Query: 117 VVTIMGHVDHGKTTLLDTL--RNTSVVKSEFGGITQHIGAFVVTLKSGEQVTFLDTPG-- 172
VV I+G + GK+TL++ + R +VV+ + G+T+ ++ +G +DT G
Sbjct: 277 VVAIVGRPNVGKSTLVNRILGRREAVVE-DTPGVTRDRVSYDAEW-AGTDFKLVDTGGWE 334
Query: 173 ------HAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMAREAKVPIIVAINKID 226
+A ++ D VV VV G+ +RM R A P+++A+NKID
Sbjct: 335 ADVEGIDSAIASQAQIAVSLADAVVFVVDGQVGLTSTDERIVRMLRRAGKPVVLAVNKID 394
Query: 227 KPAADIERTKNMLLAQGITVE--DLGGDIQAVPISALTGTNV-DNLTEAIERTK 277
A++ E LG + PISA+ G V D L EA++ K
Sbjct: 395 DQASE-----------YDAAEFWKLGLG-EPYPISAMHGRGVGDLLDEALDSLK 436
>gnl|CDD|238652 cd01342, Translation_Factor_II_like, Translation_Factor_II_like:
Elongation factor Tu (EF-Tu) domain II-like proteins.
Elongation factor Tu consists of three structural
domains, this family represents the second domain.
Domain II adopts a beta barrel structure and is involved
in binding to charged tRNA. Domain II is found in other
proteins such as elongation factor G and translation
initiation factor IF-2. This group also includes the C2
subdomain of domain IV of IF-2 that has the same fold as
domain II of (EF-Tu). Like IF-2 from certain prokaryotes
such as Thermus thermophilus, mitochondrial IF-2 lacks
domain II, which is thought to be involved in binding
of E.coli IF-2 to 30S subunits.
Length = 83
Score = 42.3 bits (100), Expect = 3e-05
Identities = 25/88 (28%), Positives = 38/88 (43%), Gaps = 5/88 (5%)
Query: 569 GEANVLQMFLITDGKKKVPVAGCRCSKGVLKKNALFKLVRRNEVLFEGKLESMKHLKEEV 628
A V ++F K + VA R G LKK + V +GK++S+K K EV
Sbjct: 1 LRALVFKVFKD---KGRGTVATGRVESGTLKKGDKVR-VGPGGGGVKGKVKSLKRFKGEV 56
Query: 629 TSIKKELECGLRLEDPSIEFEPGDTIVC 656
G+ L+D + + GDT+
Sbjct: 57 DEAVAGDIVGIVLKD-KDDIKIGDTLTD 83
Score = 41.5 bits (98), Expect = 6e-05
Identities = 16/44 (36%), Positives = 23/44 (52%)
Query: 331 VEAMIVESKFDTHRGKLATALVQRGTLKKGAIVVAGQAWAKVRS 374
+ A++ + D RG +AT V+ GTLKKG V G V+
Sbjct: 1 LRALVFKVFKDKGRGTVATGRVESGTLKKGDKVRVGPGGGGVKG 44
>gnl|CDD|206727 cd04164, trmE, trmE is a tRNA modification GTPase. TrmE (MnmE,
ThdF, MSS1) is a 3-domain protein found in bacteria and
eukaryotes. It controls modification of the uridine at
the wobble position (U34) of tRNAs that read codons
ending with A or G in the mixed codon family boxes. TrmE
contains a GTPase domain that forms a canonical Ras-like
fold. It functions a molecular switch GTPase, and
apparently uses a conformational change associated with
GTP hydrolysis to promote the tRNA modification
reaction, in which the conserved cysteine in the
C-terminal domain is thought to function as a catalytic
residue. In bacteria that are able to survive in
extremely low pH conditions, TrmE regulates
glutamate-dependent acid resistance.
Length = 159
Score = 43.6 bits (104), Expect = 5e-05
Identities = 25/90 (27%), Positives = 33/90 (36%), Gaps = 17/90 (18%)
Query: 188 DIVVLVVAADDGVMEQTVE-SIRMAREAKVPIIVAINKIDKPAADIERTKNMLLAQGITV 246
D+V+LVV D E + AK P+IV +NK D L
Sbjct: 84 DLVLLVV---DASEGLDEEDLEILELPAKKPVIVVLNKSD-------------LLSDAEG 127
Query: 247 EDLGGDIQAVPISALTGTNVDNLTEAIERT 276
+ ISA TG +D L EA+
Sbjct: 128 ISELNGKPIIAISAKTGEGIDELKEALLEL 157
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 45.6 bits (109), Expect = 6e-05
Identities = 25/88 (28%), Positives = 41/88 (46%), Gaps = 12/88 (13%)
Query: 188 DIVVLVVAADDGVMEQTVESIRMAREAKVPIIVAINKIDKPAADIERTKNMLLAQGITVE 247
D+V+ V+ A + ++ + I + + K PIIV +NK D + + E
Sbjct: 298 DLVLFVLDASQPLDKEDLALIELLPKKK-PIIVVLNKADLVSKIE-----------LESE 345
Query: 248 DLGGDIQAVPISALTGTNVDNLTEAIER 275
L + ISA TG +D L EAI++
Sbjct: 346 KLANGDAIISISAKTGEGLDALREAIKQ 373
>gnl|CDD|151168 pfam10662, PduV-EutP, Ethanolamine utilisation - propanediol
utilisation. Members of this family function in
ethanolamine and propanediol degradation pathways,
however the exact roles of these proteins is poorly
understood.
Length = 143
Score = 43.0 bits (102), Expect = 6e-05
Identities = 39/172 (22%), Positives = 64/172 (37%), Gaps = 39/172 (22%)
Query: 112 MKRPPVVTIMGHVDHGKTTLLDTLRNTSVVKSEFGGITQHIGAFVVTLKSGEQVTFLDTP 171
MK+ + ++G GKTTL L + + TQ I + + + +DTP
Sbjct: 1 MKK---IMLIGRSGCGKTTLTQALNGEELKYKK----TQAI-------EFSDNM--IDTP 44
Query: 172 G----HAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVE---SIRMAREAKVPIIVAINK 224
G + F + A D++ LV A + + + P+I I K
Sbjct: 45 GEYLENRRFYSALIVTAADADVIALVQDATE--PWSVFPPGFASMFNK----PVIGIITK 98
Query: 225 IDKPA--ADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIE 274
ID A+IE + L G + +SA+T +D L +E
Sbjct: 99 IDLAKDEANIEMVEEWLNNAGAE--------KIFEVSAVTNEGIDELFAYLE 142
>gnl|CDD|237185 PRK12739, PRK12739, elongation factor G; Reviewed.
Length = 691
Score = 45.6 bits (109), Expect = 9e-05
Identities = 48/167 (28%), Positives = 67/167 (40%), Gaps = 47/167 (28%)
Query: 120 IMGHVDHGKTTLLDTLRNTSVVKSE----FGGITQ-----HIGAFV-----------VTL 159
IM H+D GKTT +E + G + H GA +T+
Sbjct: 13 IMAHIDAGKTT-----------TTERILYYTGKSHKIGEVHDGAATMDWMEQEQERGITI 61
Query: 160 KS--------GEQVTFLDTPGHAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMA 211
S G ++ +DTPGH F+ R D V V A GV Q+ R A
Sbjct: 62 TSAATTCFWKGHRINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVSGVEPQSETVWRQA 121
Query: 212 REAKVPIIVAINKIDKPAADIERTKNMLLAQGITVEDLGGDIQAVPI 258
+ VP IV +NK+D+ AD R+ + + LG + AVPI
Sbjct: 122 DKYGVPRIVFVNKMDRIGADFFRSVEQI------KDRLGAN--AVPI 160
>gnl|CDD|185391 PRK15494, era, GTPase Era; Provisional.
Length = 339
Score = 44.7 bits (105), Expect = 1e-04
Identities = 54/192 (28%), Positives = 83/192 (43%), Gaps = 24/192 (12%)
Query: 118 VTIMGHVDHGKTTLLDTL--RNTSVVKSEFGGITQHIGAFVVTLKSGEQVTFLDTPG--- 172
V I+G + GK+TLL+ + S+V + T+ I ++TLK QV DTPG
Sbjct: 55 VCIIGRPNSGKSTLLNRIIGEKLSIVTPKVQ-TTRSIITGIITLKD-TQVILYDTPGIFE 112
Query: 173 -HAAFSNMRSRGA----HCTDIVVLVVAADDGVMEQTVESIRMAREAKVPIIVAINKIDK 227
+ R A H D+V+L++ + + T + R + I +NKID
Sbjct: 113 PKGSLEKAMVRCAWSSLHSADLVLLIIDSLKSFDDITHNILDKLRSLNIVPIFLLNKIDI 172
Query: 228 PAADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIERTKNMLLAQGITV 287
+ + K L D PISAL+G N+D L E I T ++ +
Sbjct: 173 ESKYLNDIKAFLTENH-------PDSLLFPISALSGKNIDGLLEYI--TSKAKISPWLYA 223
Query: 288 EDLGGDIQAVPI 299
ED DI +P+
Sbjct: 224 ED---DITDLPM 232
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 44.3 bits (106), Expect = 1e-04
Identities = 28/102 (27%), Positives = 44/102 (43%), Gaps = 19/102 (18%)
Query: 188 DIVVLVVAADDGVMEQTVESIRMAREAKVPIIVAINKIDKPAADIERTKNMLLAQGITVE 247
D+V+LV+ A + + E+ E + P+IV +NK D L I +E
Sbjct: 296 DLVLLVLDASEPLTEEDDEIL--EELKDKPVIVVLNKAD-------------LTGEIDLE 340
Query: 248 DLGGDIQAVPISALTGTNVDNLTEAIERTKNMLLAQGITVED 289
+ G + ISA TG +D L EAI K + ++
Sbjct: 341 EENGK-PVIRISAKTGEGIDELREAI---KELAFGGFGGNQE 378
>gnl|CDD|177730 PLN00116, PLN00116, translation elongation factor EF-2 subunit;
Provisional.
Length = 843
Score = 44.3 bits (105), Expect = 2e-04
Identities = 37/141 (26%), Positives = 62/141 (43%), Gaps = 31/141 (21%)
Query: 118 VTIMGHVDHGKTTLLDTL---------------RNTSVVKSEFG-GIT---------QHI 152
++++ HVDHGK+TL D+L R T E GIT +
Sbjct: 22 MSVIAHVDHGKSTLTDSLVAAAGIIAQEVAGDVRMTDTRADEAERGITIKSTGISLYYEM 81
Query: 153 GAFVVTLKSGEQ------VTFLDTPGHAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVE 206
+ GE+ + +D+PGH FS+ + TD ++VV +GV QT
Sbjct: 82 TDESLKDFKGERDGNEYLINLIDSPGHVDFSSEVTAALRITDGALVVVDCIEGVCVQTET 141
Query: 207 SIRMAREAKVPIIVAINKIDK 227
+R A ++ ++ +NK+D+
Sbjct: 142 VLRQALGERIRPVLTVNKMDR 162
>gnl|CDD|206714 cd04147, Ras_dva, Ras - dorsal-ventral anterior localization
(Ras-dva) family. Ras-dva subfamily. Ras-dva (Ras -
dorsal-ventral anterior localization) subfamily consists
of a set of proteins characterized only in Xenopus
leavis, to date. In Xenopus Ras-dva expression is
activated by the transcription factor Otx2 and begins
during gastrulation throughout the anterior ectoderm.
Ras-dva expression is inhibited in the anterior neural
plate by factor Xanf1. Downregulation of Ras-dva results
in head development abnormalities through the inhibition
of several regulators of the anterior neural plate and
folds patterning, including Otx2, BF-1, Xag2, Pax6,
Slug, and Sox9. Downregulation of Ras-dva also
interferes with the FGF-8a signaling within the anterior
ectoderm. Most Ras proteins contain a lipid modification
site at the C-terminus, with a typical sequence motif
CaaX, where a = an aliphatic amino acid and X = any
amino acid. Lipid binding is essential for membrane
attachment, a key feature of most Ras proteins.
Length = 197
Score = 41.7 bits (98), Expect = 4e-04
Identities = 37/121 (30%), Positives = 51/121 (42%), Gaps = 11/121 (9%)
Query: 118 VTIMGHVDHGKTTLLDT-LRNTSVVKSEFGGITQHIGAFVVTLKSGEQVTF--LDTPGHA 174
+ MG GKT L+ L +T K H + V +G +VT LDT G
Sbjct: 2 LVFMGAAGVGKTALIQRFLYDTFEPKHRRTVEELHSKEYEV---AGVKVTIDILDTSGSY 58
Query: 175 AFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESIR-----MAREAKVPIIVAINKIDKPA 229
+F MR D LV + DD + V+ +R + + VPI+V NKID A
Sbjct: 59 SFPAMRKLSIQNGDAFALVYSVDDPESFEEVKRLREEILEVKEDKFVPIVVVGNKIDSLA 118
Query: 230 A 230
Sbjct: 119 E 119
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 42.8 bits (102), Expect = 5e-04
Identities = 21/60 (35%), Positives = 27/60 (45%), Gaps = 10/60 (16%)
Query: 214 AKVPIIVAINKIDKPAADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAI 273
+ P IV NK+D P A+ E + G V PISALTG +D L A+
Sbjct: 273 LERPQIVVANKMDLPEAE-ENLEEFKEKLGPKV---------FPISALTGQGLDELLYAV 322
>gnl|CDD|206691 cd04105, SR_beta, Signal recognition particle receptor, beta
subunit (SR-beta), together with SR-alpha, forms the
heterodimeric signal recognition particle (SRP). Signal
recognition particle receptor, beta subunit (SR-beta).
SR-beta and SR-alpha form the heterodimeric signal
recognition particle (SRP or SR) receptor that binds SRP
to regulate protein translocation across the ER
membrane. Nascent polypeptide chains are synthesized
with an N-terminal hydrophobic signal sequence that
binds SRP54, a component of the SRP. SRP directs
targeting of the ribosome-nascent chain complex (RNC) to
the ER membrane via interaction with the SR, which is
localized to the ER membrane. The RNC is then
transferred to the protein-conducting channel, or
translocon, which facilitates polypeptide translation
across the ER membrane or integration into the ER
membrane. SR-beta is found only in eukaryotes; it is
believed to control the release of the signal sequence
from SRP54 upon binding of the ribosome to the
translocon. High expression of SR-beta has been observed
in human colon cancer, suggesting it may play a role in
the development of this type of cancer.
Length = 202
Score = 41.5 bits (98), Expect = 5e-04
Identities = 47/213 (22%), Positives = 81/213 (38%), Gaps = 28/213 (13%)
Query: 116 PVVTIMGHVDHGKTTLLDTLRNTSVVKSEFGGITQHIGAFVVTLKSGEQVTFLDTPGHAA 175
P V ++G D GKT L L V + I ++ +F G+++T +D PGH
Sbjct: 1 PTVLLLGPSDSGKTALFTKLTTGKVRST-VTSIEPNVASFYSNSSKGKKLTLVDVPGHEK 59
Query: 176 F-SNMRSRGAHCTDIVVLVV--AADDGVMEQTVE------SIRMAREAKVPIIVAINKID 226
+ +V VV A + E + + K+PI++A NK D
Sbjct: 60 LRDKLLEYLKASLKAIVFVVDSATFQKNIRDVAEFLYDILTDLEKIKNKIPILIACNKQD 119
Query: 227 ----KPAADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIERTKNMLLA 282
KPA I K +L E ++ +L + D+ ++ K
Sbjct: 120 LFTAKPAKKI---KELL-------EKEINTLRESRSKSLESLDGDDGSKDTLGDKG---G 166
Query: 283 QGITVEDLGGDIQAVPISAL-TGTNVDNLTEAI 314
+ + L G++ V S + +D++ E I
Sbjct: 167 KDFEFDQLEGEVDFVEGSVKKSKGGIDDIEEWI 199
>gnl|CDD|234569 PRK00007, PRK00007, elongation factor G; Reviewed.
Length = 693
Score = 42.8 bits (102), Expect = 5e-04
Identities = 46/169 (27%), Positives = 61/169 (36%), Gaps = 51/169 (30%)
Query: 120 IMGHVDHGKTT-----LLDTLRNTSVVKSEFGGITQHIG--------------------- 153
IM H+D GKTT L T G+ IG
Sbjct: 15 IMAHIDAGKTTTTERILFYT------------GVNHKIGEVHDGAATMDWMEQEQERGIT 62
Query: 154 ---AFVVTLKSGEQVTFLDTPGHAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESI-R 209
A ++ +DTPGH F+ R D V V A GV Q+ E++ R
Sbjct: 63 ITSAATTCFWKDHRINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVGGVEPQS-ETVWR 121
Query: 210 MAREAKVPIIVAINKIDKPAADIERTKNMLLAQGITVEDLGGDIQAVPI 258
A + KVP I +NK+D+ AD R + + LG VPI
Sbjct: 122 QADKYKVPRIAFVNKMDRTGADFYRVVEQI------KDRLGA--NPVPI 162
>gnl|CDD|206739 cd09912, DLP_2, Dynamin-like protein including dynamins,
mitofusins, and guanylate-binding proteins. The dynamin
family of large mechanochemical GTPases includes the
classical dynamins and dynamin-like proteins (DLPs) that
are found throughout the Eukarya. This family also
includes bacterial DLPs. These proteins catalyze
membrane fission during clathrin-mediated endocytosis.
Dynamin consists of five domains; an N-terminal G domain
that binds and hydrolyzes GTP, a middle domain (MD)
involved in self-assembly and oligomerization, a
pleckstrin homology (PH) domain responsible for
interactions with the plasma membrane, GED, which is
also involved in self-assembly, and a proline arginine
rich domain (PRD) that interacts with SH3 domains on
accessory proteins. To date, three vertebrate dynamin
genes have been identified; dynamin 1, which is brain
specific, mediates uptake of synaptic vesicles in
presynaptic terminals; dynamin-2 is expressed
ubiquitously and similarly participates in membrane
fission; mutations in the MD, PH and GED domains of
dynamin 2 have been linked to human diseases such as
Charcot-Marie-Tooth peripheral neuropathy and rare forms
of centronuclear myopathy. Dynamin 3 participates in
megakaryocyte progenitor amplification, and is also
involved in cytoplasmic enlargement and the formation of
the demarcation membrane system. This family also
includes mitofusins (MFN1 and MFN2 in mammals) that are
involved in mitochondrial fusion. Dynamin oligomerizes
into helical structures around the neck of budding
vesicles in a GTP hydrolysis-dependent manner.
Length = 180
Score = 41.0 bits (97), Expect = 6e-04
Identities = 38/154 (24%), Positives = 64/154 (41%), Gaps = 18/154 (11%)
Query: 118 VTIMGHVDHGKTTLLDTLRNTSVVKSEFGGITQHIGAFVVTLKSG--EQVTFLDTPGHAA 175
+ ++G GK+TLL+ L V+ + G+T A + L+ G + V +DTPG
Sbjct: 3 LAVVGEFSAGKSTLLNALLGEEVLPT---GVT-PTTAVITVLRYGLLKGVVLVDTPG--L 56
Query: 176 FSNMRSRGA------HCTDIVVLVVAADDGVMEQTVESIRMAREAKVP-IIVAINKIDK- 227
S + D V+ V++AD + E E ++ + I +NKID
Sbjct: 57 NSTIEHHTEITESFLPRADAVIFVLSADQPLTESEREFLKEILKWSGKKIFFVLNKIDLL 116
Query: 228 -PAADIERTKNMLLAQGITVEDLGGDIQAVPISA 260
E + G+ GG+ + P+SA
Sbjct: 117 SEEELEEVLEYSREELGVLEL-GGGEPRIFPVSA 149
>gnl|CDD|206667 cd01879, FeoB, Ferrous iron transport protein B (FeoB) family.
Ferrous iron transport protein B (FeoB) subfamily. E.
coli has an iron(II) transport system, known as feo,
which may make an important contribution to the iron
supply of the cell under anaerobic conditions. FeoB has
been identified as part of this transport system. FeoB
is a large 700-800 amino acid integral membrane protein.
The N terminus contains a P-loop motif suggesting that
iron transport may be ATP dependent.
Length = 159
Score = 40.5 bits (96), Expect = 6e-04
Identities = 42/183 (22%), Positives = 68/183 (37%), Gaps = 64/183 (34%)
Query: 127 GKTTLLDTLRNTSVVKSEFGGITQHIGAF---VVTLKSG------EQVTFLDTPGHAAFS 177
GKTTL + L T G Q +G + V K G +++ +D PG
Sbjct: 9 GKTTLFNAL--T--------GARQKVGNWPGVTVEKKEGEFKLGGKEIEIVDLPG----- 53
Query: 178 NMRSRGAHCTD------------IVVLVVAADDGVMEQ----TVESIRMAREAKVPIIVA 221
S + D ++V D +E+ T++ + + +P++VA
Sbjct: 54 -TYSLTPYSEDEKVARDFLLGEEPDLIVNVVDATNLERNLYLTLQLLEL----GLPVVVA 108
Query: 222 INKIDKPAADIERTKNMLLAQGITV------EDLGGDIQAVPISALTGTNVDNLTEAIER 275
+N ID +GI + E LG + VP SA G +D L +AI +
Sbjct: 109 LNMID-----------EAEKRGIKIDLDKLSELLG--VPVVPTSARKGEGIDELLDAIAK 155
Query: 276 TKN 278
Sbjct: 156 LAE 158
Score = 32.4 bits (75), Expect = 0.32
Identities = 18/66 (27%), Positives = 28/66 (42%), Gaps = 17/66 (25%)
Query: 269 LTEAIERTKNMLLA---------QGITV------EDLGGDIQAVPISALTGTNVDNLTEA 313
+ +E +++A +GI + E LG + VP SA G +D L +A
Sbjct: 95 TLQLLELGLPVVVALNMIDEAEKRGIKIDLDKLSELLG--VPVVPTSARKGEGIDELLDA 152
Query: 314 IVAQAE 319
I AE
Sbjct: 153 IAKLAE 158
>gnl|CDD|233986 TIGR02729, Obg_CgtA, Obg family GTPase CgtA. This model describes
a univeral, mostly one-gene-per-genome GTP-binding
protein that associates with ribosomal subunits and
appears to play a role in ribosomal RNA maturation. This
GTPase, related to the nucleolar protein Obg, is
designated CgtA in bacteria. Mutations in this gene are
pleiotropic, but it appears that effects on cellular
functions such as chromosome partition may be secondary
to the effect on ribosome structure. Recent work done in
Vibrio cholerae shows an essential role in the stringent
response, in which RelA-dependent ability to synthesize
the alarmone ppGpp is required for deletion of this
GTPase to be lethal [Protein synthesis, Other].
Length = 329
Score = 41.6 bits (99), Expect = 8e-04
Identities = 21/57 (36%), Positives = 26/57 (45%), Gaps = 7/57 (12%)
Query: 217 PIIVAINKIDKPAADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAI 273
P IV +NKID + L E LG + PISALTG +D L A+
Sbjct: 275 PRIVVLNKIDLLDEEELEELLKELK-----EALGKPV--FPISALTGEGLDELLYAL 324
>gnl|CDD|206685 cd01898, Obg, Obg GTPase. The Obg nucleotide binding protein
subfamily has been implicated in stress response,
chromosome partitioning, replication initiation,
mycelium development, and sporulation. Obg proteins are
among a large group of GTP binding proteins conserved
from bacteria to humans. The E. coli homolog, ObgE is
believed to function in ribosomal biogenesis. Members of
the subfamily contain two equally and highly conserved
domains, a C-terminal GTP binding domain and an
N-terminal glycine-rich domain.
Length = 170
Score = 40.1 bits (95), Expect = 0.001
Identities = 21/58 (36%), Positives = 27/58 (46%), Gaps = 8/58 (13%)
Query: 217 PIIVAINKIDKPAAD-IERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAI 273
P IV +NKID A+ LL E G + PISALTG +D L + +
Sbjct: 116 PRIVVLNKIDLLDAEERFEKLKELLK-----ELKGKKV--FPISALTGEGLDELLKKL 166
>gnl|CDD|206719 cd04152, Arl4_Arl7, Arf-like 4 (Arl4) and 7 (Arl7) GTPases. Arl4
(Arf-like 4) is highly expressed in testicular germ
cells, and is found in the nucleus and nucleolus. In
mice, Arl4 is developmentally expressed during
embryogenesis, and a role in somite formation and
central nervous system differentiation has been
proposed. Arl7 has been identified as the only Arf/Arl
protein to be induced by agonists of liver X-receptor
and retinoid X-receptor and by cholesterol loading in
human macrophages. Arl7 is proposed to play a role in
transport between a perinuclear compartment and the
plasma membrane, apparently linked to the ABCA1-mediated
cholesterol secretion pathway. Older literature suggests
that Arl6 is a part of the Arl4/Arl7 subfamily, but
analyses based on more recent sequence data place Arl6
in its own subfamily.
Length = 183
Score = 40.2 bits (94), Expect = 0.001
Identities = 49/177 (27%), Positives = 79/177 (44%), Gaps = 25/177 (14%)
Query: 118 VTIMGHVDHGKTTLLDTLRNTSVVKS--EFGGITQHIGAFVVTLKSGEQVTFL--DTPGH 173
+ ++G GKTT+L L+ V + G T+ I V+L + + VTF D G
Sbjct: 6 IVMLGLDSAGKTTVLYRLKFNEFVNTVPTKGFNTEKIK---VSLGNAKGVTFHFWDVGGQ 62
Query: 174 AAFSNMRSRGAHCTDIVVLVV-AADDGVMEQT-VESIRMAREAK---VPIIVAINKIDKP 228
+ CTD +V VV + D ME+ E ++ + ++ VP++V NK D P
Sbjct: 63 EKLRPLWKSYTRCTDGIVFVVDSVDVERMEEAKTELHKITKFSENQGVPVLVLANKQDLP 122
Query: 229 AA----DIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIERTKNMLL 281
A ++E+ LLA +Q P A+ G + L E +E+ M+L
Sbjct: 123 NALPVSEVEK----LLALHELSSSTPWHVQ--PACAIIG---EGLQEGLEKLYEMIL 170
>gnl|CDD|179105 PRK00741, prfC, peptide chain release factor 3; Provisional.
Length = 526
Score = 41.3 bits (98), Expect = 0.001
Identities = 32/100 (32%), Positives = 47/100 (47%), Gaps = 12/100 (12%)
Query: 162 GEQVTFLDTPGHAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMAREAKVPIIVA 221
+ LDTPGH FS R D ++V+ A GV QT + + + R PI
Sbjct: 78 DCLINLLDTPGHEDFSEDTYRTLTAVDSALMVIDAAKGVEPQTRKLMEVCRLRDTPIFTF 137
Query: 222 INKIDKPAAD-IERTKNMLLAQGITVED-LGGDIQAVPIS 259
INK+D+ + +E LL + +E+ LG I PI+
Sbjct: 138 INKLDRDGREPLE-----LLDE---IEEVLG--IACAPIT 167
>gnl|CDD|223447 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 41.1 bits (97), Expect = 0.002
Identities = 41/183 (22%), Positives = 71/183 (38%), Gaps = 45/183 (24%)
Query: 112 MKRPPVVTIMGHVDHGKTTLLDTLRNTSVVKSEFGGITQHIGAFVVTLKSG------EQV 165
MK+ V + G+ + GKTTL + L + + G+T V K G ++
Sbjct: 1 MKKLTVALV-GNPNVGKTTLFNALTGANQKVGNWPGVT-------VEKKEGKLKYKGHEI 52
Query: 166 TFLDTPGHAAFSNMRSRGAHCTDIVV------------LVVAADDGVMEQTVESIRMA-- 211
+D PG S A+ D V +V D +E+ ++ +
Sbjct: 53 EIVDLPG------TYSLTAYSEDEKVARDFLLEGKPDLIVNVVDATNLER---NLYLTLQ 103
Query: 212 -REAKVPIIVAINKIDKPAADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLT 270
E +P+I+A+N I D + + + + + LG + VP A G ++ L
Sbjct: 104 LLELGIPMILALNMI-----DEAKKRGIRIDIEKLSKLLG--VPVVPTVAKRGEGLEELK 156
Query: 271 EAI 273
AI
Sbjct: 157 RAI 159
>gnl|CDD|234770 PRK00454, engB, GTP-binding protein YsxC; Reviewed.
Length = 196
Score = 39.7 bits (94), Expect = 0.002
Identities = 28/144 (19%), Positives = 56/144 (38%), Gaps = 29/144 (20%)
Query: 149 TQHIGAFVVTLKSGEQVTFLDTPG----------HAAFSNM-----RSRGAHCTDIVVLV 193
TQ I F V +++ +D PG + + R+R VVL+
Sbjct: 60 TQLINFFEV----NDKLRLVDLPGYGYAKVSKEEKEKWQKLIEEYLRTR--ENLKGVVLL 113
Query: 194 VAADDGVMEQTVESIRMAREAKVPIIVAINKIDK-PAADIERTKNMLLAQGITVEDLGG- 251
+ + + E ++ I +E +P+++ + K DK + ++ + L
Sbjct: 114 IDSRHPLKELDLQMIEWLKEYGIPVLIVLTKADKLKKGERKKQLKKVRKA------LKFG 167
Query: 252 DIQAVPISALTGTNVDNLTEAIER 275
D + + S+L +D L AI +
Sbjct: 168 DDEVILFSSLKKQGIDELRAAIAK 191
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 40.1 bits (95), Expect = 0.002
Identities = 21/57 (36%), Positives = 29/57 (50%), Gaps = 6/57 (10%)
Query: 217 PIIVAINKIDKPAADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAI 273
P I+ +NKID + ER K L + LGG + ISA+TG +D L A+
Sbjct: 273 PRILVLNKIDLLDEEEEREKRAALE----LAALGGPV--FLISAVTGEGLDELLRAL 323
>gnl|CDD|232980 TIGR00450, mnmE_trmE_thdF, tRNA modification GTPase TrmE. TrmE,
also called MnmE and previously designated ThdF
(thiophene and furan oxidation protein), is a GTPase
involved in tRNA modification to create
5-methylaminomethyl-2-thiouridine in the wobble position
of some tRNAs. This protein and GidA form an
alpha2/beta2 heterotetramer [Protein synthesis, tRNA and
rRNA base modification].
Length = 442
Score = 40.2 bits (94), Expect = 0.003
Identities = 49/239 (20%), Positives = 95/239 (39%), Gaps = 31/239 (12%)
Query: 62 SSVIYDFQVIIDIIQKSGMKYMVINPTNSVADDSNGKDVERRPPADPSVLMKRPPVVTIM 121
V D++ D ++ + ++++ + D N +E+ + I+
Sbjct: 161 VEVNIDYEE--DDDEQDSLNQLLLSIIAELKDILNSYKLEKL---------DDGFKLAIV 209
Query: 122 GHVDHGKTTLLDTLRNT--SVVKSEFGGITQHIGAFVVTLKSGEQVTFLDTPG---HAAF 176
G + GK++LL+ L ++V S+ G T+ + L G + LDT G HA F
Sbjct: 210 GSPNVGKSSLLNALLKQDRAIV-SDIKGTTRDVVEGDFELN-GILIKLLDTAGIREHADF 267
Query: 177 SNM----RSRGA-HCTDIVVLVVAADDGVMEQTVESIRMAREAKVPIIVAINKIDKPAAD 231
+S A D+V+ V+ A + + I + + +K P I+ +NKID
Sbjct: 268 VERLGIEKSFKAIKQADLVIYVLDASQPLTKDDFLIIDLNK-SKKPFILVLNKIDLKINS 326
Query: 232 IERTKNMLLAQGITVEDLGGDIQAV------PISALTGTNVDNLTEA-IERTKNMLLAQ 283
+E + + + I+A+ I+A L + I + M+L +
Sbjct: 327 LEFFVSSKVLNSSNLSAKQLKIKALVDLLTQKINAFYSKERVELDDYLISSWQAMILLE 385
>gnl|CDD|206748 cd01855, YqeH, Circularly permuted YqeH GTPase. YqeH is an
essential GTP-binding protein. Depletion of YqeH induces
an excess initiation of DNA replication, suggesting that
it negatively controls initiation of chromosome
replication. The YqeH subfamily is common in eukaryotes
and sporadically present in bacteria with probable
acquisition by plants from chloroplasts. Proteins of the
YqeH family contain all sequence motifs typical of the
vast class of P-loop-containing GTPases, but show a
circular permutation, with a G4-G1-G3 pattern of motifs
as opposed to the regular G1-G3-G4 pattern seen in most
GTPases.
Length = 191
Score = 38.4 bits (90), Expect = 0.004
Identities = 25/119 (21%), Positives = 41/119 (34%), Gaps = 26/119 (21%)
Query: 215 KVPIIVAINKID--KPAADIERTKNMLLAQGITVEDLGGDIQAVP-ISALTGTNVDNLTE 271
P+I+ NKID R K + ++ G I+ V +SA G V+ L E
Sbjct: 60 AKPVILVGNKIDLLPKDVKPNRLKQWVKK---RLKIGGLKIKDVILVSAKKGWGVEELIE 116
Query: 272 AIERTK--------------------NMLLAQGITVEDLGGDIQAVPISALTGTNVDNL 310
I++ N LL +Q + +S + GT + +
Sbjct: 117 EIKKLAKYRGDVYVVGATNVGKSTLINALLKSNGGKVQAQALVQRLTVSPIPGTTLGLI 175
>gnl|CDD|206747 cd01854, YjeQ_EngC, Ribosomal interacting GTPase YjeQ/EngC, a
circularly permuted subfamily of the Ras GTPases. YjeQ
(YloQ in Bacillus subtilis) is a ribosomal small
subunit-dependent GTPase; hence also known as RsgA. YjeQ
is a late-stage ribosomal biogenesis factor involved in
the 30S subunit maturation, and it represents a protein
family whose members are broadly conserved in bacteria
and have been shown to be essential to the growth of E.
coli and B. subtilis. Proteins of the YjeQ family
contain all sequence motifs typical of the vast class of
P-loop-containing GTPases, but show a circular
permutation, with a G4-G1-G3 pattern of motifs as
opposed to the regular G1-G3-G4 pattern seen in most
GTPases. All YjeQ family proteins display a unique
domain architecture, which includes an N-terminal
OB-fold RNA-binding domain, the central permuted GTPase
domain, and a zinc knuckle-like C-terminal cysteine
domain.
Length = 211
Score = 38.9 bits (92), Expect = 0.004
Identities = 18/95 (18%), Positives = 37/95 (38%), Gaps = 22/95 (23%)
Query: 188 DIVVLVVAADDGVMEQTVESIR-------MAREAKVPIIVAINKID-KPAADIERTKNML 239
D V++V + + ++R A + + ++ +NK D ++E +
Sbjct: 4 DQVLIVFSLKEPFF-----NLRLLDRYLVAAEASGIEPVIVLNKADLVDDEELEELLEIY 58
Query: 240 LAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIE 274
G V + +SA TG +D L E ++
Sbjct: 59 EKLGYPV---------LAVSAKTGEGLDELRELLK 84
>gnl|CDD|217025 pfam02421, FeoB_N, Ferrous iron transport protein B. Escherichia
coli has an iron(II) transport system (feo) which may
make an important contribution to the iron supply of the
cell under anaerobic conditions. FeoB has been
identified as part of this transport system. FeoB is a
large 700-800 amino acid integral membrane protein. The
N terminus contains a P-loop motif suggesting that iron
transport may be ATP dependent.
Length = 190
Score = 38.2 bits (90), Expect = 0.006
Identities = 21/74 (28%), Positives = 32/74 (43%), Gaps = 21/74 (28%)
Query: 212 REAKVPIIVAINKIDKPAA-------DIERTKNMLLAQGITVEDLGGDIQAVPISALTGT 264
E +P++VA+N +D A DI++ +L G+ V VP SA G
Sbjct: 102 LELGIPVVVALNMMD--EAEKKGIKIDIKKLSELL---GVPV---------VPTSARKGE 147
Query: 265 NVDNLTEAIERTKN 278
+D L +AI
Sbjct: 148 GIDELKDAIIEVAE 161
Score = 37.5 bits (88), Expect = 0.008
Identities = 24/88 (27%), Positives = 38/88 (43%), Gaps = 21/88 (23%)
Query: 269 LTEAIERTKNMLLA---------QGITV------EDLGGDIQAVPISALTGTNVDNLTEA 313
+ +E +++A +GI + E LG + VP SA G +D L +A
Sbjct: 98 TLQLLELGIPVVVALNMMDEAEKKGIKIDIKKLSELLG--VPVVPTSARKGEGIDELKDA 155
Query: 314 IVAQAE----IMHLKADYGGPVEAMIVE 337
I+ AE L+ +YG +E I E
Sbjct: 156 IIEVAEGKVPPAPLRINYGPEIEEAISE 183
>gnl|CDD|133343 cd04143, Rhes_like, Ras homolog enriched in striatum (Rhes) and
activator of G-protein signaling 1 (Dexras1/AGS1). This
subfamily includes Rhes (Ras homolog enriched in
striatum) and Dexras1/AGS1 (activator of G-protein
signaling 1). These proteins are homologous, but exhibit
significant differences in tissue distribution and
subcellular localization. Rhes is found primarily in the
striatum of the brain, but is also expressed in other
areas of the brain, such as the cerebral cortex,
hippocampus, inferior colliculus, and cerebellum. Rhes
expression is controlled by thyroid hormones. In rat
PC12 cells, Rhes is farnesylated and localizes to the
plasma membrane. Rhes binds and activates PI3K, and
plays a role in coupling serpentine membrane receptors
with heterotrimeric G-protein signaling. Rhes has
recently been shown to be reduced under conditions of
dopamine supersensitivity and may play a role in
determining dopamine receptor sensitivity. Dexras1/AGS1
is a dexamethasone-induced Ras protein that is expressed
primarily in the brain, with low expression levels in
other tissues. Dexras1 localizes primarily to the
cytoplasm, and is a critical regulator of the circadian
master clock to photic and nonphotic input. Most Ras
proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Ras proteins.
Length = 247
Score = 38.2 bits (89), Expect = 0.008
Identities = 30/126 (23%), Positives = 53/126 (42%), Gaps = 24/126 (19%)
Query: 164 QVTFLDTPGHAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMA-REAK------- 215
Q+ LDT G+ F MR D+ +LV + D+ + V +R E K
Sbjct: 49 QLDILDTSGNHPFPAMRRLSILTGDVFILVFSLDNRESFEEVCRLREQILETKSCLKNKT 108
Query: 216 -----VPIIVAINKIDKPAA-DIERTKNMLLAQGITVEDLGGDIQAV--PISALTGTNVD 267
+P+++ NK D+ +++R + L +GGD +SA +N+D
Sbjct: 109 KENVKIPMVICGNKADRDFPREVQRDEVEQL--------VGGDENCAYFEVSAKKNSNLD 160
Query: 268 NLTEAI 273
+ A+
Sbjct: 161 EMFRAL 166
>gnl|CDD|206640 cd00154, Rab, Ras-related in brain (Rab) family of small guanosine
triphosphatases (GTPases). Rab GTPases form the largest
family within the Ras superfamily. There are at least 60
Rab genes in the human genome, and a number of Rab
GTPases are conserved from yeast to humans. Rab GTPases
are small, monomeric proteins that function as molecular
switches to regulate vesicle trafficking pathways. The
different Rab GTPases are localized to the cytosolic
face of specific intracellular membranes, where they
regulate distinct steps in membrane traffic pathways. In
the GTP-bound form, Rab GTPases recruit specific sets of
effector proteins onto membranes. Through their
effectors, Rab GTPases regulate vesicle formation,
actin- and tubulin-dependent vesicle movement, and
membrane fusion. GTPase activating proteins (GAPs)
interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which mask C-terminal lipid binding and promote
cytosolic localization. While most unicellular organisms
possess 5-20 Rab members, several have been found to
possess 60 or more Rabs; for many of these Rab isoforms,
homologous proteins are not found in other organisms.
Most Rab GTPases contain a lipid modification site at
the C-terminus, with sequence motifs CC, CXC, or CCX.
Lipid binding is essential for membrane attachment, a
key feature of most Rab proteins. Since crystal
structures often lack C-terminal residues, the lipid
modification site is not available for annotation in
many of the CDs in the hierarchy, but is included where
possible.
Length = 159
Score = 37.1 bits (87), Expect = 0.009
Identities = 39/160 (24%), Positives = 62/160 (38%), Gaps = 35/160 (21%)
Query: 127 GKTTLLDTLRNTSVVKSEFGGITQH-IGA--FVVTLK-SGEQVTFL--DTPGHAAFSNMR 180
GKT+LL V ++F + IG T++ G++V DT G F ++
Sbjct: 12 GKTSLL-----LRFVDNKFSENYKSTIGVDFKSKTIEVDGKKVKLQIWDTAGQERFRSIT 66
Query: 181 S---RGAHCTDIVVLVVAADDGVMEQTVESIRM----AREA---KVPIIVAINKIDKPAA 230
S RGAH +LV + ++ E++ +E +PII+ NK D
Sbjct: 67 SSYYRGAHG---AILVYDVTN---RESFENLDKWLNELKEYAPPNIPIILVGNKSDLEDE 120
Query: 231 -DIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNL 269
+ + A+ + SA TG NVD
Sbjct: 121 RQVSTEEAQQFAKE-------NGLLFFETSAKTGENVDEA 153
>gnl|CDD|206645 cd00879, Sar1, Sar1 is an essential component of COPII vesicle
coats. Sar1 is an essential component of COPII vesicle
coats involved in export of cargo from the ER. The
GTPase activity of Sar1 functions as a molecular switch
to control protein-protein and protein-lipid
interactions that direct vesicle budding from the ER.
Activation of the GDP to the GTP-bound form of Sar1
involves the membrane-associated guanine nucleotide
exchange factor (GEF) Sec12. Sar1 is unlike all Ras
superfamily GTPases that use either myristoyl or prenyl
groups to direct membrane association and function, in
that Sar1 lacks such modification. Instead, Sar1
contains a unique nine-amino-acid N-terminal extension.
This extension contains an evolutionarily conserved
cluster of bulky hydrophobic amino acids, referred to as
the Sar1-N-terminal activation recruitment (STAR) motif.
The STAR motif mediates the recruitment of Sar1 to ER
membranes and facilitates its interaction with mammalian
Sec12 GEF leading to activation.
Length = 191
Score = 37.3 bits (87), Expect = 0.010
Identities = 39/127 (30%), Positives = 61/127 (48%), Gaps = 13/127 (10%)
Query: 111 LMKRPPVVTIMGHVDHGKTTLLDTLRNTSVVKSEFGGITQHIGAFVVTLKSGEQVTFLDT 170
L K+ + +G + GKTTLL L++ + + T H + +T+ + + TF D
Sbjct: 15 LYKKEAKIVFLGLDNAGKTTLLHMLKDDRLAQHV---PTLHPTSEELTIGNVKFTTF-DL 70
Query: 171 PGHAAFSNMRSRGAHCTD---IVVLVVAADDGVMEQTVESIR--MARE--AKVPIIVAIN 223
GH R + + IV LV AAD +++ E + + E A VPI++ N
Sbjct: 71 GGHEQA--RRVWKDYFPEVDGIVFLVDAADPERFQESKEELDSLLNDEELANVPILILGN 128
Query: 224 KIDKPAA 230
KIDKP A
Sbjct: 129 KIDKPGA 135
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 37.9 bits (89), Expect = 0.013
Identities = 19/57 (33%), Positives = 27/57 (47%), Gaps = 5/57 (8%)
Query: 217 PIIVAINKIDKPAADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAI 273
P IV +NKID P + E + L + + + G ISALT +D L A+
Sbjct: 277 PRIVVLNKIDLPLDEEELEE---LKKAL--AEALGWEVFYLISALTREGLDELLRAL 328
>gnl|CDD|240362 PTZ00327, PTZ00327, eukaryotic translation initiation factor 2
gamma subunit; Provisional.
Length = 460
Score = 37.7 bits (88), Expect = 0.018
Identities = 58/234 (24%), Positives = 94/234 (40%), Gaps = 49/234 (20%)
Query: 83 MVINPTNSVADDSNGKDVERRPPADPSVLMKRPPVVTI--MGHVDHGKTTLLDTLR--NT 138
++ D + D+++ P P V + R + I +GHV HGK+T++ L T
Sbjct: 1 VIDTDDGLAKQDLSKLDLDKLTPLTPEV-ISRQATINIGTIGHVAHGKSTVVKALSGVKT 59
Query: 139 SVVKSEF-GGITQHIG-------------------AF---------------VVTLKSGE 163
K E IT +G ++ +TLK
Sbjct: 60 VRFKREKVRNITIKLGYANAKIYKCPKCPRPTCYQSYGSSKPDNPPCPGCGHKMTLK--R 117
Query: 164 QVTFLDTPGHAAFSNMRSRGAHCTDIVVLVVAADDGVME-QTVESIRMAREAKVP-IIVA 221
V+F+D PGH GA D +L++AA++ + QT E + K+ II+
Sbjct: 118 HVSFVDCPGHDILMATMLNGAAVMDAALLLIAANESCPQPQTSEHLAAVEIMKLKHIIIL 177
Query: 222 INKID--KPAADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAI 273
NKID K A ++ + + T+ D + +PISA N+D + E I
Sbjct: 178 QNKIDLVKEAQAQDQYEEIRNFVKGTIAD---NAPIIPISAQLKYNIDVVLEYI 228
>gnl|CDD|232975 TIGR00437, feoB, ferrous iron transporter FeoB. FeoB (773 amino
acids in E. coli), a cytoplasmic membrane protein
required for iron(II) update, is encoded in an operon
with FeoA (75 amino acids), which is also required, and
is regulated by Fur. There appear to be two copies in
Archaeoglobus fulgidus and Clostridium acetobutylicum
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 591
Score = 37.4 bits (87), Expect = 0.027
Identities = 38/161 (23%), Positives = 68/161 (42%), Gaps = 30/161 (18%)
Query: 127 GKTTLLDTLRNTSVVKSEFGGITQHIGAFVVTLKSGEQVTFLDTPGHAAFS--NMRSRGA 184
GK+TL + L + + G+T + + GE + +D PG + + ++ A
Sbjct: 6 GKSTLFNALTGANQTVGNWPGVTVEKKEGKLGFQ-GEDIEIVDLPGIYSLTTFSLEEEVA 64
Query: 185 ------HCTDIVVLVVAADDGVMEQTVESIRMAREAKVPIIVAINKIDKPAADIERTKNM 238
D+VV VV D +E+ + E +P+I+A+N +D
Sbjct: 65 RDYLLNEKPDLVVNVV--DASNLERNLYLTLQLLELGIPMILALNLVD-----------E 111
Query: 239 LLAQGITVED------LGGDIQAVPISALTGTNVDNLTEAI 273
+GI +++ LG + VP SA G ++ L +AI
Sbjct: 112 AEKKGIRIDEEKLEERLG--VPVVPTSATEGRGIERLKDAI 150
>gnl|CDD|185364 PRK15467, PRK15467, ethanolamine utilization protein EutP;
Provisional.
Length = 158
Score = 35.3 bits (81), Expect = 0.034
Identities = 41/153 (26%), Positives = 62/153 (40%), Gaps = 55/153 (35%)
Query: 112 MKRPPVVTIMGHVDHGKTTLLDTLRNTSVVKSEFGGITQHIGAFVVTLKSGEQVTF---- 167
MKR + +G V GKTTL + L+ G + + K+ + V F
Sbjct: 1 MKR---IAFVGAVGAGKTTLFNALQ----------------GNYTLARKT-QAVEFNDKG 40
Query: 168 -LDTPGHAAFSNMRSRGAHCT-----DIVVLVVAADDGVMEQTVESIRMAREAKVP---- 217
+DTPG FS+ R A T D+++ V A+D E+++P
Sbjct: 41 DIDTPGEY-FSHPRWYHALITTLQDVDMLIYVHGAND-------------PESRLPAGLL 86
Query: 218 -------IIVAINKIDKPAADIERTKNMLLAQG 243
I I+K D P AD+ T+ +LL G
Sbjct: 87 DIGVSKRQIAVISKTDMPDADVAATRKLLLETG 119
>gnl|CDD|206708 cd04136, Rap_like, Rap-like family consists of Rap1, Rap2 and RSR1.
The Rap subfamily consists of the Rap1, Rap2, and RSR1.
Rap subfamily proteins perform different cellular
functions, depending on the isoform and its subcellular
localization. For example, in rat salivary gland,
neutrophils, and platelets, Rap1 localizes to secretory
granules and is believed to regulate exocytosis or the
formation of secretory granules. Rap1 has also been
shown to localize in the Golgi of rat fibroblasts,
zymogen granules, plasma membrane, and microsomal
membrane of the pancreatic acini, as well as in the
endocytic compartment of skeletal muscle cells and
fibroblasts. Rap1 localizes in the nucleus of human
oropharyngeal squamous cell carcinomas (SCCs) and cell
lines. Rap1 plays a role in phagocytosis by controlling
the binding of adhesion receptors (typically integrins)
to their ligands. In yeast, Rap1 has been implicated in
multiple functions, including activation and silencing
of transcription and maintenance of telomeres. Rap2 is
involved in multiple functions, including activation of
c-Jun N-terminal kinase (JNK) to regulate the actin
cytoskeleton and activation of the Wnt/beta-catenin
signaling pathway in embryonic Xenopus. A number of
effector proteins for Rap2 have been identified,
including isoform 3 of the human mitogen-activated
protein kinase kinase kinase kinase 4 (MAP4K4) and
Traf2- and Nck-interacting kinase (TNIK), and the
RalGEFs RalGDS, RGL, and Rlf, which also interact with
Rap1 and Ras. RSR1 is the fungal homolog of Rap1 and
Rap2. In budding yeasts, it is involved in selecting a
site for bud growth, which directs the establishment of
cell polarization. The Rho family GTPase Cdc42 and its
GEF, Cdc24, then establish an axis of polarized growth.
It is believed that Cdc42 interacts directly with RSR1
in vivo. In filamentous fungi such as Ashbya gossypii,
RSR1 is a key regulator of polar growth in the hypha.
Most Ras proteins contain a lipid modification site at
the C-terminus, with a typical sequence motif CaaX,
where a = an aliphatic amino acid and X = any amino
acid. Lipid binding is essential for membrane
attachment, a key feature of most Ras proteins. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for annotation.
Length = 164
Score = 35.2 bits (81), Expect = 0.039
Identities = 26/116 (22%), Positives = 45/116 (38%), Gaps = 10/116 (8%)
Query: 168 LDTPGHAAFSNMRSRGAHCTDIVVLVVAADD-----GVMEQTVESIRMAREAKVPIIVAI 222
LDT G F+ MR LV + + + + +R+ VP+I+
Sbjct: 54 LDTAGTEQFTAMRDLYIKNGQGFALVYSITAQQSFNDLQDLREQILRVKDTEDVPMILVG 113
Query: 223 NKIDKPAADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIERTKN 278
NK D+E + + +G + G+ + SA + NVD + + R N
Sbjct: 114 NK-----CDLEDERVVSKEEGQNLARQWGNCPFLETSAKSKINVDEIFYDLVRQIN 164
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 35.3 bits (82), Expect = 0.040
Identities = 41/164 (25%), Positives = 64/164 (39%), Gaps = 25/164 (15%)
Query: 127 GKTTLLDTLRNTSVVKSEFGGITQHIGAFVVTLKSGE-QVTFLDTPGHAAFSNMRSRGAH 185
GKTT+L L+ E IG V T+ + T D G ++R +
Sbjct: 26 GKTTILYKLKL-----GEIVTTIPTIGFNVETVTYKNVKFTVWDVGGQ---ESLRPLWRN 77
Query: 186 ---CTDIVVLVV-AAD-DGVMEQTVESIRMARE---AKVPIIVAINKIDKP-AADIERTK 236
TD V+ VV +AD D + E E + E A P+++ NK D P A +
Sbjct: 78 YFPNTDAVIFVVDSADRDRIEEAKEELHALLNEEELADAPLLILANKQDLPGAMSEAEIR 137
Query: 237 NMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIERTKNML 280
+L + + SA+TG + L E ++ N +
Sbjct: 138 ELLGLHELKDR----PWEIQGCSAVTG---EGLDEGLDWLSNYI 174
>gnl|CDD|213835 TIGR03598, GTPase_YsxC, ribosome biogenesis GTP-binding protein
YsxC/EngB. Members of this protein family are a GTPase
associated with ribosome biogenesis, typified by YsxC
from Bacillus subutilis. The family is widely but not
universally distributed among bacteria. Members commonly
are called EngB based on homology to EngA, one of
several other GTPases of ribosome biogenesis. Cutoffs as
set find essentially all bacterial members, but also
identify large numbers of eukaryotic (probably
organellar) sequences. This protein is found in about 80
percent of bacterial genomes [Protein synthesis, Other].
Length = 178
Score = 35.1 bits (82), Expect = 0.049
Identities = 35/161 (21%), Positives = 61/161 (37%), Gaps = 32/161 (19%)
Query: 127 GKTTLLDTL-RNTSVVK-SEFGGITQHIGAFVVTLKSGEQVTFLDTPG----------HA 174
GK++L++ L + + S+ G TQ I F V + +D PG
Sbjct: 30 GKSSLINALTNRKKLARTSKTPGRTQLINFFEV----NDGFRLVDLPGYGYAKVSKEEKE 85
Query: 175 AFSNM-----RSRGAHCTDIVVLVVAADDGVMEQTVESIRMAREAKVPIIVAINKIDK-P 228
+ + R VVL++ + E +E I RE +P+++ + K DK
Sbjct: 86 KWQKLIEEYLEKRENLKG--VVLLMDIRHPLKELDLEMIEWLRERGIPVLIVLTKADKLK 143
Query: 229 AADIERTKNMLLAQGITVEDLGG--DIQAVPISALTGTNVD 267
+ E K + + + L D S+L T +D
Sbjct: 144 KS--ELNKQLKKIK----KALKKDADDSVQLFSSLKKTGID 178
>gnl|CDD|112137 pfam03308, ArgK, ArgK protein. The ArgK protein acts as an ATPase
enzyme and as a kinase, and phosphorylates periplasmic
binding proteins involved in the LAO (lysine, arginine,
ornithine)/AO transport systems.
Length = 267
Score = 35.8 bits (83), Expect = 0.055
Identities = 30/110 (27%), Positives = 44/110 (40%), Gaps = 22/110 (20%)
Query: 184 AHCTDIVVLVV---AADD------GVMEQTVESIRMAREAKVPIIVAINKIDKPAADIER 234
A+ D VLV DD G+ME + I +NK D P A+
Sbjct: 140 ANMADTFVLVTIPGGGDDLQGIKAGLME-------------IADIYVVNKADLPGAERTA 186
Query: 235 TKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIERTKNMLLAQG 284
+ +T ++ G + SA+TG +D L +AIE + L A G
Sbjct: 187 RELRSALHLLTPKEAGWRPPVLTTSAVTGEGIDELWDAIEEHREFLTATG 236
>gnl|CDD|129833 TIGR00750, lao, LAO/AO transport system ATPase. In E. coli,
mutation of this kinase blocks phosphorylation of two
transporter system periplasmic binding proteins and
consequently inhibits those transporters. This kinase is
also found in Gram-positive bacteria, archaea, and the
roundworm C. elegans. It may have a more general, but
still unknown function. Mutations have also been found
that do not phosphorylate the periplasmic binding
proteins, yet still allow transport. The ATPase activity
of this protein seems to be necessary, however
[Transport and binding proteins, Amino acids, peptides
and amines, Regulatory functions, Protein interactions].
Length = 300
Score = 35.9 bits (83), Expect = 0.057
Identities = 38/151 (25%), Positives = 59/151 (39%), Gaps = 27/151 (17%)
Query: 146 GGITQHIGAFVVTLKS-GEQVTFLDTPGHAAFSNMRSRGAHCTDIVVLVVAADD------ 198
GG++Q V+ L + G V ++T G + A +V + DD
Sbjct: 109 GGLSQATRELVLLLDAAGYDVIIVETVGVGQSEVDIANMADTFVLVTIPGTGDDLQGIKA 168
Query: 199 GVMEQTVESIRMAREAKVPIIVAINKIDKPAADIERTKNMLLAQGITVEDL-----GGDI 253
GVME + I +NK D A R ++L+ + E++ G
Sbjct: 169 GVME-------------IADIYVVNKADGEGATNVRIARLMLSLAL--EEIRRREDGWRP 213
Query: 254 QAVPISALTGTNVDNLTEAIERTKNMLLAQG 284
+ SA+ G +D L +AIE K L A G
Sbjct: 214 PVLTTSAVEGRGIDELWDAIEEHKTFLTASG 244
>gnl|CDD|206749 cd01856, YlqF, Circularly permuted YlqF GTPase. Proteins of the
YlqF family contain all sequence motifs typical of the
vast class of P-loop-containing GTPases, but show a
circular permutation, with a G4-G1-G3 pattern of motifs
as opposed to the regular G1-G3-G4 pattern seen in most
GTPases. The YlqF subfamily is represented in all
eukaryotes as well as a phylogenetically diverse array
of bacteria (including gram-positive bacteria,
proteobacteria, Synechocystis, Borrelia, and
Thermotoga).
Length = 171
Score = 34.8 bits (81), Expect = 0.067
Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 9/49 (18%)
Query: 127 GKTTLLDTLRNTSVVKSEFG---GITQHIGAFVVTLKSGEQVTFLDTPG 172
GK+TL++ LR V K G G+T+ ++ G + LDTPG
Sbjct: 127 GKSTLINRLRGKKVAKV--GNKPGVTRGQQ----WIRIGPNIELLDTPG 169
>gnl|CDD|131580 TIGR02528, EutP, ethanolamine utilization protein, EutP. This
protein is found within operons which code for
polyhedral organelles containing the enzyme ethanolamine
ammonia lyase. The function of this gene is unknown,
although the presence of an N-terminal GxxGxGK motif
implies a GTP-binding site [Energy metabolism, Amino
acids and amines].
Length = 142
Score = 34.3 bits (79), Expect = 0.069
Identities = 39/135 (28%), Positives = 53/135 (39%), Gaps = 24/135 (17%)
Query: 118 VTIMGHVDHGKTTLLDTLRNTSVVKSEFGGITQHIGAFVVTLKSGEQVTFLDTPGHAAFS 177
+ +G V GKTTL L+ ++ + TQ V G +DTPG
Sbjct: 3 IMFIGSVGCGKTTLTQALQGEEILYKK----TQ-----AVEYNDGA----IDTPGE-YVE 48
Query: 178 NMRSRGAHCT-----DIVVLVVAADDGVMEQTVESIRMAREAKVPIIVAINKIDKPAAD- 231
N R A D++ LV +A D E + K P+I + KID AD
Sbjct: 49 NRRLYSALIVTAADADVIALVQSATDP--ESRFPPGFASIFVK-PVIGLVTKIDLAEADV 105
Query: 232 -IERTKNMLLAQGIT 245
IER K +L G
Sbjct: 106 DIERAKELLETAGAE 120
>gnl|CDD|227254 COG4917, EutP, Ethanolamine utilization protein [Amino acid
transport and metabolism].
Length = 148
Score = 34.5 bits (79), Expect = 0.074
Identities = 37/138 (26%), Positives = 52/138 (37%), Gaps = 25/138 (18%)
Query: 112 MKRPPVVTIMGHVDHGKTTLLDTLRNTSVVKSEFGGITQHIGAFVVTLKSGEQVTFLDTP 171
MKR + +G V GKTTL +L + + TQ + +DTP
Sbjct: 1 MKR---IAFVGQVGCGKTTLFQSLYGNDTLYKK----TQAVEFN--------DKGDIDTP 45
Query: 172 GHAAFSNMRSRGAHCT-----DIVVLVVAADDGVMEQTVESIRMAREAKVPIIVAINKID 226
G F + R A T D+++ V AA+D E + K +I + K D
Sbjct: 46 GE-YFEHPRWYHALITTLQDADVIIYVHAANDP--ESRFPPGFLDIGVK-KVIGVVTKAD 101
Query: 227 KPA-ADIERTKNMLLAQG 243
ADI K L G
Sbjct: 102 LAEDADISLVKRWLREAG 119
>gnl|CDD|222178 pfam13500, AAA_26, AAA domain. This domain is found in a number of
proteins involved in cofactor biosynthesis such as
dethiobiotin synthase and cobyric acid synthase. This
domain contains a P-loop motif.
Length = 197
Score = 34.5 bits (80), Expect = 0.089
Identities = 12/45 (26%), Positives = 22/45 (48%), Gaps = 2/45 (4%)
Query: 190 VVLVVAADDGVMEQTVESIRMAREAKVPII-VAINKIDKPAADIE 233
V+LV G + T+ +I R + I+ V +N + A++E
Sbjct: 130 VILVARGGLGTINHTLLTIEALRSRGINILGVILNGV-PNPANVE 173
>gnl|CDD|206724 cd04159, Arl10_like, Arf-like 9 (Arl9) and 10 (Arl10) GTPases.
Arl10-like subfamily. Arl9/Arl10 was identified from a
human cancer-derived EST dataset. No functional
information about the subfamily is available at the
current time, but crystal structures of human Arl10b and
Arl10c have been solved.
Length = 159
Score = 34.2 bits (79), Expect = 0.098
Identities = 39/158 (24%), Positives = 65/158 (41%), Gaps = 17/158 (10%)
Query: 118 VTIMGHVDHGKTTLLDTLRNTSVVKSEFGGITQHIGAFVV--TLKSGEQVTFLDTPGHAA 175
+T++G + GKTTL++ + + +F T F + K + D G
Sbjct: 2 ITLVGLQNSGKTTLVNVIAS-----GQFSEDTIPTVGFNMRKVTKGNVTIKVWDLGGQPR 56
Query: 176 FSNMRSRGAHCTDIVVLVV-AADDGVMEQTVESIRMAREAK----VPIIVAINKIDKP-A 229
F +M R + +V VV AAD +E + E +P++V NK D P A
Sbjct: 57 FRSMWERYCRGVNAIVYVVDAADREKLEVAKNELHDLLEKPSLEGIPLLVLGNKNDLPGA 116
Query: 230 ADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVD 267
++ + + IT ++ ISA TN+D
Sbjct: 117 LSVDELIEQMNLKSIT----DREVSCYSISAKEKTNID 150
>gnl|CDD|206669 cd01882, BMS1, Bms1, an essential GTPase, promotes assembly of
preribosomal RNA processing complexes. Bms1 is an
essential, evolutionarily conserved, nucleolar protein.
Its depletion interferes with processing of the 35S
pre-rRNA at sites A0, A1, and A2, and the formation of
40S subunits. Bms1, the putative endonuclease Rc11, and
the essential U3 small nucleolar RNA form a stable
subcomplex that is believed to control an early step in
the formation of the 40S subumit. The C-terminal domain
of Bms1 contains a GTPase-activating protein (GAP) that
functions intramolecularly. It is believed that Rc11
activates Bms1 by acting as a guanine-nucleotide
exchange factor (GEF) to promote GDP/GTP exchange, and
that activated (GTP-bound) Bms1 delivers Rc11 to the
preribosomes.
Length = 231
Score = 34.6 bits (80), Expect = 0.10
Identities = 31/116 (26%), Positives = 51/116 (43%), Gaps = 19/116 (16%)
Query: 102 RRPPADPSVLMKRPPVVTIMGHVDHGKTTLLDTL------RNTSVVKSEFGGITQHIGAF 155
P D + P VV ++G GK+TL+ +L +N S +K G IT
Sbjct: 26 HVPVVDRTPEEPPPLVVVVVGPPGVGKSTLIRSLIKRYTKQNLSDIK---GPIT------ 76
Query: 156 VVTLKSGEQVTFLDTPGHAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMA 211
+VT K ++TF++ P N A D+V+L++ G +T E + +
Sbjct: 77 IVTGKK-RRLTFIECPND---INSMIDVAKIADLVLLLIDGSYGFEMETFEFLNIL 128
>gnl|CDD|206684 cd01897, NOG, Nucleolar GTP-binding protein (NOG). NOG1 is a
nucleolar GTP-binding protein present in eukaryotes
ranging from trypanosomes to humans. NOG1 is
functionally linked to ribosome biogenesis and found in
association with the nuclear pore complexes and
identified in many preribosomal complexes. Thus, defects
in NOG1 can lead to defects in 60S biogenesis. The S.
cerevisiae NOG1 gene is essential for cell viability,
and mutations in the predicted G motifs abrogate
function. It is a member of the ODN family of
GTP-binding proteins that also includes the bacterial
Obg and DRG proteins.
Length = 167
Score = 34.1 bits (79), Expect = 0.12
Identities = 19/67 (28%), Positives = 29/67 (43%), Gaps = 11/67 (16%)
Query: 215 KVPIIVAINKIDKPAADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIE 274
P+IV +NKID E L++ + G+ + + IS LT VD E
Sbjct: 112 NKPVIVVLNKIDL--LTEED-----LSEIEKELEKEGE-EVIKISTLTEEGVD---ELKN 160
Query: 275 RTKNMLL 281
+ +LL
Sbjct: 161 KACELLL 167
>gnl|CDD|206655 cd01862, Rab7, Rab GTPase family 7 (Rab7). Rab7 subfamily. Rab7 is
a small Rab GTPase that regulates vesicular traffic from
early to late endosomal stages of the endocytic pathway.
The yeast Ypt7 and mammalian Rab7 are both involved in
transport to the vacuole/lysosome, whereas Ypt7 is also
required for homotypic vacuole fusion. Mammalian Rab7 is
an essential participant in the autophagic pathway for
sequestration and targeting of cytoplasmic components to
the lytic compartment. Mammalian Rab7 is also proposed
to function as a tumor suppressor. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 172
Score = 34.2 bits (79), Expect = 0.12
Identities = 34/121 (28%), Positives = 45/121 (37%), Gaps = 25/121 (20%)
Query: 169 DTPGHAAFSNMRS---RGAHCTDIVVLVVAADDGVMEQTVESIRMARE-----------A 214
DT G F ++ RGA C VLV D ++ ES+ R+
Sbjct: 55 DTAGQERFQSLGVAFYRGADC---CVLVY---DVTNPKSFESLDSWRDEFLIQASPRDPE 108
Query: 215 KVPIIVAINKIDKPAADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIE 274
P +V NKID + +R + AQ G+I SA NVD E I
Sbjct: 109 NFPFVVLGNKIDL---EEKRQVSTKKAQQWCKSK--GNIPYFETSAKEAINVDQAFETIA 163
Query: 275 R 275
R
Sbjct: 164 R 164
>gnl|CDD|204242 pfam09439, SRPRB, Signal recognition particle receptor beta
subunit. The beta subunit of the signal recognition
particle receptor (SRP) is a transmembrane GTPase which
anchors the alpha subunit to the endoplasmic reticulum
membrane.
Length = 181
Score = 33.9 bits (78), Expect = 0.15
Identities = 30/137 (21%), Positives = 48/137 (35%), Gaps = 21/137 (15%)
Query: 113 KRPPVVTIMGHVDHGKTTLLDTLRNTSVVKSEFGGITQHIGAFV--VTLKSGEQVTFLDT 170
P V I G D GKT+L L +V K+ +T + L G T +D
Sbjct: 1 SSQPAVIIAGLCDSGKTSLFTLLTTGTVKKT----VTSQEPSAAYKYMLHKGFSFTLIDF 56
Query: 171 PGHAAF-SNMRSRGAHCTDIVVLVVAADDGVMEQ----------TVESIRMAREAKVPII 219
PGH + + + +V D + + SI + + I+
Sbjct: 57 PGHVKLRQKLLETIKDSSSLRGIVFVVDSTAFPKEVTDTAEFLYEILSITELLKNGIDIL 116
Query: 220 VAINKID----KPAADI 232
+A NK + +P I
Sbjct: 117 IACNKQESFTARPPKKI 133
>gnl|CDD|224617 COG1703, ArgK, Putative periplasmic protein kinase ArgK and related
GTPases of G3E family [Amino acid transport and
metabolism].
Length = 323
Score = 34.6 bits (80), Expect = 0.15
Identities = 30/115 (26%), Positives = 45/115 (39%), Gaps = 28/115 (24%)
Query: 184 AHCTDIVVLVVAA---DD------GVMEQTVESIRMAREAKVPIIVAINKIDKPAADIER 234
A+ D ++V+ DD G+ME +A I+ INK D+ A E+
Sbjct: 162 ANMADTFLVVMIPGAGDDLQGIKAGIME-------IAD------IIVINKADRKGA--EK 206
Query: 235 TKNMLLAQ----GITVEDLGGDIQAVPISALTGTNVDNLTEAIERTKNMLLAQGI 285
L + + G V SAL G +D L +AIE + L G+
Sbjct: 207 AARELRSALDLLREVWRENGWRPPVVTTSALEGEGIDELWDAIEDHRKFLTESGL 261
>gnl|CDD|213833 TIGR03596, GTPase_YlqF, ribosome biogenesis GTP-binding protein
YlqF. Members of this protein family are GTP-binding
proteins involved in ribosome biogenesis, including the
essential YlqF protein of Bacillus subtilis, which is an
essential protein. They are related to Era, EngA, and
other GTPases of ribosome biogenesis, but are circularly
permuted. This family is not universal, and is not
present in Escherichia coli, and so is not as well
studied as some other GTPases. This model is built for
bacterial members [Protein synthesis, Other].
Length = 276
Score = 34.4 bits (80), Expect = 0.16
Identities = 27/106 (25%), Positives = 46/106 (43%), Gaps = 17/106 (16%)
Query: 70 VIIDIIQKSGMKYMVINPTNSVADDSNGKDVERRPPADPSVLMKRPPVVTIMGHVDHGKT 129
+ I+ + G+K +I + + N K + L+ RP I+G + GK+
Sbjct: 81 LAINAKKGKGVK-KIIKAAKKLLKEKNEKLKAKG-------LLNRPIRAMIVGIPNVGKS 132
Query: 130 TLLDTLRNTSVVKSEFG---GITQHIGAFVVTLKSGEQVTFLDTPG 172
TL++ L V K G G+T+ +K + + LDTPG
Sbjct: 133 TLINRLAGKKVAKV--GNRPGVTKGQQ----WIKLSDGLELLDTPG 172
>gnl|CDD|197556 smart00178, SAR, Sar1p-like members of the Ras-family of small
GTPases. Yeast SAR1 is an essential gene required for
transport of secretory proteins from the endoplasmic
reticulum to the Golgi apparatus.
Length = 184
Score = 33.8 bits (77), Expect = 0.17
Identities = 35/112 (31%), Positives = 49/112 (43%), Gaps = 15/112 (13%)
Query: 127 GKTTLLDTLRNTSVVKSEFGGITQHIGAFVVTLKSGEQVTFLDTPGHAAFSNM-RSRGAH 185
GKTTLL L+N + + + TQH + + + + + TF D GH + +
Sbjct: 29 GKTTLLHMLKNDRLAQHQ---PTQHPTSEELAIGNIKFTTF-DLGGHQQARRLWKDYFPE 84
Query: 186 CTDIVVLVVAADDGVMEQTVESIR-------MAREAKVPIIVAINKIDKPAA 230
IV LV A D E+ ES R A VP ++ NKID P A
Sbjct: 85 VNGIVYLVDAYD---KERFAESKRELDALLSDEELATVPFLILGNKIDAPYA 133
>gnl|CDD|206710 cd04139, RalA_RalB, Ral (Ras-like) family containing highly
homologous RalA and RalB. The Ral (Ras-like) subfamily
consists of the highly homologous RalA and RalB. Ral
proteins are believed to play a crucial role in
tumorigenesis, metastasis, endocytosis, and actin
cytoskeleton dynamics. Despite their high sequence
similarity (>80% sequence identity), nonoverlapping and
opposing functions have been assigned to RalA and RalBs
in tumor migration. In human bladder and prostate cancer
cells, RalB promotes migration while RalA inhibits it. A
Ral-specific set of GEFs has been identified that are
activated by Ras binding. This RalGEF activity is
enhanced by Ras binding to another of its target
proteins, phosphatidylinositol 3-kinase (PI3K). Ral
effectors include RLIP76/RalBP1, a Rac/cdc42 GAP, and
the exocyst (Sec6/8) complex, a heterooctomeric protein
complex that is involved in tethering vesicles to
specific sites on the plasma membrane prior to
exocytosis. In rat kidney cells, RalB is required for
functional assembly of the exocyst and for localizing
the exocyst to the leading edge of migrating cells. In
human cancer cells, RalA is required to support
anchorage-independent proliferation and RalB is required
to suppress apoptosis. RalA has been shown to localize
to the plasma membrane while RalB is localized to the
intracellular vesicles. Most Ras proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of most
Ras proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 163
Score = 33.2 bits (76), Expect = 0.19
Identities = 27/118 (22%), Positives = 47/118 (39%), Gaps = 12/118 (10%)
Query: 156 VVTLKSGE-QVTFLDTPGHAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESI-----R 209
V L E Q+ LDT G ++ +R + +LV + D + R
Sbjct: 40 KVVLDGEEVQLNILDTAGQEDYAAIRDNYFRSGEGFLLVFSITDMESFTALAEFREQILR 99
Query: 210 MAREAKVPIIVAINKIDKPAADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVD 267
+ + VP+++ NK D + +R ++ A + + + V SA T NVD
Sbjct: 100 VKEDDNVPLLLVGNKCD---LEDKRQVSVEEAANLAEQ---WGVNYVETSAKTRANVD 151
>gnl|CDD|224009 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 33.8 bits (78), Expect = 0.23
Identities = 47/197 (23%), Positives = 86/197 (43%), Gaps = 35/197 (17%)
Query: 98 KDVERRPPA-DPSVLMKRPPVVTIMGHVDHGKTTLLDTLRNTSVVKSEFGGITQ--HIGA 154
+D ++ PA DP + P + + G+ + GK++L+ L + + T+ H+G
Sbjct: 155 RDHLKKLPAIDPDL-----PTIVVAGYPNVGKSSLVRKLTTAKPEVAPYPFTTKGIHVGH 209
Query: 155 FVVTLKSGEQVTFLDTPG--HAAFSNM-----RSRGA--HCTDIVVLVVAADD----GVM 201
F + ++ +DTPG ++ A H +++ + + +
Sbjct: 210 FE---RGYLRIQVIDTPGLLDRPLEERNEIERQAILALRHLAGVILFLFDPSETCGYSLE 266
Query: 202 EQT--VESIRMAREAKVPIIVAINKIDKPAADIERTKNMLLAQGITVEDLGGDIQAVPIS 259
EQ +E I+ K PI+V INKID AD E+ + + + E G + + IS
Sbjct: 267 EQISLLEEIK--ELFKAPIVVVINKID--IADEEKLEE--IEASVLEE---GGEEPLKIS 317
Query: 260 ALTGTNVDNLTEAIERT 276
A G +D L E + +T
Sbjct: 318 ATKGCGLDKLREEVRKT 334
>gnl|CDD|133356 cd04156, ARLTS1, Arf-like tumor suppressor gene 1 (ARLTS1 or
Arl11). ARLTS1 (Arf-like tumor suppressor gene 1), also
known as Arl11, is a member of the Arf family of small
GTPases that is believed to play a major role in
apoptotic signaling. ARLTS1 is widely expressed and
functions as a tumor suppressor gene in several human
cancers. ARLTS1 is a low-penetrance suppressor that
accounts for a small percentage of familial melanoma or
familial chronic lymphocytic leukemia (CLL). ARLTS1
inactivation seems to occur most frequently through
biallelic down-regulation by hypermethylation of the
promoter. In breast cancer, ARLTS1 alterations were
typically a combination of a hypomorphic polymorphism
plus loss of heterozygosity. In a case of thyroid
adenoma, ARLTS1 alterations were polymorphism plus
promoter hypermethylation. The nonsense polymorphism
Trp149Stop occurs with significantly greater frequency
in familial cancer cases than in sporadic cancer cases,
and the Cys148Arg polymorphism is associated with an
increase in high-risk familial breast cancer.
Length = 160
Score = 32.8 bits (75), Expect = 0.26
Identities = 39/170 (22%), Positives = 62/170 (36%), Gaps = 40/170 (23%)
Query: 118 VTIMGHVDHGKTTLLDTLRNTSVVKSEFGGITQHIGAFVVTLKS-GEQVTFLDTPGHAAF 176
V ++G GK+TLL L++ V T+ + G V L H +
Sbjct: 2 VLLLGLDSAGKSTLLYKLKH---------------AELVTTIPTVGFNVEMLQLEKHLSL 46
Query: 177 S--------NMRSR-GAHC--TDIVVLVVAADDGVMEQTVESIRMARE-------AKVPI 218
+ MR+ + TD +V VV + D + ES + + VP+
Sbjct: 47 TVWDVGGQEKMRTVWKCYLENTDGLVYVVDSSDE--ARLDESQKELKHILKNEHIKGVPV 104
Query: 219 IVAINKIDKPAA-DIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVD 267
++ NK D P A E + D +Q P SA+TG +
Sbjct: 105 VLLANKQDLPGALTAEEITRRFKLKKYC-SDRDWYVQ--PCSAVTGEGLA 151
>gnl|CDD|224085 COG1163, DRG, Predicted GTPase [General function prediction only].
Length = 365
Score = 33.4 bits (77), Expect = 0.34
Identities = 30/130 (23%), Positives = 51/130 (39%), Gaps = 36/130 (27%)
Query: 179 MRSRGAHCTDIVVLVVAADDGVMEQTVESIRMAREAKVPIIVAINKIDKPAADIERTKNM 238
+R H D+++ +D ++ ++++ P + +NKID P +
Sbjct: 208 LREYRIHNADVLI----REDVTLDDLIDAL-EGNRVYKPALYVVNKIDLPGLE------- 255
Query: 239 LLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIER--------TKN----------ML 280
+E L +VPISA G N+D L E I TK ++
Sbjct: 256 ------ELERLARKPNSVPISAKKGINLDELKERIWDVLGLIRVYTKPPGEEPDFDEPLI 309
Query: 281 LAQGITVEDL 290
L +G TV D+
Sbjct: 310 LRRGSTVGDV 319
>gnl|CDD|179790 PRK04213, PRK04213, GTP-binding protein; Provisional.
Length = 201
Score = 33.0 bits (76), Expect = 0.35
Identities = 24/72 (33%), Positives = 34/72 (47%), Gaps = 17/72 (23%)
Query: 212 REAKVPIIVAINKIDKPAADIERTKNMLLAQGITVEDLG--------GDIQAVPISALTG 263
RE +P IVA+NK+DK + + + + E LG DI PISA G
Sbjct: 127 RELGIPPIVAVNKMDK-IKNRDEVLDEI------AERLGLYPPWRQWQDI-IAPISAKKG 178
Query: 264 TNVDNLTEAIER 275
++ L EAI +
Sbjct: 179 -GIEELKEAIRK 189
>gnl|CDD|217730 pfam03792, PBC, PBC domain. The PBC domain is a member of the TALE
(three-amino-acid loop extension) superclass of
homeodomain proteins.
Length = 192
Score = 32.9 bits (75), Expect = 0.36
Identities = 17/66 (25%), Positives = 25/66 (37%), Gaps = 11/66 (16%)
Query: 202 EQTVESIRMAREAKVPIIVAINKIDKPAADIERTKNMLLAQGITVEDLGGDIQAVPISAL 261
E+T S R E D P + R NMLLA+G+ D G + A
Sbjct: 52 EKTALSTRNMPED-----------DPPDPQLLRLDNMLLAEGVAGPDKSGLLAAAAAGTG 100
Query: 262 TGTNVD 267
+++
Sbjct: 101 PDNSIE 106
>gnl|CDD|237498 PRK13768, PRK13768, GTPase; Provisional.
Length = 253
Score = 32.9 bits (76), Expect = 0.43
Identities = 22/101 (21%), Positives = 38/101 (37%), Gaps = 29/101 (28%)
Query: 215 KVPIIVAINKIDK-PAADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAI 273
+P I +NK D ++ER L + + L E +
Sbjct: 162 GLPQIPVLNKADLLSEEELERILKWL------------------------EDPEYLLEEL 197
Query: 274 --ERTKNMLLAQGI--TVEDLGGDIQAVPISALTGTNVDNL 310
E+ LL+ + +E+ G ++ +P+SA TG D L
Sbjct: 198 KLEKGLQGLLSLELLRALEETGLPVRVIPVSAKTGEGFDEL 238
>gnl|CDD|206725 cd04160, Arfrp1, Arf-related protein 1 (Arfrp1). Arfrp1
(Arf-related protein 1), formerly known as ARP, is a
membrane-associated Arf family member that lacks the
N-terminal myristoylation motif. Arfrp1 is mainly
associated with the trans-Golgi compartment and the
trans-Golgi network, where it regulates the targeting of
Arl1 and the GRIP domain-containing proteins, golgin-97
and golgin-245, onto Golgi membranes. It is also
involved in the anterograde transport of the vesicular
stomatitis virus G protein from the Golgi to the plasma
membrane, and in the retrograde transport of TGN38 and
Shiga toxin from endosomes to the trans-Golgi network.
Arfrp1 also inhibits Arf/Sec7-dependent activation of
phospholipase D. Deletion of Arfrp1 in mice causes
embryonic lethality at the gastrulation stage and
apoptosis of mesodermal cells, indicating its importance
in development.
Length = 168
Score = 32.3 bits (74), Expect = 0.44
Identities = 39/170 (22%), Positives = 68/170 (40%), Gaps = 21/170 (12%)
Query: 118 VTIMGHVDHGKTTLLDTLRNTSVVKSEF---GGITQHIGAFVVTLKSGEQ-VTFLDTPGH 173
V I+G + GKTT L+ + + IT +G + T++ G+ + F D G
Sbjct: 2 VLILGLDNAGKTTFLEQTKTKFSKNYKGLNPSKITPTVGLNIGTIEVGKARLMFWDLGGQ 61
Query: 174 AAFSNMRSR-GAHCTDIVVLVVAADDGVMEQTVES----IRMAREAKVPIIVAINKIDKP 228
++ + A ++ ++ + D ++ + I VP++V NK D P
Sbjct: 62 EELRSLWDKYYAESHGVIYVIDSTDRERFNESKSAFEKVINNEALEGVPLLVLANKQDLP 121
Query: 229 ----AADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIE 274
A+I+ + I D P+SAL G V+ E IE
Sbjct: 122 DALSVAEIKEVFD-DCIALIGRRDC----LVQPVSALEGEGVE---EGIE 163
>gnl|CDD|165621 PLN00043, PLN00043, elongation factor 1-alpha; Provisional.
Length = 447
Score = 33.1 bits (75), Expect = 0.46
Identities = 31/132 (23%), Positives = 53/132 (40%), Gaps = 13/132 (9%)
Query: 166 TFLDTPGHAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMAREAKV--------P 217
T +D PGH F G D VL++ + G E + RE +
Sbjct: 88 TVIDAPGHRDFIKNMITGTSQADCAVLIIDSTTGGFEAGISKDGQTREHALLAFTLGVKQ 147
Query: 218 IIVAINKID--KPAADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIER 275
+I NK+D P R ++ ++ +G + +P ++G DN+ IER
Sbjct: 148 MICCCNKMDATTPKYSKARYDEIVKEVSSYLKKVGYNPDKIPFVPISGFEGDNM---IER 204
Query: 276 TKNMLLAQGITV 287
+ N+ +G T+
Sbjct: 205 STNLDWYKGPTL 216
>gnl|CDD|133377 cd04177, RSR1, RSR1/Bud1p family GTPase. RSR1/Bud1p is a member of
the Rap subfamily of the Ras family that is found in
fungi. In budding yeasts, RSR1 is involved in selecting
a site for bud growth on the cell cortex, which directs
the establishment of cell polarization. The Rho family
GTPase cdc42 and its GEF, cdc24, then establish an axis
of polarized growth by organizing the actin cytoskeleton
and secretory apparatus at the bud site. It is believed
that cdc42 interacts directly with RSR1 in vivo. In
filamentous fungi, polar growth occurs at the tips of
hypha and at novel growth sites along the extending
hypha. In Ashbya gossypii, RSR1 is a key regulator of
hyphal growth, localizing at the tip region and
regulating in apical polarization of the actin
cytoskeleton. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras proteins.
Length = 168
Score = 32.1 bits (73), Expect = 0.52
Identities = 29/116 (25%), Positives = 46/116 (39%), Gaps = 18/116 (15%)
Query: 162 GEQVTF--LDTPGHAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMAREA----- 214
G Q LDT G F+ MR +LV + E ++ + RE
Sbjct: 46 GRQCDLEILDTAGTEQFTAMRELYIKSGQGFLLVYSVTS---EASLNELGELREQVLRIK 102
Query: 215 ---KVPIIVAINKIDKPAADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVD 267
VP+++ NK AD+E + + G+++ G++ SA TNVD
Sbjct: 103 DSDNVPMVLVGNK-----ADLEDDRQVSREDGVSLSQQWGNVPFYETSARKRTNVD 153
>gnl|CDD|206722 cd04157, Arl6, Arf-like 6 (Arl6) GTPase. Arl6 (Arf-like 6) forms a
subfamily of the Arf family of small GTPases. Arl6
expression is limited to the brain and kidney in adult
mice, but it is expressed in the neural plate and
somites during embryogenesis, suggesting a possible role
for Arl6 in early development. Arl6 is also believed to
have a role in cilia or flagella function. Several
proteins have been identified that bind Arl6, including
Arl6 interacting protein (Arl6ip), and SEC61beta, a
subunit of the heterotrimeric conducting channel SEC61p.
Based on Arl6 binding to these effectors, Arl6 is also
proposed to play a role in protein transport, membrane
trafficking, or cell signaling during hematopoietic
maturation. At least three specific homozygous Arl6
mutations in humans have been found to cause
Bardet-Biedl syndrome, a disorder characterized by
obesity, retinopathy, polydactyly, renal and cardiac
malformations, learning disabilities, and
hypogenitalism. Older literature suggests that Arl6 is a
part of the Arl4/Arl7 subfamily, but analyses based on
more recent sequence data place Arl6 in its own
subfamily.
Length = 162
Score = 32.0 bits (73), Expect = 0.55
Identities = 24/125 (19%), Positives = 50/125 (40%), Gaps = 19/125 (15%)
Query: 118 VTIMGHVDHGKTTLLDTLRNTSVVKSEFGGITQHIGA---FVVTL--KSGEQVTFLDTPG 172
+ ++G + GKTT+++ L+ ++ +Q+I F V K T D G
Sbjct: 2 ILVLGLDNSGKTTIINQLKPSNAQ-------SQNIVPTVGFNVESFKKGNLSFTAFDMSG 54
Query: 173 HAAFSNMRSRGAHCTDIVVLVVAADDGV-MEQTVESIRMARE------AKVPIIVAINKI 225
+ + ++ V+ + D + M + + + ++PI+ NK+
Sbjct: 55 QGKYRGLWEHYYKNIQGIIFVIDSSDRLRMVVAKDELELLLNHPDIKHRRIPILFYANKM 114
Query: 226 DKPAA 230
D P A
Sbjct: 115 DLPDA 119
>gnl|CDD|215692 pfam00071, Ras, Ras family. Includes sub-families Ras, Rab, Rac,
Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with
GTP_EFTU, arf and myosin_head. See pfam00009 pfam00025,
pfam00063. As regards Rab GTPases, these are important
regulators of vesicle formation, motility and fusion.
They share a fold in common with all Ras GTPases: this
is a six-stranded beta-sheet surrounded by five
alpha-helices.
Length = 162
Score = 31.7 bits (73), Expect = 0.64
Identities = 39/169 (23%), Positives = 68/169 (40%), Gaps = 39/169 (23%)
Query: 127 GKTTLLDTLRNTSVVKSEFGGITQH---IGA--FVVTLK-SGEQVTF--LDTPGHAAFSN 178
GK++LL +++F ++ IG + T++ G+ V DT G F
Sbjct: 11 GKSSLL-----IRFTQNKF--PEEYIPTIGVDFYTKTIEVDGKTVKLQIWDTAGQERFRA 63
Query: 179 MRS---RGAHCTDIVVLVVAADDGVMEQT-------VESIRMAREAKVPIIVAINKIDKP 228
+R RGA +LV + +E I + VPI++ NK
Sbjct: 64 LRPLYYRGAQG---FLLVYDITS---RDSFENVKKWLEEILRHADENVPIVLVGNK---- 113
Query: 229 AADIERTKNMLLAQGITV-EDLGGDIQAVPISALTGTNVDNLTEAIERT 276
D+E + + +G + ++LG + + SA T NV+ E + R
Sbjct: 114 -CDLEDQRVVSTEEGEALAKELG--LPFMETSAKTNENVEEAFEELARE 159
>gnl|CDD|206752 cd01859, MJ1464, An uncharacterized, circularly permuted subfamily
of the Ras GTPases. This family represents archaeal
GTPase typified by the protein MJ1464 from Methanococcus
jannaschii. The members of this family show a circular
permutation of the GTPase signature motifs so that
C-terminal strands 5, 6, and 7 (strands 6 contain the
NKxD motif) are relocated to the N terminus.
Length = 157
Score = 31.5 bits (72), Expect = 0.72
Identities = 19/60 (31%), Positives = 34/60 (56%), Gaps = 1/60 (1%)
Query: 188 DIVVLVVAADDGVMEQTVESIRMAREAKVPIIVAINKID-KPAADIERTKNMLLAQGITV 246
D+V+ VV A D + ++ + RMA E +I+ +NK D P +E+ K + ++G+ V
Sbjct: 13 DVVLEVVDARDPELTRSRKLERMALELGKKLIIVLNKADLVPREVLEKWKEVFESEGLPV 72
>gnl|CDD|221914 pfam13088, BNR_2, BNR repeat-like domain. This family of proteins
contains BNR-like repeats suggesting these proteins may
act as sialidases.
Length = 279
Score = 32.3 bits (74), Expect = 0.80
Identities = 15/55 (27%), Positives = 21/55 (38%), Gaps = 4/55 (7%)
Query: 146 GGITQHIGAFVVTLKSGE-QVTFLDTPGHAAFSNMRSRGAHCTDIVVLVVAADDG 199
GG T G GE Q + L P + RSR A ++ ++D G
Sbjct: 144 GGKTWTKGRPPNAGTGGEIQPSILPLPDGRLLALFRSRNAGR---ILRSESSDGG 195
>gnl|CDD|236570 PRK09563, rbgA, GTPase YlqF; Reviewed.
Length = 287
Score = 32.1 bits (74), Expect = 0.82
Identities = 24/107 (22%), Positives = 45/107 (42%), Gaps = 19/107 (17%)
Query: 70 VIIDIIQKSGMKYMVINPTNSVADDSNGKDVERRPPADPSVLMKRPPVVTIMGHVDHGKT 129
+ I+ + G+K ++ + + N + + + R I+G + GK+
Sbjct: 84 LAINAKKGQGVK-KILKAAKKLLKEKNERRKAK-------GMRPRAIRAMIIGIPNVGKS 135
Query: 130 TLLDTLRNTSVVKSE-FGGIT---QHIGAFVVTLKSGEQVTFLDTPG 172
TL++ L + K+ G+T Q I K G+ + LDTPG
Sbjct: 136 TLINRLAGKKIAKTGNRPGVTKAQQWI-------KLGKGLELLDTPG 175
>gnl|CDD|133361 cd04161, Arl2l1_Arl13_like, Arl2-like protein 1 (Arl2l1) and Arl13.
Arl2l1 (Arl2-like protein 1) and Arl13 form a subfamily
of the Arf family of small GTPases. Arl2l1 was
identified in human cells during a search for the
gene(s) responsible for Bardet-Biedl syndrome (BBS).
Like Arl6, the identified BBS gene, Arl2l1 is proposed
to have cilia-specific functions. Arl13 is found on the
X chromosome, but its expression has not been confirmed;
it may be a pseudogene.
Length = 167
Score = 31.2 bits (71), Expect = 0.84
Identities = 32/116 (27%), Positives = 50/116 (43%), Gaps = 23/116 (19%)
Query: 127 GKTTLLDTLRNTSVVKSEFGGITQHIGAFV-VTLKSGE-QVTFLDTPGHAAFSNMRSRG- 183
GKTTL+ S ++ E F L+ + +V D G A F RG
Sbjct: 11 GKTTLV------SALQGEIPKKVAPTVGFTPTKLRLDKYEVCIFDLGGGANF-----RGI 59
Query: 184 -----AHCTDIVVLVVAADDGVMEQTVESIR-MAREAKV---PIIVAINKIDKPAA 230
A +V +V ++DD +++ E +R + + +V PI+V NK DK A
Sbjct: 60 WVNYYAEAHGLVFVVDSSDDDRVQEVKEILRELLQHPRVSGKPILVLANKQDKKNA 115
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 32.1 bits (74), Expect = 0.88
Identities = 18/57 (31%), Positives = 25/57 (43%), Gaps = 5/57 (8%)
Query: 217 PIIVAINKIDKPAADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAI 273
P + NKID + E + A+ I VE LG + ISA +G V L +
Sbjct: 277 PRWLVFNKIDLLDEE-EAEE---RAKAI-VEALGWEGPVYLISAASGLGVKELCWDL 328
>gnl|CDD|173885 cd08520, PBP2_NikA_DppA_OppA_like_21, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
represents the substrate-binding domain of an
uncharacterized ATP-binding cassette (ABC) type
nickel/dipeptide/oligopeptide-like transporter. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA, the initial nickel receptor. The
DppA binds dipeptides and some tripeptides and is
involved in chemotaxis toward dipeptides, whereas the
OppA binds peptides of a wide range of lengths (2-35
amino acid residues) and plays a role in recycling of
cell wall peptides, which precludes any involvement in
chemotaxis. Most of other periplasmic binding proteins
are comprised of only two globular subdomains
corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 468
Score = 32.3 bits (74), Expect = 0.95
Identities = 19/62 (30%), Positives = 26/62 (41%), Gaps = 3/62 (4%)
Query: 229 AADIERTKNMLLAQGITVEDLGGDIQAVPISA--LTGTNVDNLTEAIERTKNMLLAQGIT 286
D E+ K +L G T G+ P+S LT ++ D + A E K L GI
Sbjct: 301 PYDPEKAKELLKGLGYTDNGGDGEKDGEPLSLELLTSSSGDEVRVA-ELIKEQLERVGIK 359
Query: 287 VE 288
V
Sbjct: 360 VN 361
>gnl|CDD|236018 PRK07431, PRK07431, aspartate kinase; Provisional.
Length = 587
Score = 32.2 bits (74), Expect = 1.0
Identities = 34/111 (30%), Positives = 53/111 (47%), Gaps = 19/111 (17%)
Query: 230 ADIERTKNMLLAQGI--TVEDLGGDIQAVPISALTGTNVDNLTE-AIERTKN-------M 279
+ER + +AQ I T E G D+ V +SA+ G D L + A E + N M
Sbjct: 14 GSVERIQA--VAQRIARTKEA-GNDVVVV-VSAM-GKTTDELVKLAKEISSNPPRREMDM 68
Query: 280 LLAQG--ITVEDLGGDIQAVPISA--LTGTNVDNLTEAIVAQAEIMHLKAD 326
LL+ G +++ L + + A LTG V +TE+ +A I+ +K D
Sbjct: 69 LLSTGEQVSIALLSMALHELGQPAISLTGAQVGIVTESEHGRARILEIKTD 119
>gnl|CDD|192832 pfam11789, zf-Nse, Zinc-finger of the MIZ type in Nse subunit.
Nse1 and Nse2 are novel non-SMC subunits of the fission
yeast Smc5-6 DNA repair complex. This family is the
zinc-finger domain similar to the MIZ type of
zinc-finger.
Length = 57
Score = 28.8 bits (65), Expect = 1.1
Identities = 9/37 (24%), Positives = 14/37 (37%), Gaps = 6/37 (16%)
Query: 555 INAMLPHTYAEEVLGEANVLQMFLITDGKKKVPVAGC 591
+ H + E + + L + K PVAGC
Sbjct: 26 TSKKCNHVF------EKDAILSMLRRNKTVKCPVAGC 56
>gnl|CDD|206683 cd01896, DRG, Developmentally Regulated GTP-binding protein (DRG).
The developmentally regulated GTP-binding protein (DRG)
subfamily is an uncharacterized member of the Obg
family, an evolutionary branch of GTPase superfamily
proteins. GTPases act as molecular switches regulating
diverse cellular processes. DRG2 and DRG1 comprise the
DRG subfamily in eukaryotes. In view of their widespread
expression in various tissues and high conservation
among distantly related species in eukaryotes and
archaea, DRG proteins may regulate fundamental cellular
processes. It is proposed that the DRG subfamily
proteins play their physiological roles through RNA
binding.
Length = 233
Score = 31.4 bits (72), Expect = 1.3
Identities = 17/58 (29%), Positives = 23/58 (39%), Gaps = 13/58 (22%)
Query: 216 VPIIVAINKIDKPAADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAI 273
+P + NKID IE ++ L +V ISA N+D L E I
Sbjct: 177 IPCLYVYNKID--LISIEE-----------LDRLARIPNSVVISAEKDLNLDELLERI 221
>gnl|CDD|234988 PRK01889, PRK01889, GTPase RsgA; Reviewed.
Length = 356
Score = 31.4 bits (72), Expect = 1.4
Identities = 29/111 (26%), Positives = 45/111 (40%), Gaps = 29/111 (26%)
Query: 188 DIVVLVVAADD----GVMEQTVESIRMAREAKV-PIIVAINKIDKPAADIERTKNML--L 240
D V +V + + +E+ + +A E+ P+IV + K D D E + L
Sbjct: 114 DTVFIVCSLNHDFNLRRIERY---LALAWESGAEPVIV-LTKADL-CEDAEEKIAEVEAL 168
Query: 241 AQGITVEDLGGDIQAVPISALTGTNVDNLTEAIERTKNMLLAQGITVEDLG 291
A G+ V + +SAL G +D L L+ G TV LG
Sbjct: 169 APGVPV---------LAVSALDGEGLDVLA--------AWLSGGKTVALLG 202
>gnl|CDD|213834 TIGR03597, GTPase_YqeH, ribosome biogenesis GTPase YqeH. This
family describes YqeH, a member of a larger family of
GTPases involved in ribosome biogenesis. Like YqlF, it
shows a cyclical permutation relative to GTPases EngA
(in which the GTPase domain is duplicated), Era, and
others. Members of this protein family are found in a
relatively small number of bacterial species, including
Bacillus subtilis but not Escherichia coli [Protein
synthesis, Other].
Length = 360
Score = 31.1 bits (71), Expect = 1.7
Identities = 16/68 (23%), Positives = 29/68 (42%), Gaps = 12/68 (17%)
Query: 217 PIIVAINKID------KPAADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLT 270
P+++ NKID + E K G+ D+ + +SA G +D L
Sbjct: 92 PVLLVGNKIDLLPKSVNLSKIKEWMKKRAKELGLKPVDI------ILVSAKKGNGIDELL 145
Query: 271 EAIERTKN 278
+ I++ +N
Sbjct: 146 DKIKKARN 153
>gnl|CDD|224083 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 30.8 bits (70), Expect = 2.0
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 5/47 (10%)
Query: 127 GKTTLLDTLRNTSVVK-SEFGGITQHIGAFVVTLKSGEQVTFLDTPG 172
GK+TL++ L V K S G T+ I +K + + LDTPG
Sbjct: 144 GKSTLINRLLGKKVAKTSNRPGTTKGI----QWIKLDDGIYLLDTPG 186
>gnl|CDD|217388 pfam03144, GTP_EFTU_D2, Elongation factor Tu domain 2. Elongation
factor Tu consists of three structural domains, this is
the second domain. This domain adopts a beta barrel
structure. This the second domain is involved in binding
to charged tRNA. This domain is also found in other
proteins such as elongation factor G and translation
initiation factor IF-2. This domain is structurally
related to pfam03143, and in fact has weak sequence
matches to this domain.
Length = 70
Score = 28.4 bits (64), Expect = 2.0
Identities = 15/37 (40%), Positives = 19/37 (51%), Gaps = 4/37 (10%)
Query: 345 GKLATALVQRGTLKKGAIVVAG----QAWAKVRSISR 377
G +AT V+ GTLKKG VV G +V S+
Sbjct: 1 GTVATGRVESGTLKKGDKVVIGPNGTGKKGRVTSLEM 37
>gnl|CDD|133376 cd04176, Rap2, Rap2 family GTPase consists of Rap2a, Rap2b, and
Rap2c. The Rap2 subgroup is part of the Rap subfamily
of the Ras family. It consists of Rap2a, Rap2b, and
Rap2c. Both isoform 3 of the human mitogen-activated
protein kinase kinase kinase kinase 4 (MAP4K4) and
Traf2- and Nck-interacting kinase (TNIK) are putative
effectors of Rap2 in mediating the activation of c-Jun
N-terminal kinase (JNK) to regulate the actin
cytoskeleton. In human platelets, Rap2 was shown to
interact with the cytoskeleton by binding the actin
filaments. In embryonic Xenopus development, Rap2 is
necessary for the Wnt/beta-catenin signaling pathway.
The Rap2 interacting protein 9 (RPIP9) is highly
expressed in human breast carcinomas and correlates with
a poor prognosis, suggesting a role for Rap2 in breast
cancer oncogenesis. Rap2b, but not Rap2a, Rap2c, Rap1a,
or Rap1b, is expressed in human red blood cells, where
it is believed to be involved in vesiculation. A number
of additional effector proteins for Rap2 have been
identified, including the RalGEFs RalGDS, RGL, and Rlf,
which also interact with Rap1 and Ras. Most Ras proteins
contain a lipid modification site at the C-terminus,
with a typical sequence motif CaaX, where a = an
aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Ras proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 163
Score = 30.2 bits (68), Expect = 2.1
Identities = 33/122 (27%), Positives = 52/122 (42%), Gaps = 23/122 (18%)
Query: 168 LDTPGHAAFSNMRS---RGAHCTDIVVLVVAADDGVMEQTVESIRMAREA--------KV 216
LDT G F++MR + +V +V +QT + I+ R+ KV
Sbjct: 54 LDTAGTEQFASMRDLYIKNGQGFIVVYSLVN------QQTFQDIKPMRDQIVRVKGYEKV 107
Query: 217 PIIVAINKIDKPAADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIERT 276
PII+ NK D+E + + A+G + + G + SA + T V+ L I R
Sbjct: 108 PIILVGNK-----VDLESEREVSSAEGRALAEEWG-CPFMETSAKSKTMVNELFAEIVRQ 161
Query: 277 KN 278
N
Sbjct: 162 MN 163
>gnl|CDD|227519 COG5192, BMS1, GTP-binding protein required for 40S ribosome
biogenesis [Translation, ribosomal structure and
biogenesis].
Length = 1077
Score = 31.2 bits (70), Expect = 2.1
Identities = 32/129 (24%), Positives = 60/129 (46%), Gaps = 24/129 (18%)
Query: 100 VERRPPADPSVLMKRPP-VVTIMGHVDHGKTTLLDTL--RNTSVVKSEFGGITQHIGAFV 156
V+R P P PP +V ++G GK+TL+ +L R T E G
Sbjct: 59 VDRTPKDLP------PPFIVAVVGPPGTGKSTLIRSLVRRFTKQTIDEIRG--------P 104
Query: 157 VTLKSGE--QVTFLDTPGH-AAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESIRMARE 213
+T+ SG+ ++TFL+ P ++ A D+V+L++ + G +T+E + +
Sbjct: 105 ITVVSGKTRRITFLECPSDLHQMIDV----AKIADLVLLLIDGNFGFEMETMEFLNILIS 160
Query: 214 AKVPIIVAI 222
+P ++ +
Sbjct: 161 HGMPRVLGV 169
>gnl|CDD|236078 PRK07726, PRK07726, DNA topoisomerase III; Provisional.
Length = 658
Score = 31.3 bits (72), Expect = 2.2
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 537 TVKQFNVIYKLVEDVKEEINA 557
T KQFNV+ KL++ E + A
Sbjct: 79 TAKQFNVVKKLLKQATEIVIA 99
>gnl|CDD|99800 cd06203, methionine_synthase_red, Human methionine synthase
reductase (MSR) restores methionine sythase which is
responsible for the regeneration of methionine from
homocysteine, as well as the coversion of
methyltetrahydrofolate to tetrahydrofolate. In MSR,
electrons are transferred from NADPH to FAD to FMN to
cob(II)alamin. MSR resembles proteins of the cytochrome
p450 family including nitric oxide synthase, the alpha
subunit of sulfite reductase, but contains an extended
hinge region. NADPH cytochrome p450 reductase (CYPOR)
serves as an electron donor in several oxygenase systems
and is a component of nitric oxide synthases and
methionine synthase reductases. CYPOR transfers two
electrons from NADPH to the heme of cytochrome p450 via
FAD and FMN. CYPORs resemble ferredoxin reductase (FNR)
but have a connecting subdomain inserted within the
flavin binding region, which helps orient the FMN
binding doamin with the FNR module. Ferredoxin-NADP+
(oxido)reductase is an FAD-containing enzyme that
catalyzes the reversible electron transfer between
NADP(H) and electron carrier proteins such as ferredoxin
and flavodoxin. Isoforms of these flavoproteins (i.e.
having a non-covalently bound FAD as a prosthetic group)
are present in chloroplasts, mitochondria, and bacteria
in which they participate in a wide variety of redox
metabolic pathways. The C-terminal domain contains most
of the NADP(H) binding residues and the N-terminal
domain interacts non-covalently with the isoalloxazine
rings of the flavin molecule which lies largely in a
large gap betweed the two domains. Ferredoxin-NADP+
reductase first accepts one electron from reduced
ferredoxin to form a flavin semiquinone intermediate.
The enzyme then accepts a second electron to form FADH2
which then transfers two electrons and a proton to NADP+
to form NADPH.
Length = 398
Score = 30.8 bits (70), Expect = 2.3
Identities = 13/48 (27%), Positives = 21/48 (43%), Gaps = 1/48 (2%)
Query: 617 KLESMKHLKEEVTSIKKELECGLRLEDPSIEFEPGDTIVCFVKNKVPQ 664
+ S K L E +K ++ L L +++PGDTI N +
Sbjct: 1 PISSAKKLTEG-DDVKTVVDLTLDLSPTGFDYQPGDTIGILPPNTASE 47
>gnl|CDD|236584 PRK09602, PRK09602, translation-associated GTPase; Reviewed.
Length = 396
Score = 30.5 bits (70), Expect = 2.7
Identities = 20/62 (32%), Positives = 27/62 (43%), Gaps = 14/62 (22%)
Query: 201 MEQTVESIRMAREAKVPIIVAINKIDKPAAD--IERTKNMLLAQGITVEDLGGDIQAVPI 258
E +E R R+ P+++A NK D P A+ IER K + V VP
Sbjct: 203 DEDLLELARELRKISKPMVIAANKADLPPAEENIERLKE---EKYYIV---------VPT 250
Query: 259 SA 260
SA
Sbjct: 251 SA 252
>gnl|CDD|206686 cd01899, Ygr210, Ygr210 GTPase. Ygr210 is a member of Obg-like
family and present in archaea and fungi. They are
characterized by a distinct glycine-rich motif
immediately following the Walker B motif. The Ygr210 and
YyaF/YchF subfamilies appear to form one major branch of
the Obg-like family. Among eukaryotes, the Ygr210
subfamily is represented only in fungi. These fungal
proteins form a tight cluster with their archaeal
orthologs, which suggests the possibility of horizontal
transfer from archaea to fungi.
Length = 318
Score = 30.3 bits (69), Expect = 3.6
Identities = 15/51 (29%), Positives = 22/51 (43%), Gaps = 9/51 (17%)
Query: 212 REAKVPIIVAINKIDKPAADIERTKNMLLAQGITVEDLGGDIQAVPISALT 262
R+ + P+++A NK D P A+ +K L V VP SA
Sbjct: 211 RKRRKPMVIAANKADIPDAEENISKLRLKYPDEIV---------VPTSAEA 252
>gnl|CDD|236515 PRK09435, PRK09435, membrane ATPase/protein kinase; Provisional.
Length = 332
Score = 30.2 bits (69), Expect = 3.7
Identities = 27/115 (23%), Positives = 42/115 (36%), Gaps = 35/115 (30%)
Query: 187 TDIVVLVVAA---DD------GVMEQTVESIRMAREAKVPIIVAINKIDKP--------A 229
D +L+ D+ G+ME +A ++ INK D A
Sbjct: 170 VDFFLLLQLPGAGDELQGIKKGIME-------LAD------LIVINKADGDNKTAARRAA 216
Query: 230 ADIERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEAIERTKNMLLAQG 284
A+ +L +D G + SAL G +D + +AIE + L A G
Sbjct: 217 AEYRSALRLL-----RPKDPGWQPPVLTCSALEGEGIDEIWQAIEDHRAALTASG 266
>gnl|CDD|206680 cd01893, Miro1, Mitochondrial Rho family 1 (Miro1), N-terminal.
Miro1 subfamily. Miro (mitochondrial Rho) proteins have
tandem GTP-binding domains separated by a linker region
containing putative calcium-binding EF hand motifs.
Genes encoding Miro-like proteins were found in several
eukaryotic organisms. This CD represents the N-terminal
GTPase domain of Miro proteins. These atypical Rho
GTPases have roles in mitochondrial homeostasis and
apoptosis. Most Rho proteins contain a lipid
modification site at the C-terminus; however, Miro is
one of few Rho subfamilies that lack this feature.
Length = 168
Score = 29.2 bits (66), Expect = 4.2
Identities = 15/46 (32%), Positives = 21/46 (45%), Gaps = 10/46 (21%)
Query: 188 DIVVLVVAADDGVMEQTVESIRM-------AREAKVPIIVAINKID 226
+++ LV + D T+E IR KVPII+ NK D
Sbjct: 74 NVICLVYSVDR---PSTLERIRTKWLPLIRRLGVKVPIILVGNKSD 116
>gnl|CDD|240337 PTZ00261, PTZ00261, acyltransferase; Provisional.
Length = 355
Score = 29.9 bits (67), Expect = 4.9
Identities = 14/51 (27%), Positives = 23/51 (45%), Gaps = 4/51 (7%)
Query: 117 VVTIMGHVDHGKTTLLDTLRNTSVVKSEFGGITQHIGAFVVTLKSGEQVTF 167
+T H+ + +T + +LR + FGG+ +G F V KS F
Sbjct: 148 GLTPFRHLLNTRTLMKSSLRKIPI----FGGVFDRVGHFPVHFKSDSDGNF 194
>gnl|CDD|226124 COG3596, COG3596, Predicted GTPase [General function prediction
only].
Length = 296
Score = 29.8 bits (67), Expect = 5.1
Identities = 25/133 (18%), Positives = 51/133 (38%), Gaps = 17/133 (12%)
Query: 108 PSVLMKRPPVVTIMGHVDHGKTTLLDTLRNTSVVKSEFGGITQHIGAFVVTLKSGEQVTF 167
+ K P V +MG GK++L++ L V + G+ I + GE +
Sbjct: 32 LQLTEKEPVNVLLMGATGAGKSSLINALFQGEVKEVSKVGVGTDITTRLRLSYDGENLVL 91
Query: 168 LDTPG-----------HAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVESIR--MAREA 214
DTPG + + + D+V+ ++ ADD + + +R +
Sbjct: 92 WDTPGLGDGKDKDAEHRQLYRDYLPK----LDLVLWLIKADDRALGTDEDFLRDVIILGL 147
Query: 215 KVPIIVAINKIDK 227
++ + + D+
Sbjct: 148 DKRVLFVVTQADR 160
>gnl|CDD|239668 cd03697, EFTU_II, EFTU_II: Elongation factor Tu domain II.
Elongation factors Tu (EF-Tu) are three-domain GTPases
with an essential function in the elongation phase of
mRNA translation. The GTPase center of EF-Tu is in the
N-terminal domain (domain I), also known as the
catalytic or G-domain. The G-domain is composed of about
200 amino acid residues, arranged into a predominantly
parallel six-stranded beta-sheet core surrounded by
seven a-helices. Non-catalytic domains II and III are
beta-barrels of seven and six, respectively,
antiparallel beta-strands that share an extended
interface. Either non-catalytic domain is composed of
about 100 amino acid residues. EF-Tu proteins exist in
two principal conformations: in a compact one,
EF-Tu*GTP, with tight interfaces between all three
domains and a high affinity for aminoacyl-tRNA, and in
an open one, EF-Tu*GDP, with essentially no
G-domain-domain II interactions and a low affinity for
aminoacyl-tRNA. EF-Tu has approximately a 100-fold
higher affinity for GDP than for GTP.
Length = 87
Score = 27.9 bits (63), Expect = 5.3
Identities = 12/31 (38%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 334 MIVESKFD-THRGKLATALVQRGTLKKGAIV 363
M +E F RG + T ++RGT+K G V
Sbjct: 3 MPIEDVFSIPGRGTVVTGRIERGTIKVGDEV 33
>gnl|CDD|235537 PRK05632, PRK05632, phosphate acetyltransferase; Reviewed.
Length = 684
Score = 29.7 bits (68), Expect = 5.6
Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 6/53 (11%)
Query: 190 VVLVVAADDGVMEQTVESIRMAREA-----KVPII-VAINKIDKPAADIERTK 236
VVLV + + E+ E I +A + I+ V INK++ P + RT+
Sbjct: 109 VVLVSSGGNDTPEELAERIELAASSFGGAKNANILGVIINKLNAPVDEQGRTR 161
>gnl|CDD|223563 COG0489, Mrp, ATPases involved in chromosome partitioning [Cell
division and chromosome partitioning].
Length = 265
Score = 29.3 bits (66), Expect = 5.7
Identities = 9/36 (25%), Positives = 18/36 (50%)
Query: 187 TDIVVLVVAADDGVMEQTVESIRMAREAKVPIIVAI 222
D VV+V +E ++I M +A +P++ +
Sbjct: 190 PDGVVIVTTPGKTALEDVKKAIDMLEKAGIPVLGVV 225
>gnl|CDD|236637 PRK09970, PRK09970, xanthine dehydrogenase subunit XdhA;
Provisional.
Length = 759
Score = 29.7 bits (67), Expect = 6.7
Identities = 18/72 (25%), Positives = 32/72 (44%), Gaps = 1/72 (1%)
Query: 185 HCTDIVVLVVAADDGVMEQTVESIRMAREAKVPIIVAINKIDKPAADIERTKNMLLAQ-G 243
H D V VVA D+ E+ ++ I++ E I + + A I + LL Q
Sbjct: 102 HHGDAVAAVVARDELTAEKALKLIKVEYEELPVITDPEAALAEGAPPIHNGRGNLLKQST 161
Query: 244 ITVEDLGGDIQA 255
++ ++ I+A
Sbjct: 162 MSTGNVQQTIKA 173
>gnl|CDD|234449 TIGR04053, sam_11, radical SAM protein, BA_1875 family. Members of
this subfamily of the radical SAM domain superfamily
show closer sequence relationships to peptide-modifying
proteins of bacteriocin and PQQ biosynthesis than to
other characterized radical SAM proteins. Within this
subfamily, targets are likely to be diverse [Unknown
function, Enzymes of unknown specificity].
Length = 365
Score = 29.2 bits (66), Expect = 6.9
Identities = 11/26 (42%), Positives = 15/26 (57%), Gaps = 2/26 (7%)
Query: 198 DGVMEQTVESIRMAREAKVPIIVAIN 223
G ++TV +IR A E +P V IN
Sbjct: 132 PGSFDRTVNAIRAALELGIP--VQIN 155
>gnl|CDD|232853 TIGR00169, leuB, 3-isopropylmalate dehydrogenase. Several NAD- or
NADP-dependent dehydrogenases, including
3-isopropylmalate dehydrogenase, tartrate dehydrogenase,
and the dimeric forms of isocitrate dehydrogenase, share
a nucleotide binding domain unrelated to that of lactate
dehydrogenase and its homologs. These enzymes
dehydrogenate their substates at a H-C-OH site adjacent
to a H-C-COOH site; the latter carbon, now adjacent to a
carbonyl group, readily decarboxylates.Among these
decarboxylating dehydrogenases of hydroxyacids, overall
sequence homology indicates evolutionary history rather
than actual substrate or cofactor specifity, which may
be toggled experimentally by replacement of just a few
amino acids. 3-isopropylmalate dehydrogenase is an
NAD-dependent enzyme and should have a sequence
resembling HGSAPDI around residue 340. The subtrate
binding loop should include a sequence resembling
E[KQR]X(0,1)LLXXR around residue 115. Other contacts of
importance are known from crystallography but not
detailed here.This model will not find all
isopropylmalate dehydrogenases; the enzyme from
Sulfolobus sp. strain 7 is more similar to mitochondrial
NAD-dependent isocitrate dehydrogenases than to other
known isopropylmalate dehydrogenases and was omitted to
improve the specificity of the model. It scores below
the cutoff and below some enzymes known not to be
isopropylmalate dehydrogenase [Amino acid biosynthesis,
Pyruvate family].
Length = 346
Score = 29.3 bits (66), Expect = 7.8
Identities = 15/54 (27%), Positives = 23/54 (42%), Gaps = 8/54 (14%)
Query: 248 DLGGDIQAVPISAL--------TGTNVDNLTEAIERTKNMLLAQGITVEDLGGD 293
D+ G A PI+ + N++ +AIE +LA+G DLG
Sbjct: 279 DIAGKGIANPIAQILSAAMLLRYSFNLEEAADAIEAAVKKVLAEGYRTPDLGSS 332
>gnl|CDD|239662 cd03691, BipA_TypA_II, BipA_TypA_II: domain II of BipA (also called
TypA) having homology to domain II of the elongation
factors (EFs) EF-G and EF-Tu. BipA is a highly
conserved protein with global regulatory properties in
Escherichia coli. BipA is phosphorylated on a tyrosine
residue under some cellular conditions. Mutants show
altered regulation of some pathways. BipA functions as a
translation factor that is required specifically for the
expression of the transcriptional modulator Fis. BipA
binds to ribosomes at a site that coincides with that of
EF-G and has a GTPase activity that is sensitive to high
GDP:GTP ratios and, is stimulated by 70S ribosomes
programmed with mRNA and aminoacylated tRNAs. The growth
rate-dependent induction of BipA allows the efficient
expression of Fis, thereby modulating a range of
downstream processes, including DNA metabolism and type
III secretion.
Length = 86
Score = 27.1 bits (61), Expect = 8.4
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 341 DTHRGKLATALVQRGTLKKGAIVVA 365
D + G++A + RGT+K G V
Sbjct: 11 DDYVGRIAIGRIFRGTVKVGQQVAV 35
>gnl|CDD|215724 pfam00110, wnt, wnt family. Wnt genes have been identified in
vertebrates and invertebrates but not in plants,
unicellular eukaryotes or prokaryotes. In humans, 19 WNT
proteins are known. Because of their insolubility little
is known about Wnt protein structure, but all have 23 or
24 Cys residues whose spacing is highly conserved.
Signal transduction by Wnt proteins (including the
Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity
pathway) is mediated by receptors of the Frizzled and
LDL-receptor-related protein (LRP) families.
Length = 308
Score = 28.7 bits (65), Expect = 8.6
Identities = 10/24 (41%), Positives = 12/24 (50%), Gaps = 1/24 (4%)
Query: 445 QWRRYWTCSTPTRESKHGRIYLIG 468
+ RR W CST S G+I G
Sbjct: 42 RNRR-WNCSTLDSSSVFGKILKRG 64
>gnl|CDD|214829 smart00812, Alpha_L_fucos, Alpha-L-fucosidase. O-Glycosyl
hydrolases (EC 3.2.1.-) are a widespread group of
enzymes that hydrolyse the glycosidic bond between two
or more carbohydrates, or between a carbohydrate and a
non-carbohydrate moiety. A classification system for
glycosyl hydrolases, based on sequence similarity, has
led to the definition of 85 different families. This
classification is available on the CAZy
(CArbohydrate-Active EnZymes) web site. Because the fold
of proteins is better conserved than their sequences,
some of the families can be grouped in 'clans'. Family
29 encompasses alpha-L-fucosidases, which is a lysosomal
enzyme responsible for hydrolyzing the alpha-1,6-linked
fucose joined to the reducing-end N-acetylglucosamine of
the carbohydrate moieties of glycoproteins. Deficiency
of alpha-L-fucosidase results in the lysosomal storage
disease fucosidosis.
Length = 384
Score = 28.8 bits (65), Expect = 9.2
Identities = 7/20 (35%), Positives = 14/20 (70%)
Query: 66 YDFQVIIDIIQKSGMKYMVI 85
+D + D+ +K+G KY+V+
Sbjct: 81 FDPEEWADLFKKAGAKYVVL 100
>gnl|CDD|237045 PRK12296, obgE, GTPase CgtA; Reviewed.
Length = 500
Score = 29.1 bits (66), Expect = 9.9
Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 11/58 (18%)
Query: 217 PIIVAINKIDKP-AADI-ERTKNMLLAQGITVEDLGGDIQAVPISALTGTNVDNLTEA 272
P +V +NKID P A ++ E + L A+G V +SA + + L+ A
Sbjct: 286 PRLVVLNKIDVPDARELAEFVRPELEARGWPV---------FEVSAASREGLRELSFA 334
>gnl|CDD|206706 cd04134, Rho3, Ras homology family 3 (Rho3) of small guanosine
triphosphatases (GTPases). Rho3 is a member of the Rho
family found only in fungi. Rho3 is believed to regulate
cell polarity by interacting with the diaphanous/formin
family protein For3 to control both the actin
cytoskeleton and microtubules. Rho3 is also believed to
have a direct role in exocytosis that is independent of
its role in regulating actin polarity. The function in
exocytosis may be two-pronged: first, in the transport
of post-Golgi vesicles from the mother cell to the bud,
mediated by myosin (Myo2); second, in the docking and
fusion of vesicles to the plasma membrane, mediated by
an exocyst (Exo70) protein. Most Rho proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of most
Rho proteins.
Length = 185
Score = 28.3 bits (63), Expect = 9.9
Identities = 22/101 (21%), Positives = 37/101 (36%), Gaps = 22/101 (21%)
Query: 118 VTIMGHVDHGKTTLLDTLRNTSVVKSEFGGI-----------TQHIGAFVVTLKSGEQVT 166
V ++G GKT+LL+ + F + + V L +
Sbjct: 3 VVVLGDGACGKTSLLNVF-----TRGYFPQVYEPTVFENYIHDIFVDGLAVEL------S 51
Query: 167 FLDTPGHAAFSNMRSRGAHCTDIVVLVVAADDGVMEQTVES 207
DT G F +RS T +++L + D+ + VES
Sbjct: 52 LWDTAGQEEFDRLRSLSYADTHVIMLCFSVDNPDSLENVES 92
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.135 0.387
Gapped
Lambda K H
0.267 0.0739 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 34,385,305
Number of extensions: 3475394
Number of successful extensions: 4455
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4245
Number of HSP's successfully gapped: 322
Length of query: 673
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 570
Effective length of database: 6,369,140
Effective search space: 3630409800
Effective search space used: 3630409800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 62 (27.6 bits)