RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780787|ref|YP_003065200.1| translation initiation factor
IF-2 [Candidatus Liberibacter asiaticus str. psy62]
(884 letters)
>gnl|CDD|30878 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 594 bits (1532), Expect = e-170
Identities = 266/509 (52%), Positives = 359/509 (70%), Gaps = 5/509 (0%)
Query: 379 LDIRPPVVTIMGHVDHGKTSLLDAIRKADVAKGEIGGITQHIGAYQVAY---QGKNITFL 435
L++RPPVVTIMGHVDHGKT+LLD IRK +VA GE GGITQHIGAYQV + ITF+
Sbjct: 1 LELRPPVVTIMGHVDHGKTTLLDKIRKTNVAAGEAGGITQHIGAYQVPLDVIKIPGITFI 60
Query: 436 DTPGHAAFYEMRARGARVTDIAVLVLAADEEIMPQAIESINHAKAADVSIIVAINKIDKL 495
DTPGH AF MRARGA VTDIA+LV+AAD+ +MPQ IE+INHAKAA V I+VAINKIDK
Sbjct: 61 DTPGHEAFTAMRARGASVTDIAILVVAADDGVMPQTIEAINHAKAAGVPIVVAINKIDKP 120
Query: 496 GADPQKVRMSLLKHDVFVESMGGDILDVEISAKNNLNLDKLLDAILLQAEMLDLKTSINR 555
A+P KV+ L ++ + E GGD++ V +SAK +D+LL+ ILL AE+L+LK +
Sbjct: 121 EANPDKVKQELQEYGLVPEEWGGDVIFVPVSAKTGEGIDELLELILLLAEVLELKANPEG 180
Query: 556 KAEGIVVEGKLDRGRGPVVTVLVQKGTLSKGNILVVGDQWGKIRALFNDRGQGISKAVPS 615
A G V+E KLD+G GPV TV+VQ GTL KG+I+V G ++G++R + +D G+ I +A PS
Sbjct: 181 PARGTVIEVKLDKGLGPVATVIVQDGTLKKGDIIVAGGEYGRVRTMVDDLGKPIKEAGPS 240
Query: 616 MPIEVLGLQGMPMAGDKFGVVDSESRAREIAQYRQRVTRNKSMARRLGSHSALEKLVKNA 675
P+E+LGL +P AGD F VV E +AR IA+ R + R +A + LE+L+
Sbjct: 241 KPVEILGLSEVPAAGDVFIVVKDEKKARAIAELRVVLLREAELASKK--KGELEELIAEI 298
Query: 676 NISSKMKEFPVIIKGDVQGSVEAIVDSLGALKNSEVCLSIVHSSVGAINETDVSLAKASG 735
I ++KE VI+K D QGS+EA+ SL L EV + I+H+ VG I E+DV LA AS
Sbjct: 299 KIRGELKELNVILKADTQGSLEALKGSLKKLGVDEVKVRIIHAGVGGITESDVMLAAASD 358
Query: 736 AVIFGFNVRASSQARVLAIKDEIKILYYKIIYDLLDSIKDSMSELLSPEIRETFLGNAEV 795
AVI GFNVR +AR LA + +KI YY +IY L++ ++ +M +L PE +E +G AEV
Sbjct: 359 AVIIGFNVRVDPEARRLAESEGVKIRYYDVIYKLIEDVEAAMKGMLEPEKKERVIGLAEV 418
Query: 796 LEVFAVTKLGNVAGCKVSEGKVERGSGVRLIRNSTVIYEGKLKTLKRFKDEVSEVHAGQD 855
VF + K+G +AGC V+EG ++RG+ VR++R+ VIYEG++++LKRFKD+V EV GQ+
Sbjct: 419 RAVFKLPKVGAIAGCMVTEGVIKRGAPVRVVRDGVVIYEGEVESLKRFKDDVKEVRKGQE 478
Query: 856 CGMAFEKYDNIQAGDMIECFSIEHIKRSL 884
CG+A E Y +I+ GD++E F +KR+L
Sbjct: 479 CGIAIENYRDIKEGDILEVFEPVEVKRTL 507
>gnl|CDD|36360 KOG1145, KOG1145, KOG1145, Mitochondrial translation initiation
factor 2 (IF-2; GTPase) [Translation, ribosomal
structure and biogenesis].
Length = 683
Score = 551 bits (1420), Expect = e-157
Identities = 265/631 (41%), Positives = 386/631 (61%), Gaps = 32/631 (5%)
Query: 277 SAMRRRQEKFRRNQQQEKREKISREIVVPETITIQELSQRMSERSADVIKFLM--KEGQI 334
+RR +R +Q K + V +T +L+ + +V + L+
Sbjct: 37 ILSQRRYLVGKRREQISKSRLKKKNFSVWNYMTAAKLAAALKCSVDEVQEALLSVGFAYN 96
Query: 335 MKPGD-----VIDADLSEIIANEFGNTVKRVLESDIEVGIFDVADSESD---LDIRPPVV 386
+ D ++ E+I ++ + S E E+D L+ RPPVV
Sbjct: 97 LAIADSNLDTKGILEVVELILMKYRFVLLPAETSVEEKAADVAPQPEADPKLLEPRPPVV 156
Query: 387 TIMGHVDHGKTSLLDAIRKADVAKGEIGGITQHIGAYQVAY-QGKNITFLDTPGHAAFYE 445
TIMGHVDHGKT+LLDA+RK+ VA GE GGITQHIGA+ V GK+ITFLDTPGHAAF
Sbjct: 157 TIMGHVDHGKTTLLDALRKSSVAAGEAGGITQHIGAFTVTLPSGKSITFLDTPGHAAFSA 216
Query: 446 MRARGARVTDIAVLVLAADEEIMPQAIESINHAKAADVSIIVAINKIDKLGADPQKVRMS 505
MRARGA VTDI VLV+AAD+ +MPQ +E+I HAK+A+V I+VAINKIDK GA+P+KV+
Sbjct: 217 MRARGANVTDIVVLVVAADDGVMPQTLEAIKHAKSANVPIVVAINKIDKPGANPEKVKRE 276
Query: 506 LLKHDVFVESMGGDILDVEISAKNNLNLDKLLDAILLQAEMLDLKTSINRKAEGIVVEGK 565
LL + VE +GGD+ + ISA NLD L +AILL AE++DLK AEG V+E
Sbjct: 277 LLSQGIVVEDLGGDVQVIPISALTGENLDLLEEAILLLAEVMDLKADPKGPAEGWVIESS 336
Query: 566 LDRGRGPVVTVLVQKGTLSKGNILVVGDQWGKIRALFNDRGQGISKAVPSMPIEVLGLQG 625
+D+GRGPV TV+V++GTL KG++LV G W K+RALF+ G+ I +A PS P+EVLG +
Sbjct: 337 VDKGRGPVATVIVKRGTLKKGSVLVAGKSWCKVRALFDHNGKPIDEATPSQPVEVLGWKD 396
Query: 626 MPMAGDKFGVVDSESRAREIAQYRQRVTRNKSMARRLGSHSALEKLVKNANISSKM---- 681
+P+AGD+ V+SE RAR++ R+ + + ++R L + A ++ +
Sbjct: 397 LPIAGDEVLEVESEDRARKVLSKRKDESEQEKISRDLEDIEEQREEAAEALLAKREEGEN 456
Query: 682 -------------KEFPVIIKGDVQGSVEAIVDSLGALKNSEVCLSIVHSSVGAINETDV 728
F +IIK DVQGS EA++D+L L + +V L++VHS VG + E+D+
Sbjct: 457 IGRKTRVELHEQNPLFNIIIKCDVQGSAEAVLDALSTLNSEQVKLNVVHSGVGPVTESDL 516
Query: 729 SLAKASGAVIFGFNVRASSQARVLAIKDEIKILYYKIIYDLLDSIKDSMSELLSPEIRET 788
LA+AS A+I+GFNV+AS + LA +KI Y +IY L++ +++ +SE L P +
Sbjct: 517 ELAQASDAIIYGFNVKASPSVKQLAAAKGVKIRLYNVIYRLIEDVRELLSERLPPVEEQE 576
Query: 789 FLGNAEVLEVFAVT---KLGNVAGCKVSEGKVERGSGVRLIRNSTVIYEGKLKTLKRFKD 845
+G AEVL F + K VAGC+V+ G +++ +RL+RN V++EG+L +LK K+
Sbjct: 577 VVGEAEVLATFDIREKRKRVPVAGCRVNNGVIKKSCKIRLVRNGKVVFEGELDSLKHLKE 636
Query: 846 EVSEVHAGQDCGMAFEKYD-NIQAGDMIECF 875
+V+EV G +CG+ F+ + + + GD I+C+
Sbjct: 637 DVTEVKKGHECGLTFDDGNEDFKEGDKIQCY 667
>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional.
Length = 742
Score = 502 bits (1294), Expect = e-142
Identities = 266/761 (34%), Positives = 415/761 (54%), Gaps = 51/761 (6%)
Query: 147 SQESSIDL--PEVCDSQQVPEQVLEDPCKEKD-LEIKDVDVGTEVESSVILSHDMGDSDS 203
S E++IDL P + + + KD L D++ + D
Sbjct: 10 SSENTIDLKNPLFIKNLKHSSYKIRLESDIKDSLLNLDINKKLHEKL-----------DK 58
Query: 204 SSVVNNKFRESSSDASSNRGKSRGGAGK-----------YASVNSSKPVTRNKVGDDDKK 252
+ NK + D+ + K + K + S N+SK +K
Sbjct: 59 KNKKFNK-TDDLKDSKKTKLKQKKKIKKKLHIDDDYDNFFDSKNNSKQFAGPLAISLMRK 117
Query: 253 YKKVRIAVAADVDEEGGASRGRSLSAMRRRQEKFRRNQQQEKREKIS--REIVVPETITI 310
K E + + ++++K ++ + + + + I + +TI
Sbjct: 118 PKP---------KTEKLKKKITVNKSTNKKKKKVLSSKDELIKYDNNKPKSISIHSPLTI 168
Query: 311 QELSQRMSERSADVIKFLMKEGQIMKPGDVIDADLSEIIANEFGNTVKRVLESDIE---V 367
QELS + ++IK L +G + +ID + +A++FG + +++I
Sbjct: 169 QELSTLLCIPETEIIKSLFLKGISVTVNQIIDISIISQVADDFGINIISEEKNNINEKTS 228
Query: 368 GIFDVADSESDLDIRPPVVTIMGHVDHGKTSLLDAIRKADVAKGEIGGITQHIGAYQVAY 427
+ + + + RPP+VTI+GHVDHGKT+LLD IRK +A+ E GGITQ IGAY+V +
Sbjct: 229 NLDNTSAFTENSINRPPIVTILGHVDHGKTTLLDKIRKTQIAQKEAGGITQKIGAYEVEF 288
Query: 428 QGKN----ITFLDTPGHAAFYEMRARGARVTDIAVLVLAADEEIMPQAIESINHAKAADV 483
+ K+ I FLDTPGH AF MR+RGA VTDIA+L++AAD+ + PQ IE+IN+ +AA+V
Sbjct: 289 EYKDENQKIVFLDTPGHEAFSSMRSRGANVTDIAILIIAADDGVKPQTIEAINYIQAANV 348
Query: 484 SIIVAINKIDKLGADPQKVRMSLLKHDVFVESMGGDILDVEISAKNNLNLDKLLDAILLQ 543
IIVAINKIDK A+ ++++ L K+++ E GGD + ISA N+DKLL+ ILL
Sbjct: 349 PIIVAINKIDKANANTERIKQQLAKYNLIPEKWGGDTPMIPISASQGTNIDKLLETILLL 408
Query: 544 AEMLDLKTSINRKAEGIVVEGKLDRGRGPVVTVLVQKGTLSKGNILVVGDQWGKIRALFN 603
AE+ DLK + A+GI++E LD+ +GPV T+LVQ GTL G+I+V+G + KIR + N
Sbjct: 409 AEIEDLKADPTQLAQGIILEAHLDKTKGPVATILVQNGTLHIGDIIVIGTSYAKIRGMIN 468
Query: 604 DRGQGISKAVPSMPIEVLGLQGMPMAGDKFGVVDSESRAREIAQYRQRVTRNKSMARRLG 663
G I+ A PS +E+ GL +P G+ F V +SE A+ +NK ++
Sbjct: 469 SLGNKINLATPSSVVEIWGLSSVPATGEHFQVFNSEKEAKLKII------KNKENNKKDT 522
Query: 664 SHSALEKLVKNANISSKMKEFPVIIKGDVQGSVEAIVDSLGALKNSEVCLSIVHSSVGAI 723
+ K N K+ +IIK D QGS+EAI++S+ + +V L+I+++S+G +
Sbjct: 523 TKRITLSTTKTINKKDNKKQINLIIKTDTQGSIEAIINSISQIPQKKVQLNILYASLGEV 582
Query: 724 NETDVSLAKASGAVIFGFNVRASSQARVLAIKDEIKILYYKIIYDLLDSIKDSMSELLSP 783
ETDV A + A I FN + A+ A K I I Y++IYDLL+ I+ M +LL P
Sbjct: 583 TETDVEFASTTNAEILAFNTNLAPGAKKAARKLNIIIKEYQVIYDLLEYIEALMEDLLDP 642
Query: 784 EIRETFLGNAEVLEVFAVTKLGNVAGCKVSEGKVERGSGVRLIRNSTVIYEGKLKTLKRF 843
E ++ +G AEV VF + K VAGC+V+EGK+ + + +++IR + +IYEGK+ +LKR
Sbjct: 643 EYKKVPIGEAEVKTVFPLAK-RFVAGCRVTEGKITKNALIKVIRENKLIYEGKITSLKRV 701
Query: 844 KDEVSEVHAGQDCGMAFEKYDNIQAGDMIECFSIEHIKRSL 884
K++V E G +CG+ E++ Q+GD I F + K+SL
Sbjct: 702 KEDVEEAQEGNECGIFIEEFQLWQSGDKIHAFELIPKKKSL 742
>gnl|CDD|133287 cd01887, IF2_eIF5B, IF2/eIF5B (initiation factors 2/ eukaryotic
initiation factor 5B) subfamily. 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 = 168
Score = 266 bits (682), Expect = 2e-71
Identities = 99/168 (58%), Positives = 123/168 (73%), Gaps = 4/168 (2%)
Query: 384 PVVTIMGHVDHGKTSLLDAIRKADVAKGEIGGITQHIGAYQV---AYQGKNITFLDTPGH 440
PVVT+MGHVDHGKT+LLD IRK +VA GE GGITQHIGA++V + ITF+DTPGH
Sbjct: 1 PVVTVMGHVDHGKTTLLDKIRKTNVAAGEAGGITQHIGAFEVPAEVLKIPGITFIDTPGH 60
Query: 441 AAFYEMRARGARVTDIAVLVLAADEEIMPQAIESINHAKAADVSIIVAINKIDKLGADPQ 500
AF MRARGA +TDIA+LV+AAD+ +MPQ IE+I AKAA+V IVA+NKIDK A+P+
Sbjct: 61 EAFTNMRARGASLTDIAILVVAADDGVMPQTIEAIKLAKAANVPFIVALNKIDKPNANPE 120
Query: 501 KVRMSLLKHDVFVES-MGGDILDVEISAKNNLNLDKLLDAILLQAEML 547
+V+ L + + E GGD+ V SAK +D LL+AILL AE L
Sbjct: 121 RVKNELSELGLQGEDEWGGDVQIVPTSAKTGEGIDDLLEAILLLAEKL 168
>gnl|CDD|143801 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 = 185
Score = 168 bits (427), Expect = 8e-42
Identities = 62/184 (33%), Positives = 89/184 (48%), Gaps = 19/184 (10%)
Query: 382 RPPVVTIMGHVDHGKTSLLDAIRKADVAKGEIG-----------------GITQHIGAYQ 424
R + I+GHVDHGKT+L DA+ A + G GIT I A
Sbjct: 2 RHRNIGIIGHVDHGKTTLTDALLYVTGAIDKRGEVKQEGELDRLKEERERGITIKIAAVS 61
Query: 425 VAYQGKNITFLDTPGHAAFYEMRARGARVTDIAVLVLAADEEIMPQAIESINHAKAADVS 484
+ ++I +DTPGH F + RGA D A+LV+ A E +MPQ E + AK V
Sbjct: 62 FETKKRHINIIDTPGHVDFTKEMIRGAAQADGAILVVDAVEGVMPQTREHLLLAKQLGVP 121
Query: 485 IIVAINKIDKL-GADPQKVRMSLLKHDVFVESMGGDILDV-EISAKNNLNLDKLLDAILL 542
IIV INK+D++ A+ +V + + + GG+ + V SA +D LL+A+ L
Sbjct: 122 IIVFINKMDRVDDAELDEVVEEISRELLEKYGFGGETIPVIPGSALTGEGIDTLLEALDL 181
Query: 543 QAEM 546
Sbjct: 182 YLPS 185
>gnl|CDD|58093 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 = 132 bits (333), Expect = 6e-31
Identities = 56/95 (58%), Positives = 77/95 (81%)
Query: 557 AEGIVVEGKLDRGRGPVVTVLVQKGTLSKGNILVVGDQWGKIRALFNDRGQGISKAVPSM 616
AEG+V+E KLD+GRGPV TVLVQ GTL G++LV G +GK+RA+F++ G+ + +A PS
Sbjct: 1 AEGVVIESKLDKGRGPVATVLVQNGTLKVGDVLVAGTTYGKVRAMFDENGKRVKEAGPST 60
Query: 617 PIEVLGLQGMPMAGDKFGVVDSESRAREIAQYRQR 651
P+E+LGL+G+P AGDKF VV+SE A+EIA+YR+
Sbjct: 61 PVEILGLKGVPQAGDKFLVVESEKEAKEIAEYRKE 95
>gnl|CDD|133257 cd00881, GTP_translation_factor, GTP translation factor family.
This 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 = 189
Score = 122 bits (308), Expect = 4e-28
Identities = 61/183 (33%), Positives = 89/183 (48%), Gaps = 26/183 (14%)
Query: 386 VTIMGHVDHGKTSLLDAI---------------RKADVAKGEI-GGITQHIGAYQVAYQG 429
V I GHVDHGKT+L + + DV K E GIT G +
Sbjct: 2 VGIAGHVDHGKTTLTERLLYVTGDIERDGTVEETFLDVLKEERERGITIKSGVATFEWPD 61
Query: 430 KNITFLDTPGHAAFYEMRARGARVTDIAVLVLAADEEIMPQAIESINHAKAADVSIIVAI 489
+ + F+DTPGH F RG V+D A+LV+ A+E + PQ E + A+ + IIVAI
Sbjct: 62 RRVNFIDTPGHEDFSSEVIRGLSVSDGAILVVDANEGVQPQTREHLRIAREGGLPIIVAI 121
Query: 490 NKIDKLG-ADPQKVRM---SLLKHDVFVESMGGDILD------VEISAKNNLNLDKLLDA 539
NKID++G D ++V LL F+ + + V SA + +++LL+A
Sbjct: 122 NKIDRVGEEDLEEVLREIKELLGLIGFISTKEEGTRNGLLVPIVPGSALTGIGVEELLEA 181
Query: 540 ILL 542
I+
Sbjct: 182 IVE 184
>gnl|CDD|58092 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 = 118 bits (297), Expect = 8e-27
Identities = 50/95 (52%), Positives = 68/95 (71%)
Query: 557 AEGIVVEGKLDRGRGPVVTVLVQKGTLSKGNILVVGDQWGKIRALFNDRGQGISKAVPSM 616
AEG V+E KLD+GRGPV TV+VQ GTL KG+++V G +GKIR + ++ G+ + +A PS
Sbjct: 1 AEGTVIESKLDKGRGPVATVIVQNGTLKKGDVIVAGGTYGKIRTMVDENGKALLEAGPST 60
Query: 617 PIEVLGLQGMPMAGDKFGVVDSESRAREIAQYRQR 651
P+E+LGL+ +P AGD VV SE A+EI YR
Sbjct: 61 PVEILGLKDVPKAGDGVLVVASEKEAKEIGSYRLV 95
>gnl|CDD|58083 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 = 116 bits (293), Expect = 3e-26
Identities = 44/84 (52%), Positives = 65/84 (77%)
Query: 791 GNAEVLEVFAVTKLGNVAGCKVSEGKVERGSGVRLIRNSTVIYEGKLKTLKRFKDEVSEV 850
G AEV VF ++K+GN+AGC V++GK++R + VR++RN VIYEGK+ +LKRFKD+V EV
Sbjct: 1 GEAEVRAVFKISKVGNIAGCYVTDGKIKRNAKVRVLRNGEVIYEGKISSLKRFKDDVKEV 60
Query: 851 HAGQDCGMAFEKYDNIQAGDMIEC 874
G +CG+ E +++I+ GD+IE
Sbjct: 61 KKGYECGITLENFNDIKVGDIIEA 84
>gnl|CDD|36359 KOG1144, KOG1144, KOG1144, Translation initiation factor 5B (eIF-5B)
[Translation, ribosomal structure and biogenesis].
Length = 1064
Score = 116 bits (291), Expect = 3e-26
Identities = 194/923 (21%), Positives = 351/923 (38%), Gaps = 147/923 (15%)
Query: 33 QNQGANQGRARSVVVETRKRRSYVQGEEKVSVFRKSSRVIESSSDSSQDLSQAKAKGNFR 92
+N + E + + +EK S+ S +++ + K+
Sbjct: 137 ENVAPVEAAGEKEKKEKAAAKKKKEKKEKEKKKEDSAAAAAEKSVEAKEEKKEKSVTEPA 196
Query: 93 RASRSDKVSSQKNDSSFAGLSQ-GEIESRRRALHEAQVREEELR-KRLEQQSLEQPSQES 150
+ + + G+ E ++R+ E Q REEE R +R E++ + +E+
Sbjct: 197 EPEKKEAKGKKAEKKKPKGVRAMQEALAKRQEEEERQKREEEERLRREEEEERRREEEEA 256
Query: 151 SIDLPEVCDSQQVPEQVLEDPCKEKDLEIKDVDVGTEVES----------SVILSHDMGD 200
+ + ++ E+ + K L K + E+ + ++ GD
Sbjct: 257 QEEEAKEKKKEKEKEKKERKKAEGKLLTAKQKEEAALAEAFLKQLLASGGGLPVADKDGD 316
Query: 201 SDSSSVVNNKFRESSSDASSNRGKSRGGAGKYASVNSSKPVTRN--KVGDDDKKYKKVRI 258
S + NK +++ + + G + ++ + + +V ++ +
Sbjct: 317 SKKRPIYANKKKKARQKGNDRTSVEKLGEVEAKENHAGDVGSVDTEEVDLEEDSNTDEKE 376
Query: 259 AVAADVDEEGGASRGRSLSAMRRRQEKFRRNQQQEKREKISREIVVPETITIQELSQRMS 318
DVD+E G + + + + ++E +E++ +E+ E +E S++ +
Sbjct: 377 GTPEDVDQEEGEEEDDWDAKVDLAIDGDDDDDEEELQEEVDKEL--KEAEEEEEDSEKPT 434
Query: 319 ERSADVIKFLMKEGQIMKPGDVIDADLSEIIANEFGNTVKRVLESDIEVGIFDVADSESD 378
E +A I K D IA KR ES
Sbjct: 435 EDAA--------VKAISKVEDAATRTKRAKIA-------KRATNESAN---------EST 470
Query: 379 LDIRPPVVTIMGHVDHGKTSLLDAIRKADVAKGEIGGITQHIGA---------------- 422
++R P+ I+GHVD GKT LLD IR +V +GE GGITQ IGA
Sbjct: 471 ENLRSPICCILGHVDTGKTKLLDKIRGTNVQEGEAGGITQQIGATYFPAENIREKTKELK 530
Query: 423 --YQVAYQGKNITFLDTPGHAAFYEMRARGARVTDIAVLVLAADEEIMPQAIESINHAKA 480
+ + + +DTPGH +F +R+RG+ + D+A+LV+ + PQ IESIN +
Sbjct: 531 KDAKKRLKVPGLLVIDTPGHESFTNLRSRGSSLCDLAILVVDIMHGLEPQTIESINLLRM 590
Query: 481 ADVSIIVAINKIDKLGA------DPQKVRMSLLKHDVFVE-------------------- 514
IVA+NKID+L P + K DV E
Sbjct: 591 RKTPFIVALNKIDRLYGWKSCPNAPIVEALKKQKKDVQNEFKERLNNIIVEFAEQGLNAE 650
Query: 515 ------SMGGDILDVEISAKNNLNLDKLLDAILLQAE-MLDLKTSINRKAEGIVVEGKLD 567
MG + V SA + + LL ++ + + K + + + V+E K+
Sbjct: 651 LYYKNKEMGETVSIVPTSAISGEGIPDLLLLLVQLTQKTMVEKLAYVDEVQCTVLEVKVI 710
Query: 568 RGRGPVVTVLVQKGTLSKGNILVVGDQWG----KIRALFND--------RGQGIS----K 611
G G + V++ G L +G+ +VV G IRAL +G + K
Sbjct: 711 EGHGTTIDVILVNGELHEGDQIVVCGLQGPIVTTIRALLTPQPLKELRVKGTYVHHKEVK 770
Query: 612 AVPSMPIEVLGLQGMPMAGDKFGVVDSESRAREIAQYRQRVTRNKSMARRLGSHSALEKL 671
A + I L+ +AG + VV E E+ A+E L
Sbjct: 771 AAQGIKIAAKDLEKA-IAGTRLLVVGPEDDIEELK------------------EEAMEDL 811
Query: 672 VKNANISSKMKEFPVIIKGDVQGSVEAIVDSLGALKNSEVCLSIVHSSVGAINETDVSLA 731
++ V ++ GS+EA+++ L +K + + +G +++ DV A
Sbjct: 812 -ESVLSRIDKSGEGVYVQASTLGSLEALLEFLKTVK-----IPVSGIGIGPVHKKDVMKA 865
Query: 732 ------KASGAVIFGFNVRASSQARVLAIKDEIKILYYKIIYDLLDSIKDSMSELLSPEI 785
K A I F+V+ +AR LA + +KI IIY L D+ + E+ E
Sbjct: 866 SVMLEKKKEYATILAFDVKVEREARELADEMGVKIFCADIIYHLFDAFTKYIEEIKE-EK 924
Query: 786 RETFLGNA------EVLEVFAVTKLGN-VAGCKVSEGKVERGSGVRLIRNSTVIYEGKLK 838
++ A ++L K V G V EG ++ G+ + + + + G++
Sbjct: 925 KKESADEAVFPCVLQILPNCIFNKRDPIVLGVDVEEGILKIGTPICVPKREFIDL-GRVA 983
Query: 839 TLKRFKDEVSEVHAGQDCGMAFE 861
+++ V GQ+ + E
Sbjct: 984 SIENNHKPVDYAKKGQEVAIKIE 1006
>gnl|CDD|30828 COG0480, FusA, Translation elongation factors (GTPases)
[Translation, ribosomal structure and biogenesis].
Length = 697
Score = 86.4 bits (214), Expect = 3e-17
Identities = 46/143 (32%), Positives = 65/143 (45%), Gaps = 19/143 (13%)
Query: 386 VTIMGHVDHGKTSLLDAI--------RKADVAKG---------EIG-GITQHIGAYQVAY 427
+ I+ H+D GKT+L + I + +V G E GIT A + +
Sbjct: 13 IGIVAHIDAGKTTLTERILFYTGIISKIGEVHDGAATMDWMEQEQERGITITSAATTLFW 72
Query: 428 QGKN-ITFLDTPGHAAFYEMRARGARVTDIAVLVLAADEEIMPQAIESINHAKAADVSII 486
+G I +DTPGH F R RV D AV+V+ A E + PQ A V I
Sbjct: 73 KGDYRINLIDTPGHVDFTIEVERSLRVLDGAVVVVDAVEGVEPQTETVWRQADKYGVPRI 132
Query: 487 VAINKIDKLGADPQKVRMSLLKH 509
+ +NK+D+LGAD V L +
Sbjct: 133 LFVNKMDRLGADFYLVVEQLKER 155
>gnl|CDD|133371 cd04171, SelB, SelB subfamily. 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 = 164
Score = 79.9 bits (198), Expect = 3e-15
Identities = 50/160 (31%), Positives = 78/160 (48%), Gaps = 12/160 (7%)
Query: 390 GHVDHGKTSLLDAI--RKADVAKGEIG-GITQHIG-AYQVAYQGKNITFLDTPGHAAFYE 445
GH+DHGKT+L+ A+ + D E GIT +G AY GK + F+D PGH F +
Sbjct: 7 GHIDHGKTTLIKALTGIETDRLPEEKKRGITIDLGFAYLDLPSGKRLGFIDVPGHEKFIK 66
Query: 446 MRARGARVTDIAVLVLAADEEIMPQAIESINHAKAADV-SIIVAINKIDKLGADPQKVRM 504
GA D+ +LV+AADE IMPQ E + + + +V + K D D +
Sbjct: 67 NMLAGAGGIDLVLLVVAADEGIMPQTREHLEILELLGIKRGLVVLTKADL--VDED--WL 122
Query: 505 SLLKHDVFVESMGGDILDVEI---SAKNNLNLDKLLDAIL 541
L++ ++ G + D I SA +++L + +
Sbjct: 123 ELVEEEIRELLAGTFLADAPIFPVSAVTGEGIEELKEYLD 162
>gnl|CDD|35683 KOG0462, KOG0462, KOG0462, Elongation factor-type GTP-binding
protein [Translation, ribosomal structure and
biogenesis].
Length = 650
Score = 79.2 bits (195), Expect = 5e-15
Identities = 62/219 (28%), Positives = 97/219 (44%), Gaps = 25/219 (11%)
Query: 386 VTIMGHVDHGKTSLLDAI-RKADVAKGEIG--------------GITQHIGAYQVAYQGK 430
+I+ HVDHGK++L D + IG GIT + Y+
Sbjct: 63 FSIIAHVDHGKSTLADRLLELTGTIDNNIGQEQVLDKLQVERERGITIKAQTASIFYKDG 122
Query: 431 NITFL---DTPGHAAFYEMRARGARVTDIAVLVLAADEEIMPQAIESINHAKAADVSIIV 487
L DTPGH F +R D A+LV+ A + + Q + + A A ++II
Sbjct: 123 QSYLLNLIDTPGHVDFSGEVSRSLAACDGALLVVDASQGVQAQTVANFYLAFEAGLAIIP 182
Query: 488 AINKIDKLGADPQKVRMSLLKHDVFVESMGGDILDVEISAKNNLNLDKLLDAILLQAEML 547
+NKID ADP++V L ++F I +SAK LN+++LL+AI+ +
Sbjct: 183 VLNKIDLPSADPERVENQL--FELFDIPPAEVIY---VSAKTGLNVEELLEAIIRRVP-- 235
Query: 548 DLKTSINRKAEGIVVEGKLDRGRGPVVTVLVQKGTLSKG 586
K + ++ + + D RG + V V G + KG
Sbjct: 236 PPKGIRDAPLRMLIFDSEYDEYRGVIALVRVVDGVVRKG 274
>gnl|CDD|31410 COG1217, TypA, Predicted membrane GTPase involved in stress
response [Signal transduction mechanisms].
Length = 603
Score = 77.9 bits (192), Expect = 1e-14
Identities = 71/251 (28%), Positives = 103/251 (41%), Gaps = 49/251 (19%)
Query: 386 VTIMGHVDHGKTSLLDAIRKAD---VAKGEIG-------------GITQHIGAYQVAYQG 429
+ I+ HVDHGKT+L+DA+ K + E+ GIT V Y G
Sbjct: 8 IAIIAHVDHGKTTLVDALLKQSGTFREREEVAERVMDSNDLEKERGITILAKNTAVNYNG 67
Query: 430 KNITFLDTPGHAAFYEMRARGARVTDIAVLVLAADEEIMPQAIESINHAKAADVSIIVAI 489
I +DTPGHA F R + D +L++ A E MPQ + A A + IV I
Sbjct: 68 TRINIVDTPGHADFGGEVERVLSMVDGVLLLVDASEGPMPQTRFVLKKALALGLKPIVVI 127
Query: 490 NKIDKLGADPQKVRMSLLKHDVFVE-SMGGDILDVEI---SAKN----------NLNLDK 535
NKID+ A P +V + D+FVE + LD I SA+N ++
Sbjct: 128 NKIDRPDARPDEVVDEV--FDLFVELGATDEQLDFPIVYASARNGTASLDPEDEADDMAP 185
Query: 536 LLDAIL---------------LQAEMLDLKTSINRKAEGIVVEGKLDRGRGPVVTVLVQK 580
L + IL +Q LD + + R G + G + + V ++
Sbjct: 186 LFETILDHVPAPKGDLDEPLQMQVTQLDYNSYVGRIGIGRIFRGTVKPNQ--QVALIKSD 243
Query: 581 GTLSKGNILVV 591
GT G I +
Sbjct: 244 GTTENGRITKL 254
>gnl|CDD|133291 cd01891, TypA_BipA, TypA (tyrosine phosphorylated protein A)/BipA
subfamily. 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 = 75.3 bits (186), Expect = 7e-14
Identities = 64/195 (32%), Positives = 91/195 (46%), Gaps = 40/195 (20%)
Query: 380 DIRPPVVTIMGHVDHGKTSLLDAIRK---ADVAKGEIG-------------GITQHIGAY 423
DIR + I+ HVDHGKT+L+DA+ K E+ GIT I A
Sbjct: 1 DIRN--IAIIAHVDHGKTTLVDALLKQSGTFRENEEVEERVMDSNDLERERGIT--ILAK 56
Query: 424 QVA--YQGKNITFLDTPGHAAFYEMRARGARVTDIAVLVLAADEEIMPQAIESINHAKAA 481
A Y+ I +DTPGHA F R + D +L++ A E MPQ + A
Sbjct: 57 NTAVTYKDTKINIVDTPGHADFGGEVERVLSMVDGVLLLVDASEGPMPQTRFVLKKALEL 116
Query: 482 DVSIIVAINKIDKLGADPQKVRMSLLKHDVFVESMGG--DILDVEI---SAKN------- 529
+ IV INKID+ A P++V + D+F+E +G + LD + SAKN
Sbjct: 117 GLKPIVVINKIDRPDARPEEVVDEVF--DLFIE-LGATEEQLDFPVLYASAKNGWASLNL 173
Query: 530 ---NLNLDKLLDAIL 541
+ +L+ L D I+
Sbjct: 174 EDPSEDLEPLFDTII 188
>gnl|CDD|30829 COG0481, LepA, Membrane GTPase LepA [Cell envelope biogenesis,
outer membrane].
Length = 603
Score = 74.8 bits (184), Expect = 1e-13
Identities = 62/221 (28%), Positives = 110/221 (49%), Gaps = 31/221 (14%)
Query: 388 IMGHVDHGKTSLLDAI--RKADVAKGEIG-------------GITQHIGAYQVAYQGKN- 431
I+ H+DHGK++L D + +++ E+ GIT A ++ Y+ K+
Sbjct: 14 IIAHIDHGKSTLADRLLELTGGLSEREMRAQVLDSMDIERERGITIKAQAVRLNYKAKDG 73
Query: 432 ----ITFLDTPGHAAF-YEMRARGARVTDIAVLVLAADEEIMPQAIESINHAKAADVSII 486
+ +DTPGH F YE+ +R + A+LV+ A + + Q + ++ A ++ II
Sbjct: 74 ETYVLNLIDTPGHVDFSYEV-SRSLAACEGALLVVDASQGVEAQTLANVYLALENNLEII 132
Query: 487 VAINKIDKLGADPQKVRMSLLKHDVFVESMGGDILD-VEISAKNNLNLDKLLDAILLQAE 545
+NKID ADP++V+ + D+ G D D V +SAK + ++ +L+AI+ +
Sbjct: 133 PVLNKIDLPAADPERVKQEI--EDII----GIDASDAVLVSAKTGIGIEDVLEAIV--EK 184
Query: 546 MLDLKTSINRKAEGIVVEGKLDRGRGPVVTVLVQKGTLSKG 586
+ K + + ++ + D G VV V + GTL KG
Sbjct: 185 IPPPKGDPDAPLKALIFDSWYDNYLGVVVLVRIFDGTLKKG 225
>gnl|CDD|33087 COG3276, SelB, Selenocysteine-specific translation elongation
factor [Translation, ribosomal structure and
biogenesis].
Length = 447
Score = 73.1 bits (179), Expect = 3e-13
Identities = 60/221 (27%), Positives = 97/221 (43%), Gaps = 26/221 (11%)
Query: 385 VVTIMGHVDHGKTSLLDAIRKADVAKG-EIG--GITQHIGAYQVAYQGKNITFLDTPGHA 441
++ GH+DHGKT+LL A+ + E GIT +G Y + + F+D PGH
Sbjct: 2 IIGTAGHIDHGKTTLLKALTGGVTDRLPEEKKRGITIDLGFYYRKLEDGVMGFIDVPGHP 61
Query: 442 AFYEMRARGARVTDIAVLVLAADEEIMPQAIESINHAKAADV----SIIVAINKIDKLGA 497
F G D A+LV+AADE +M Q E H D+ + I+ + K D++
Sbjct: 62 DFISNLLAGLGGIDYALLVVAADEGLMAQTGE---HLLILDLLGIKNGIIVLTKADRVDE 118
Query: 498 DPQKVRMSLLKHDVFVESMGGDILDVEISAKNNLNLDKLLDAILLQAEMLDLKTSINRKA 557
+ ++ + D+ + + + SAK ++ L+ E++DL I R
Sbjct: 119 ARIEQKIKQILADLSLA----NAKIFKTSAKTGRGIE------ELKNELIDLLEEIERDE 168
Query: 558 EGIVVEGKLDR-----GRGPVVTVLVQKGTLSKGNILVVGD 593
+ +DR G G VVT V G + G+ L +
Sbjct: 169 QKPFRIA-IDRAFTVKGVGTVVTGTVLSGEVKVGDKLYLSP 208
>gnl|CDD|133290 cd01890, LepA, LepA subfamily. LepA belongs to the GTPase family
of 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 = 73.3 bits (181), Expect = 3e-13
Identities = 51/175 (29%), Positives = 87/175 (49%), Gaps = 29/175 (16%)
Query: 388 IMGHVDHGKTSLLDAI--RKADVAKGEIG-------------GITQHIGAYQVAYQGKN- 431
I+ H+DHGK++L D + V+K E+ GIT ++ Y+ K+
Sbjct: 5 IIAHIDHGKSTLADRLLELTGTVSKREMKEQVLDSMDLERERGITIKAQTVRLNYKAKDG 64
Query: 432 ----ITFLDTPGHAAF-YEMRARGARVTDIAVLVLAADEEIMPQAIESINHAKAADVSII 486
+ +DTPGH F YE+ +R + A+L++ A + + Q + + A ++ II
Sbjct: 65 QEYLLNLIDTPGHVDFSYEV-SRSLAACEGALLLVDATQGVEAQTLANFYLALENNLEII 123
Query: 487 VAINKIDKLGADPQKVRMSLLKHDVFVESMGGDILDV-EISAKNNLNLDKLLDAI 540
INKID ADP++V+ + + +G D + +SAK L ++ LL+AI
Sbjct: 124 PVINKIDLPSADPERVKQQI------EDVLGLDPSEAILVSAKTGLGVEDLLEAI 172
>gnl|CDD|133370 cd04170, EF-G_bact, Elongation factor G (EF-G) subfamily.
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 = 71.4 bits (176), Expect = 1e-12
Identities = 37/136 (27%), Positives = 60/136 (44%), Gaps = 20/136 (14%)
Query: 386 VTIMGHVDHGKTSLLDAI--------RKADVAKG---------EIG-GITQHIGAYQVAY 427
+ ++GH GKT+L +A+ R V G EI ++ + +
Sbjct: 2 IALVGHSGSGKTTLAEALLYATGAIDRLGSVEDGTTVSDYDPEEIKRKMSISTSVAPLEW 61
Query: 428 QGKNITFLDTPGHAAFYEMRARGA-RVTDIAVLVLAADEEIMPQAIESINHAKAADVSII 486
+G I +DTPG+A F R A R D A++V++A + + A A + I
Sbjct: 62 KGHKINLIDTPGYADFVG-ETRAALRAADAALVVVSAQSGVEVGTEKLWEFADEAGIPRI 120
Query: 487 VAINKIDKLGADPQKV 502
+ INK+D+ AD K
Sbjct: 121 IFINKMDRERADFDKT 136
>gnl|CDD|133367 cd04167, Snu114p, 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 = 69.9 bits (172), Expect = 3e-12
Identities = 41/134 (30%), Positives = 56/134 (41%), Gaps = 24/134 (17%)
Query: 386 VTIMGHVDHGKTSLLDAI------------------RKADVAKGEIG-GITQHIGAYQVA 426
V I GH+ HGKTSLLD + R D+ K E GI+ +
Sbjct: 3 VAIAGHLHHGKTSLLDMLIEQTHDLTPSGKDGWKPLRYTDIRKDEQERGISIKSSPISLV 62
Query: 427 YQGKN-----ITFLDTPGHAAFYEMRARGARVTDIAVLVLAADEEIMPQAIESINHAKAA 481
+DTPGH F + A R++D VLV+ E + I HA
Sbjct: 63 LPDSKGKSYLFNIIDTPGHVNFMDEVAAALRLSDGVVLVVDVVEGVTSNTERLIRHAILE 122
Query: 482 DVSIIVAINKIDKL 495
+ I++ INKID+L
Sbjct: 123 GLPIVLVINKIDRL 136
>gnl|CDD|35681 KOG0460, KOG0460, KOG0460, Mitochondrial translation elongation
factor Tu [Translation, ribosomal structure and
biogenesis].
Length = 449
Score = 69.6 bits (170), Expect = 3e-12
Identities = 72/231 (31%), Positives = 103/231 (44%), Gaps = 33/231 (14%)
Query: 386 VTIMGHVDHGKTSLLDAIRKADVAKG--------EIG--------GITQHIGAYQVAYQG 429
V +GHVDHGKT+L AI K KG EI GIT I A V Y+
Sbjct: 57 VGTIGHVDHGKTTLTAAITKILAEKGGAKFKKYDEIDKAPEEKARGIT--INAAHVEYET 114
Query: 430 KNITF--LDTPGHAAFYEMRARGARVTDIAVLVLAADEEIMPQAIESINHAKAADV-SII 486
+ D PGHA + + GA D A+LV+AA + MPQ E + A+ V I+
Sbjct: 115 AKRHYAHTDCPGHADYIKNMITGAAQMDGAILVVAATDGPMPQTREHLLLARQVGVKHIV 174
Query: 487 VAINKIDKLGADPQKVRMSLLKHDVFVESMG--GD----ILDVEISAKNNLNLDKLLDAI 540
V INK+D + DP+ + + ++ + G GD I + A + L+AI
Sbjct: 175 VFINKVDLV-DDPEMLELVEMEIRELLSEFGFDGDNTPVIRGSALCALEGRQPEIGLEAI 233
Query: 541 LLQAEMLDLKTSI-NRKAEG---IVVEGKLD-RGRGPVVTVLVQKGTLSKG 586
+ +D R + + +E GRG VVT +++G L KG
Sbjct: 234 EKLLDAVDSYIPTPERDLDKPFLLPIEDVFSIPGRGTVVTGRLERGVLKKG 284
Score = 31.8 bits (72), Expect = 0.95
Identities = 30/139 (21%), Positives = 66/139 (47%), Gaps = 15/139 (10%)
Query: 739 FGFN------VRASSQARVLAIKDEIKILYYKIIYDLLDSIKDSMSELLSPEIRETFLGN 792
FGF+ +R S+ + + EI + + I LLD++ DS ++ + FL
Sbjct: 203 FGFDGDNTPVIRGSALCALEGRQPEIGL---EAIEKLLDAV-DSYIPTPERDLDKPFLLP 258
Query: 793 AEVLEVFAVTKLGNVAGCKVSEGKVERGSGVRLIRNSTVIYEGKLKTLKRFKDEVSEVHA 852
E +VF++ G V ++ G +++G V ++ ++ + + + ++ F+ + E A
Sbjct: 259 IE--DVFSIPGRGTVVTGRLERGVLKKGDEVEIVGHNKTL-KTTVTGIEMFRKSLDEAQA 315
Query: 853 GQDCGMAFE--KYDNIQAG 869
G + G K ++++ G
Sbjct: 316 GDNLGALLRGIKREDVKRG 334
>gnl|CDD|133256 cd00880, Era_like, Era (E. coli Ras-like protein)-like. This
family includes several distinct subfamilies (TrmE/ThdF,
FeoB, YihA (EngG), 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 = 163
Score = 69.3 bits (170), Expect = 4e-12
Identities = 33/168 (19%), Positives = 65/168 (38%), Gaps = 22/168 (13%)
Query: 388 IMGHVDHGKTSLLDAIRKADVAK-GEIGGITQHIGAYQVAYQ-GKNITFLDTPGH----- 440
+ G + GK+SLL+A+ +VA + G T Y + +DTPG
Sbjct: 1 LFGRTNAGKSSLLNALLGQEVAIVSPVPGTTTDPVEYVWELGPLGPVVLIDTPGIDEAGG 60
Query: 441 ------AAFYEMRARGARVTDIAVLVLAADEEIMPQAIESINHAKAADVSIIVAINKIDK 494
+ D+ + V+ AD + + + + +++ +NKID
Sbjct: 61 LGREREELARRV----LERADLILFVVDADLRADEEEEKLLELLRERGKPVLLVLNKIDL 116
Query: 495 LGADPQKVRMSLLKHDVFVESMGGDILDV-EISAKNNLNLDKLLDAIL 541
L + ++ L + + L V +SA +D+L +A++
Sbjct: 117 LPEEEEE----ELLELRLLILLLLLGLPVIAVSALTGEGIDELREALI 160
>gnl|CDD|35688 KOG0467, KOG0467, KOG0467, Translation elongation factor 2/ribosome
biogenesis protein RIA1 and related proteins
[Translation, ribosomal structure and biogenesis].
Length = 887
Score = 68.1 bits (166), Expect = 1e-11
Identities = 38/140 (27%), Positives = 64/140 (45%), Gaps = 16/140 (11%)
Query: 386 VTIMGHVDHGKTSLLDA---------------IRKADVAKGEIG-GITQHIGAYQVAYQG 429
+ ++ HVDHGKTSL D+ IR D + E GIT A + ++
Sbjct: 12 ICLVAHVDHGKTSLADSLVASNGVISSRLAGKIRFLDTREDEQTRGITMKSSAISLLHKD 71
Query: 430 KNITFLDTPGHAAFYEMRARGARVTDIAVLVLAADEEIMPQAIESINHAKAADVSIIVAI 489
I +D+PGH F + +R++D A++++ E + Q + A + I+ I
Sbjct: 72 YLINLIDSPGHVDFSSEVSSASRLSDGALVLVDVVEGVCSQTYAVLRQAWIEGLKPILVI 131
Query: 490 NKIDKLGADPQKVRMSLLKH 509
NKID+L + + +H
Sbjct: 132 NKIDRLITELKLSPQEAYEH 151
>gnl|CDD|133284 cd01884, EF_Tu, 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 = 67.6 bits (166), Expect = 1e-11
Identities = 49/132 (37%), Positives = 64/132 (48%), Gaps = 23/132 (17%)
Query: 387 TIMGHVDHGKTSLLDAIRKADVAKG--------EIG--------GITQHIGAYQVAYQGK 430
TI GHVDHGKT+L AI K KG EI GIT I V Y+
Sbjct: 7 TI-GHVDHGKTTLTAAITKVLAKKGGAKFKKYDEIDKAPEEKARGIT--INTAHVEYETA 63
Query: 431 NITF--LDTPGHAAFYEMRARGARVTDIAVLVLAADEEIMPQAIESINHAKAADV-SIIV 487
N + +D PGHA + + GA D A+LV++A + MPQ E + A+ V I+V
Sbjct: 64 NRHYAHVDCPGHADYIKNMITGAAQMDGAILVVSATDGPMPQTREHLLLARQVGVPYIVV 123
Query: 488 AINKIDKLGADP 499
+NK D + D
Sbjct: 124 FLNKADMV-DDE 134
>gnl|CDD|133258 cd00882, Ras_like_GTPase, 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 regulate
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 = 157
Score = 67.5 bits (165), Expect = 2e-11
Identities = 33/161 (20%), Positives = 60/161 (37%), Gaps = 12/161 (7%)
Query: 388 IMGHVDHGKTSLLDAIRKADVAKGEIGGITQHIGAYQVAYQGKN--ITFLDTPGHAAFYE 445
++G GKTSLL+ + + E + + GK + DT G F
Sbjct: 1 VVGDSGVGKTSLLNRLLGGEFVPEEYETTIIDFYSKTIEVDGKKVKLQIWDTAGQERFRS 60
Query: 446 MRARGARVTDIAVLVLAAD-----EEIMPQAIESINHAKAADVSIIVAINKIDKLGADPQ 500
+R R D +LV E + + + + + ++ II+ NKID
Sbjct: 61 LRRLYYRGADGIILVYDVTDRESFENVKEWLLLILINKEGENIPIILVGNKIDLPEERVV 120
Query: 501 KVRMSLLKHDVFVESMGGDILDVEISAKNNLNLDKLLDAIL 541
+ + +G + E SAK N+++L + +
Sbjct: 121 SEEELAEQ---LAKELG--VPYFETSAKTGENVEELFEELA 156
>gnl|CDD|35689 KOG0468, KOG0468, KOG0468, U5 snRNP-specific protein [Translation,
ribosomal structure and biogenesis].
Length = 971
Score = 67.0 bits (163), Expect = 2e-11
Identities = 43/170 (25%), Positives = 68/170 (40%), Gaps = 31/170 (18%)
Query: 357 VKRVLESDIEVGIFDVADSESDLDI---------RPPVVTIMGHVDHGKTSLLDAI---- 403
++ V ++ DV ++ DL+ R V ++GH+ HGKT+L+D +
Sbjct: 93 IEPVRRLKFQIHERDVPETVYDLEYLAGLMDNPERIRNVGLVGHLHHGKTALMDLLVEQT 152
Query: 404 ------------RKADVAKGEIG-GITQHIGAYQVAYQGKN-----ITFLDTPGHAAFYE 445
R D E G + + + LDTPGH F +
Sbjct: 153 HPDFSKNTEADLRYTDTLFYEQERGCSIKSTPVTLVLSDSKGKSYLMNILDTPGHVNFSD 212
Query: 446 MRARGARVTDIAVLVLAADEEIMPQAIESINHAKAADVSIIVAINKIDKL 495
R++D VLV+ E +M I HA + I+V INK+D+L
Sbjct: 213 ETTASLRLSDGVVLVVDVAEGVMLNTERIIKHAIQNRLPIVVVINKVDRL 262
>gnl|CDD|30399 COG0050, TufB, GTPases - translation elongation factors
[Translation, ribosomal structure and biogenesis].
Length = 394
Score = 66.8 bits (163), Expect = 2e-11
Identities = 72/238 (30%), Positives = 103/238 (43%), Gaps = 38/238 (15%)
Query: 385 VVTIMGHVDHGKTSLLDAIRKADVAKGEIG----------------GITQHIGAYQVAYQ 428
V TI GHVDHGKT+L AI KG GIT I V Y+
Sbjct: 15 VGTI-GHVDHGKTTLTAAITTVLAKKGGAEAKAYDQIDNAPEEKARGIT--INTAHVEYE 71
Query: 429 GKN--ITFLDTPGHAAFYEMRARGARVTDIAVLVLAADEEIMPQAIESINHAKAADV-SI 485
N +D PGHA + + GA D A+LV+AA + MPQ E I A+ V I
Sbjct: 72 TANRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLARQVGVPYI 131
Query: 486 IVAINKIDKLGADPQ-------KVRMSLLKHDVFVES----MGGDILDVEISAKNNLNLD 534
+V +NK+D + D + +VR L ++ + G + +E AK ++
Sbjct: 132 VVFLNKVD-MVDDEELLELVEMEVRELLSEYGFPGDDTPIIRGSALKALEGDAKWEAKIE 190
Query: 535 KLLDAILLQAEMLDLKTSINRKAEGIVVEGKLD-RGRGPVVTVLVQKGTLSKGNILVV 591
+L+DA+ + K + VE GRG VVT V++G L G + +
Sbjct: 191 ELMDAV---DSYIPTPERDIDKPFLMPVEDVFSISGRGTVVTGRVERGILKVGEEVEI 245
>gnl|CDD|133289 cd01889, SelB_euk, SelB subfamily. 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 = 67.0 bits (164), Expect = 2e-11
Identities = 44/167 (26%), Positives = 76/167 (45%), Gaps = 24/167 (14%)
Query: 386 VTIMGHVDHGKTSLLDAI-RKADVA------KGEIGGITQHIG------------AYQVA 426
V ++GHVD GKTSL A+ A A + + GIT +G +
Sbjct: 3 VGVLGHVDSGKTSLAKALSEIASTAAFDKNPQSQERGITLDLGFSSFYVDKPKHLRELIN 62
Query: 427 YQGKN--ITFLDTPGHAAFYEMRARGARVTDIAVLVLAADEEIMPQAIESINHAKAADVS 484
+N IT +D PGHA+ GA++ D+ +LV+ A + I Q E + +
Sbjct: 63 PGEENLQITLVDCPGHASLIRTIIGGAQIIDLMLLVVDATKGIQTQTAECLVIGEILCKK 122
Query: 485 IIVAINKIDKLGADPQKVRMSLLK---HDVFVESMGGDILDVEISAK 528
+IV +NKID + + ++ ++ +K ++ + + +SAK
Sbjct: 123 LIVVLNKIDLIPEEERERKIEKMKKKLQKTLEKTRFKNSPIIPVSAK 169
>gnl|CDD|133368 cd04168, TetM_like, Tet(M)-like subfamily. 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-11
Identities = 52/185 (28%), Positives = 86/185 (46%), Gaps = 32/185 (17%)
Query: 388 IMGHVDHGKTSLL-------DAIRKA-DVAKG-------EIG---GITQHIGAYQVAYQG 429
I+ HVD GKT+L AIRK V KG E+ GIT I + ++Q
Sbjct: 4 ILAHVDAGKTTLTESLLYTSGAIRKLGSVDKGTTRTDTMELERQRGIT--IFSAVASFQW 61
Query: 430 KN--ITFLDTPGHAAF-YEMRARGARVTDIAVLVLAADEEIMPQAIESINHA-KAADVSI 485
++ + +DTPGH F E+ R V D A+LV++A E + Q + + ++
Sbjct: 62 EDTKVNLIDTPGHMDFIAEVE-RSLSVLDGAILVISAVEGVQAQT-RILWRLLRKLNIPT 119
Query: 486 IVAINKIDKLGADPQKVRMSL---LKHDVFVESMGGDILDVEISAKNNLNLDKLLDAILL 542
I+ +NKID+ GAD +KV + L D+ G ++ + + + D+ + +
Sbjct: 120 IIFVNKIDRAGADLEKVYQEIKEKLSSDIVPMQKVGLAPNICETNEID---DEFWETLAE 176
Query: 543 QAEML 547
+ L
Sbjct: 177 GDDEL 181
>gnl|CDD|177010 CHL00071, tufA, elongation factor Tu.
Length = 409
Score = 65.4 bits (160), Expect = 6e-11
Identities = 54/150 (36%), Positives = 73/150 (48%), Gaps = 30/150 (20%)
Query: 387 TIMGHVDHGKTSLLDAIRKA---------------DVAKGEIG-GITQHIGAYQVAYQGK 430
TI GHVDHGKT+L AI D A E GIT I V Y+ +
Sbjct: 17 TI-GHVDHGKTTLTAAITMTLAAKGGAKAKKYDEIDSAPEEKARGIT--INTAHVEYETE 73
Query: 431 NITF--LDTPGHAAFYEMRARGARVTDIAVLVLAADEEIMPQAIESINHAKAADV-SIIV 487
N + +D PGHA + + GA D A+LV++A + MPQ E I AK V +I+V
Sbjct: 74 NRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTKEHILLAKQVGVPNIVV 133
Query: 488 AINKIDKLGADPQ-------KVRMSLLKHD 510
+NK D++ D + +VR L K+D
Sbjct: 134 FLNKEDQVD-DEELLELVELEVRELLSKYD 162
Score = 33.8 bits (78), Expect = 0.19
Identities = 29/103 (28%), Positives = 49/103 (47%), Gaps = 24/103 (23%)
Query: 766 IYDLLDSIKDSMSELLSPEIRETFLGNAEVLEVFAVTKLGNVAGCKVSEGKVERGS---- 821
IY+L+D++ DS + + FL E +VF++T G VA G++ERG+
Sbjct: 199 IYNLMDAV-DSYIPTPERDTDKPFLMAIE--DVFSITGRGTVA-----TGRIERGTVKVG 250
Query: 822 ------GVRLIRNSTVIYEGKLKTLKRFKDEVSEVHAGQDCGM 858
G+R + +TV L+ F+ + E AG + G+
Sbjct: 251 DTVEIVGLRETKTTTVT------GLEMFQKTLDEGLAGDNVGI 287
>gnl|CDD|35686 KOG0465, KOG0465, KOG0465, Mitochondrial elongation factor
[Translation, ribosomal structure and biogenesis].
Length = 721
Score = 61.8 bits (150), Expect = 7e-10
Identities = 41/139 (29%), Positives = 56/139 (40%), Gaps = 18/139 (12%)
Query: 386 VTIMGHVDHGKTSLLDAIRKADVAKGEIG------------------GITQHIGAYQVAY 427
+ I H+D GKT+L + + IG GIT A +
Sbjct: 42 IGISAHIDAGKTTLTERMLYYTGRIKHIGEVRGGGATMDSMELERQRGITIQSAATYFTW 101
Query: 428 QGKNITFLDTPGHAAFYEMRARGARVTDIAVLVLAADEEIMPQAIESINHAKAADVSIIV 487
+ I +DTPGH F R RV D AVLVL A + Q K +V I
Sbjct: 102 RDYRINIIDTPGHVDFTFEVERALRVLDGAVLVLDAVAGVESQTETVWRQMKRYNVPRIC 161
Query: 488 AINKIDKLGADPQKVRMSL 506
INK+D++GA P + +
Sbjct: 162 FINKMDRMGASPFRTLNQI 180
>gnl|CDD|33865 COG4108, PrfC, Peptide chain release factor RF-3 [Translation,
ribosomal structure and biogenesis].
Length = 528
Score = 61.4 bits (149), Expect = 1e-09
Identities = 42/134 (31%), Positives = 58/134 (43%), Gaps = 22/134 (16%)
Query: 388 IMGHVDHGKTSLLD-------AIRKADVAKGEIG---------------GITQHIGAYQV 425
I+ H D GKT+L + AI++A KG GI+ Q
Sbjct: 17 IISHPDAGKTTLTEKLLLFGGAIQEAGTVKGRKSGKHAKSDWMEIEKQRGISVTSSVMQF 76
Query: 426 AYQGKNITFLDTPGHAAFYEMRARGARVTDIAVLVLAADEEIMPQAIESINHAKAADVSI 485
Y + LDTPGH F E R D AV+V+ A + I PQ ++ + D+ I
Sbjct: 77 DYADCLVNLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKGIEPQTLKLFEVCRLRDIPI 136
Query: 486 IVAINKIDKLGADP 499
INK+D+ G DP
Sbjct: 137 FTFINKLDREGRDP 150
>gnl|CDD|34854 COG5257, GCD11, Translation initiation factor 2, gamma subunit
(eIF-2gamma; GTPase) [Translation, ribosomal structure
and biogenesis].
Length = 415
Score = 61.0 bits (148), Expect = 1e-09
Identities = 58/204 (28%), Positives = 90/204 (44%), Gaps = 48/204 (23%)
Query: 377 SDLDIRPPVVTI--MGHVDHGKTSLLDAIR--KADVAKGEIG-GITQHIG---------- 421
+D P V I +GHVDHGKT+L A+ D E+ GIT +G
Sbjct: 2 ADPKHIQPEVNIGMVGHVDHGKTTLTKALSGVWTDRHSEELKRGITIKLGYADAKIYKCP 61
Query: 422 ------AYQVAYQGKN----------ITFLDTPGHAAFYEMRARGARVTDIAVLVLAADE 465
Y + N ++F+D PGH GA + D A+LV+AA+E
Sbjct: 62 ECYRPECYTTEPKCPNCGAETELVRRVSFVDAPGHETLMATMLSGAALMDGALLVIAANE 121
Query: 466 EI-MPQAIESINHAKAADV----SIIVAINKIDKLGADPQKVRMSLLKHDVFVESMGGDI 520
PQ E H A ++ +II+ NKID + ++ + + FV+ G +
Sbjct: 122 PCPQPQTRE---HLMALEIIGIKNIIIVQNKIDLV--SRERALENYEQIKEFVK---GTV 173
Query: 521 LD----VEISAKNNLNLDKLLDAI 540
+ + ISA++ N+D L++AI
Sbjct: 174 AENAPIIPISAQHKANIDALIEAI 197
>gnl|CDD|58078 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 = 61.1 bits (148), Expect = 1e-09
Identities = 30/82 (36%), Positives = 45/82 (54%), Gaps = 1/82 (1%)
Query: 793 AEVLEVFAVTKLGNVAGCKVSEGKVERGSGVRLIRNSTVIYEGKLKTLKRFKDEVSEVHA 852
A V +VF G VA +V G +++G VR+ + +GK+K+LKRFK EV E A
Sbjct: 3 ALVFKVFKDKGRGTVATGRVESGTLKKGDKVRVGPGGGGV-KGKVKSLKRFKGEVDEAVA 61
Query: 853 GQDCGMAFEKYDNIQAGDMIEC 874
G G+ + D+I+ GD +
Sbjct: 62 GDIVGIVLKDKDDIKIGDTLTD 83
Score = 38.4 bits (89), Expect = 0.010
Identities = 23/94 (24%), Positives = 37/94 (39%), Gaps = 12/94 (12%)
Query: 557 AEGIVVEGKLDRGRGPVVTVLVQKGTLSKGNILVVGDQWGKIRALFNDRGQGISKAVPSM 616
+V + D+GRG V T V+ GTL KG+ + VG G ++ + +
Sbjct: 1 LRALVFKVFKDKGRGTVATGRVESGTLKKGDKVRVGPGGGGVKGKVK----SLKRF---- 52
Query: 617 PIEVLGLQGMPMAGDKFGVVDSESRAREIAQYRQ 650
G +AGD G+V + +I
Sbjct: 53 ----KGEVDEAVAGDIVGIVLKDKDDIKIGDTLT 82
>gnl|CDD|133285 cd01885, EF2, EF2 (for 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 = 222
Score = 60.3 bits (147), Expect = 2e-09
Identities = 36/136 (26%), Positives = 56/136 (41%), Gaps = 26/136 (19%)
Query: 386 VTIMGHVDHGKTSLLDA-IRKADVAKGEIGG---------------IT--------QHIG 421
+ I+ HVDHGKT+L D+ + A + ++ G IT
Sbjct: 3 ICIIAHVDHGKTTLSDSLLASAGIISEKLAGKARYMDSREDEQERGITMKSSAISLYFEY 62
Query: 422 AYQVAYQGKN--ITFLDTPGHAAFYEMRARGARVTDIAVLVLAADEEIMPQAIESINHAK 479
+ G I +D+PGH F R+ D A++V+ A E + Q + A
Sbjct: 63 EEEDKADGNEYLINLIDSPGHVDFSSEVTAALRLCDGALVVVDAVEGVCVQTETVLRQAL 122
Query: 480 AADVSIIVAINKIDKL 495
V ++ INKID+L
Sbjct: 123 KERVKPVLVINKIDRL 138
>gnl|CDD|133283 cd01883, EF1_alpha, Eukaryotic elongation factor 1 (EF1) alpha
subfamily. 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 = 58.6 bits (143), Expect = 7e-09
Identities = 50/192 (26%), Positives = 79/192 (41%), Gaps = 44/192 (22%)
Query: 388 IMGHVDHGKTSL-------LDAIRKADVAK-----GEIG-------------------GI 416
++GHVD GK++ L + K + K E+G G+
Sbjct: 4 VIGHVDAGKSTTTGHLLYLLGGVDKRTIEKYEKEAKEMGKGSFKYAWVLDTLKEERERGV 63
Query: 417 TQHIGAYQVAYQGKNITFLDTPGHAAFYEMRARGARVTDIAVLVLAADE-------EIMP 469
T +G + + T LD PGH F GA D+AVLV+ A + E
Sbjct: 64 TIDVGLAKFETEKYRFTILDAPGHRDFVPNMITGASQADVAVLVVDARKGEFEAGFEKGG 123
Query: 470 QAIESINHAKAADVS-IIVAINKIDKLGADPQKVRMSLLKHDV--FVESMGGDILDVE-- 524
Q E A+ V +IVA+NK+D + + + R +K ++ F++ +G + DV
Sbjct: 124 QTREHALLARTLGVKQLIVAVNKMDDVTVNWSEERYDEIKKELSPFLKKVGYNPKDVPFI 183
Query: 525 -ISAKNNLNLDK 535
IS NL +
Sbjct: 184 PISGLTGDNLIE 195
>gnl|CDD|31353 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 57.5 bits (139), Expect = 1e-08
Identities = 48/172 (27%), Positives = 73/172 (42%), Gaps = 30/172 (17%)
Query: 386 VTIMGHVDHGKTSLLDAIRKADVA---------KGEIGGITQHIGAYQVAYQGKNITFLD 436
V I+G + GK++LL+A+ ++ + I GI Q I F+D
Sbjct: 9 VAIIGRPNVGKSTLLNALVGQKISIVSPKPQTTRNRIRGIV-TTDNAQ-------IIFVD 60
Query: 437 TPG----HAAFYEMRARGARVT----DIAVLVLAADEEIMPQAIESINHAKAADVSIIVA 488
TPG A E+ + AR D+ + V+ ADE P + K +I+
Sbjct: 61 TPGIHKPKHALGELMNKAARSALKDVDLILFVVDADEGWGPGDEFILEQLKKTKTPVILV 120
Query: 489 INKIDKLGADPQKVRMSLLKHDVFVESMGGDILDVEISAKNNLNLDKLLDAI 540
+NKIDK+ LLK F++ + V ISA N+D LL+ I
Sbjct: 121 VNKIDKVKPK-----TVLLKLIAFLKKLLPFKEIVPISALKGDNVDTLLEII 167
>gnl|CDD|145217 pfam01926, MMR_HSR1, GTPase of unknown function.
Length = 106
Score = 57.7 bits (140), Expect = 2e-08
Identities = 26/106 (24%), Positives = 46/106 (43%), Gaps = 9/106 (8%)
Query: 395 GKTSLLDAIRKADVAK-GEIGGITQHIGAYQVAYQGKNITFLDTPG--HAAFYEMRARGA 451
GK++L++A+ A + G T+ +V GK I +DTPG A G
Sbjct: 1 GKSTLINALTGKKRAIVSDYPGTTRDPNEGRVELDGKQIILVDTPGIIEGASKGEGELGN 60
Query: 452 RV------TDIAVLVLAADEEIMPQAIESINHAKAADVSIIVAINK 491
R D+ + V+ A E + + +E ++ +I+ +NK
Sbjct: 61 RTLEAIEEADLILHVVDASEGLTEEDLEILDLLLELGKPVILVLNK 106
>gnl|CDD|34853 COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 428
Score = 56.8 bits (137), Expect = 3e-08
Identities = 46/198 (23%), Positives = 78/198 (39%), Gaps = 44/198 (22%)
Query: 382 RPPVVTI--MGHVDHGKTSLL------------DAIRKADVAKGEIG------------- 414
P + + +GHVD GK++L+ + K + E+G
Sbjct: 4 EKPHLNLVFIGHVDAGKSTLVGRLLYDLGEIDKRTMEKLEKEAKELGKESFKFAWVLDKT 63
Query: 415 ------GITQHIGAYQVAYQGKNITFLDTPGHAAFYEMRARGARVTDIAVLVLAADE--- 465
G+T + + N T +D PGH F + GA D+AVLV+ A +
Sbjct: 64 KEERERGVTIDVAHSKFETDKYNFTIIDAPGHRDFVKNMITGASQADVAVLVVDARDGEF 123
Query: 466 ----EIMPQAIESINHAKAADVS-IIVAINKIDKLGADPQKVRMSLLKHDVFVESMGGDI 520
+ Q E A+ + +IVA+NK+D + D ++ + + ++ +G +
Sbjct: 124 EAGFGVGGQTREHAFLARTLGIKQLIVAVNKMDLVSWDEERFEEIVSEVSKLLKMVGYNP 183
Query: 521 LDVE---ISAKNNLNLDK 535
DV IS NL K
Sbjct: 184 KDVPFIPISGFKGDNLTK 201
>gnl|CDD|35685 KOG0464, KOG0464, KOG0464, Elongation factor G [Translation,
ribosomal structure and biogenesis].
Length = 753
Score = 56.3 bits (135), Expect = 3e-08
Identities = 45/149 (30%), Positives = 60/149 (40%), Gaps = 24/149 (16%)
Query: 374 DSESDLDIRPPVVT------IMGHVDHGKTSLLD-------AIRKA-DVAKGEI------ 413
D +S I P + I+ H+D GKT+ + AI A DV G+
Sbjct: 22 DIKSLHSIINPAIAKIRNIGIIAHIDAGKTTTTERILYLAGAIHSAGDVDDGDTVTDFLA 81
Query: 414 ----GGITQHIGAYQVAYQGKNITFLDTPGHAAFYEMRARGARVTDIAVLVLAADEEIMP 469
GIT A ++G I +DTPGH F R RV D AV V A +
Sbjct: 82 IERERGITIQSAAVNFDWKGHRINLIDTPGHVDFRLEVERCLRVLDGAVAVFDASAGVEA 141
Query: 470 QAIESINHAKAADVSIIVAINKIDKLGAD 498
Q + A + INK+DKL A+
Sbjct: 142 QTLTVWRQADKFKIPAHCFINKMDKLAAN 170
>gnl|CDD|133288 cd01888, eIF2_gamma, eIF2-gamma (gamma subunit of initiation factor
2). 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 = 203
Score = 54.6 bits (132), Expect = 1e-07
Identities = 54/197 (27%), Positives = 82/197 (41%), Gaps = 55/197 (27%)
Query: 390 GHVDHGKTSLLDAIR--KADVAKGEIG-GITQHIGAYQVA---------------YQGKN 431
GHV HGK++L+ A+ K E+ IT +G Y A Y+ K
Sbjct: 7 GHVAHGKSTLVKALSGVWTVRFKEELERNITIKLG-YANAKIYKCPNCGCPRPYCYRSKE 65
Query: 432 -------------------ITFLDTPGHAAFYEMRARGARVTDIAVLVLAADEEI-MPQA 471
++F+D PGH GA V D A+L++AA+E PQ
Sbjct: 66 DSPECECPGCGGETKLVRHVSFVDCPGHEILMATMLSGAAVMDGALLLIAANEPCPQPQT 125
Query: 472 IESINHAKAADV----SIIVAINKIDKLGADPQKVRMSLLKHDVFVESMGGDILD----V 523
E H A ++ II+ NKID + ++ + + FV+ G I + +
Sbjct: 126 SE---HLAALEIMGLKHIIIVQNKIDLV--KEEQALENYEQIKKFVK---GTIAENAPII 177
Query: 524 EISAKNNLNLDKLLDAI 540
ISA+ N+D LL+ I
Sbjct: 178 PISAQLKYNIDVLLEYI 194
>gnl|CDD|31354 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 54.0 bits (130), Expect = 2e-07
Identities = 55/229 (24%), Positives = 90/229 (39%), Gaps = 24/229 (10%)
Query: 374 DSESDLDIRPPVVTIMGHVDHGKTSLLDAIRKAD-VAKGEIGGITQHIGAYQVAYQGKNI 432
+ E + + P + I+G + GK+SL++AI + V +I G T+ + G+
Sbjct: 169 EEEEEEETDPIKIAIIGRPNVGKSSLINAILGEERVIVSDIAGTTRDSIDIEFERDGRKY 228
Query: 433 TFLDTPG----------HAAFYEMRARGA-RVTDIAVLVLAADEEIMPQAIESINHAKAA 481
+DT G + R A D+ +LV+ A E I Q + + A
Sbjct: 229 VLIDTAGIRRKGKITESVEKYSVARTLKAIERADVVLLVIDATEGISEQDLRIAGLIEEA 288
Query: 482 DVSIIVAINKIDKLGADPQ---KVRMSLLKHDVFVESMGGDILDVEISAKNNLNLDKLLD 538
I++ +NK D + D + + L + F+ V ISA LDKL +
Sbjct: 289 GRGIVIVVNKWDLVEEDEATMEEFKKKLRRKLPFL----DFAPIVFISALTGQGLDKLFE 344
Query: 539 AILLQAEMLDLKTS---INRKAEGIVVEGK--LDRGRGPVVTVLVQKGT 582
AI E + S +NR E V + + GR + Q T
Sbjct: 345 AIKEIYECATRRISTSLLNRVLEDAVAKHPPPVRYGRRLKIKYATQVST 393
Score = 53.6 bits (129), Expect = 2e-07
Identities = 44/172 (25%), Positives = 77/172 (44%), Gaps = 26/172 (15%)
Query: 383 PPVVTIMGHVDHGKTSLLDAI---RKADVAKGEIGGITQHIGAYQVAYQGKNITFLDTPG 439
PVV I+G + GK++L + + R A V+ + G+T+ + G+ +DT G
Sbjct: 3 TPVVAIVGRPNVGKSTLFNRLTGRRIAIVS--DTPGVTRDRIYGDAEWLGREFILIDTGG 60
Query: 440 -----HAAFYEMRARGARV----TDIAVLVLAADEEIMPQAIESINHAKAADVSIIVAIN 490
E+ A + D+ + V+ E I P E + + +I+ +N
Sbjct: 61 LDDGDEDELQELIREQALIAIEEADVILFVVDGREGITPADEEIAKILRRSKKPVILVVN 120
Query: 491 KIDKLGADPQKVRMSLLKHDVFVESMG-GDILDVEISAKNNLNLDKLLDAIL 541
KID L A+ ++ + S+G G+ V ISA++ + LLDA+L
Sbjct: 121 KIDNLKAEEL-------AYEFY--SLGFGEP--VPISAEHGRGIGDLLDAVL 161
>gnl|CDD|35682 KOG0461, KOG0461, KOG0461, Selenocysteine-specific elongation
factor [Translation, ribosomal structure and
biogenesis].
Length = 522
Score = 53.9 bits (129), Expect = 2e-07
Identities = 58/235 (24%), Positives = 99/235 (42%), Gaps = 31/235 (13%)
Query: 383 PPV---VTIMGHVDHGKTSLLDAI-----------RKADVAKG---EIG--GITQHIGAY 423
PP + I+GHVD GKT+L A+ +G ++G +T A
Sbjct: 4 PPSNLNLGILGHVDSGKTTLARALSELGSTAAFDKHPQSTERGITLDLGFSTMTVLSPAR 63
Query: 424 QVAYQGKNITFLDTPGHAAFYEMRARGARVTDIAVLVLAADEEIMPQAIESINHAKAADV 483
+ T +D PGHA+ GA++ D+ +LV+ + Q E + +
Sbjct: 64 LPQGEQLQFTLVDCPGHASLIRTIIGGAQIIDLMILVIDVQKGKQTQTAECLIIGELLCK 123
Query: 484 SIIVAINKIDKL--GADPQKVRMSLLKHDVFVESMG--GDILDVEISAKNNLNLDKLLDA 539
++V INKID L K+ S K +ES G G+ VE+SA + ++++
Sbjct: 124 KLVVVINKIDVLPENQRASKIEKSAKKVRKTLESTGFDGNSPIVEVSAADGYFKEEMIQE 183
Query: 540 ILLQAEMLDLKTSINRKAEGIVVEGKLD-----RGRGPVVTVLVQKGTLSKGNIL 589
+ E L+ + ++ E +D +G+G V+T V +G L +
Sbjct: 184 LK---EALESRIFEPKRDEEGPFLMAVDHCFAIKGQGTVLTGTVLRGVLRLNTEI 235
>gnl|CDD|133369 cd04169, RF3, RF3 subfamily. 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 = 267
Score = 51.0 bits (123), Expect = 1e-06
Identities = 44/134 (32%), Positives = 59/134 (44%), Gaps = 22/134 (16%)
Query: 388 IMGHVDHGKTSLLD-------AIRKADVAKG------------EIG---GITQHIGAYQV 425
I+ H D GKT+L + AIR+A K EI GI+ Q
Sbjct: 7 IISHPDAGKTTLTEKLLLFGGAIREAGAVKARKSRKHATSDWMEIEKQRGISVTSSVMQF 66
Query: 426 AYQGKNITFLDTPGHAAFYEMRARGARVTDIAVLVLAADEEIMPQAIESINHAKAADVSI 485
Y+ I LDTPGH F E R D AV+V+ A + + PQ + + + I
Sbjct: 67 EYRDCVINLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKGVEPQTRKLFEVCRLRGIPI 126
Query: 486 IVAINKIDKLGADP 499
I INK+D+ G DP
Sbjct: 127 ITFINKLDREGRDP 140
>gnl|CDD|133286 cd01886, EF-G, Elongation factor G (EF-G) subfamily. 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 = 50.9 bits (123), Expect = 2e-06
Identities = 41/133 (30%), Positives = 55/133 (41%), Gaps = 18/133 (13%)
Query: 388 IMGHVDHGKTSLLD-------AIRKA-DVAKGEIG----------GITQHIGAYQVAYQG 429
I+ H+D GKT+ + I K +V G GIT A ++
Sbjct: 4 IIAHIDAGKTTTTERILYYTGRIHKIGEVHGGGATMDFMEQERERGITIQSAATTCFWKD 63
Query: 430 KNITFLDTPGHAAFYEMRARGARVTDIAVLVLAADEEIMPQAIESINHAKAADVSIIVAI 489
I +DTPGH F R RV D AV V A + PQ A +V I +
Sbjct: 64 HRINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVAGVEPQTETVWRQADRYNVPRIAFV 123
Query: 490 NKIDKLGADPQKV 502
NK+D+ GAD +V
Sbjct: 124 NKMDRTGADFFRV 136
>gnl|CDD|133295 cd01895, EngA2, EngA2 subfamily. This 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 = 48.6 bits (117), Expect = 7e-06
Identities = 46/177 (25%), Positives = 74/177 (41%), Gaps = 23/177 (12%)
Query: 382 RPPVVTIMGHVDHGKTSLLDAIRKAD-VAKGEIGGITQHIGAYQVAYQGKNITFLDTPG- 439
P + I+G + GK+SL++A+ + V +I G T+ Y GK T +DT G
Sbjct: 1 DPIRIAIIGRPNVGKSSLVNALLGEERVIVSDIAGTTRDSIDVPFEYDGKKYTLIDTAGI 60
Query: 440 --------HAAFYE-MRARGA-RVTDIAVLVLAADEEIMPQAIESINHAKAADVSIIVAI 489
Y +R A D+ +LV+ A E I Q + ++++ +
Sbjct: 61 RRKGKVEEGIEKYSVLRTLKAIERADVVLLVIDATEGITEQDLRIAGLILEEGKALVIVV 120
Query: 490 NKIDKLGADPQKVRMSLLKHDV-----FVESMGGDILDVEISAKNNLNLDKLLDAIL 541
NK D + + M K ++ F++ I V ISA +DKL DAI
Sbjct: 121 NKWDLV--EKDSKTMKEFKKEIRRKLPFLD--YAPI--VFISALTGQGVDKLFDAID 171
>gnl|CDD|147093 pfam04760, IF2_N, Translation initiation factor IF-2, N-terminal
region. This conserved feature at the N-terminus of
bacterial translation initiation factor IF2 has recently
had its structure solved. It shows structural similarity
to the tRNA anticodon Stem Contact Fold domains of the
methionyl-tRNA and glutaminyl-tRNA synthetases, and a
similar fold is also found in the B5 domain of the
phenylalanine-tRNA synthetase.
Length = 52
Score = 48.6 bits (117), Expect = 8e-06
Identities = 16/50 (32%), Positives = 28/50 (56%)
Query: 305 PETITIQELSQRMSERSADVIKFLMKEGQIMKPGDVIDADLSEIIANEFG 354
E I + EL++ + S ++IK L K G + +D + +E++A EFG
Sbjct: 1 MEKIRVYELAKELGVSSKELIKKLFKLGIMKTHNSTLDEETAELLAEEFG 50
>gnl|CDD|30833 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 48.3 bits (115), Expect = 9e-06
Identities = 57/241 (23%), Positives = 98/241 (40%), Gaps = 31/241 (12%)
Query: 312 ELSQRMSERSADVIKFLMK-EGQIMKPGDVIDADLSEIIANEFGNTVKRVLESDIEVGIF 370
LSQ ++E +++ L + E I P + I+ + E I + + + E
Sbjct: 152 ALSQLINELREALLELLAQVEANIDFPEEDIEELVLEKIREKLEELIAELDEL------- 204
Query: 371 DVADSESDLDIRPPV-VTIMGHVDHGKTSLLDAIRKADVA-KGEIGGITQHIGAYQVAYQ 428
+A ++ +R + V I+G + GK+SLL+A+ D A +I G T+ + +
Sbjct: 205 -LATAKQGKILREGLKVVIIGRPNVGKSSLLNALLGRDRAIVTDIAGTTRDVIEEDINLN 263
Query: 429 GKNITFLDTPG---HAAFYEM----RARGARVT-DIAVLVLAADEEIMPQAIESINHAKA 480
G + +DT G E RA+ A D+ + VL A + + + + I
Sbjct: 264 GIPVRLVDTAGIRETDDVVERIGIERAKKAIEEADLVLFVLDASQPLDKEDLALIELLPK 323
Query: 481 ADVSIIVAINKIDKLGADPQKVRMSLLKHDVFVESMGGDILDVEISAKNNLNLDKLLDAI 540
IIV +NK D + + E + + ISAK LD L +AI
Sbjct: 324 -KKPIIVVLNKADLVSKIELES-----------EKLANGDAIISISAKTGEGLDALREAI 371
Query: 541 L 541
Sbjct: 372 K 372
>gnl|CDD|133363 cd04163, Era, Era subfamily. 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 = 48.2 bits (116), Expect = 1e-05
Identities = 31/118 (26%), Positives = 50/118 (42%), Gaps = 13/118 (11%)
Query: 432 ITFLDTPG----HAAFYEMRARGARVT----DIAVLVLAADEEIMPQAIESINHAKAADV 483
I F+DTPG E + A D+ + V+ A E I + K +
Sbjct: 53 IIFVDTPGIHKPKKKLGERMVKAAWSALKDVDLVLFVVDASEPIGEGDEFILELLKKSKT 112
Query: 484 SIIVAINKIDKLGADPQKVRMSLLKHDVFVESMGGDILDVEISAKNNLNLDKLLDAIL 541
+I+ +NKID + D + LL ++ +G ISA N+D+LL+ I+
Sbjct: 113 PVILVLNKIDLVK-DKED----LLPLLEKLKELGPFAEIFPISALKGENVDELLEEIV 165
>gnl|CDD|30567 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 46.8 bits (111), Expect = 2e-05
Identities = 35/174 (20%), Positives = 69/174 (39%), Gaps = 19/174 (10%)
Query: 383 PPVVTIMGHVDHGKTSLLDAI--RKADVAKGEIGGITQHIGAYQVAYQGKNITFLDTPGH 440
P + G + GK+SL++A+ +K + G TQ I ++V + +D PG+
Sbjct: 24 LPEIAFAGRSNVGKSSLINALTNQKNLARTSKTPGRTQLINFFEV---DDELRLVDLPGY 80
Query: 441 ---AAFYEMRARGARVTD----------IAVLVLAADEEIMPQAIESINHAKAADVSIIV 487
E++ + ++ + VL++ A E I + +IV
Sbjct: 81 GYAKVPKEVKEKWKKLIEEYLEKRANLKGVVLLIDARHPPKDLDREMIEFLLELGIPVIV 140
Query: 488 AINKIDKLGADPQKVRMSLLKHDVFVESMGGDILDVEISAKNNLNLDKLLDAIL 541
+ K DKL + +++ + + + D V S+ +D+L IL
Sbjct: 141 VLTKADKLKKSERNKQLNKVA-EELKKPPPDDQWVVLFSSLKKKGIDELKAKIL 193
>gnl|CDD|31297 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 46.5 bits (109), Expect = 3e-05
Identities = 36/191 (18%), Positives = 75/191 (39%), Gaps = 18/191 (9%)
Query: 386 VTIMGHVDHGKTSLLDAIRKADVAKGEIGGITQHIGAYQVAYQGKNITF--LDTPGHAAF 443
+ ++G GKT+LL+ + + +G I A + +NI DT G +
Sbjct: 8 IVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTAGQEEY 67
Query: 444 YEMRARGARVTDIAVLVLAAD-----EEIMPQAIESINHAKAADVSIIVAINKIDKLGAD 498
+R R + ++V + +E+ + +E + DV I++ NKID
Sbjct: 68 RSLRPEYYRGANGILIVYDSTLRESSDELTEEWLEELRELAPDDVPILLVGNKIDLFDEQ 127
Query: 499 PQ-KVRMSLLKHDVFVESMGGDILD--------VEISAKN--NLNLDKLLDAILLQAEML 547
+ ++ L +V + + + +E SAK+ N+++L +L +
Sbjct: 128 SSSEEILNQLNREVVLLVLAPKAVLPEVANPALLETSAKSLTGPNVNELFKELLRKLLEE 187
Query: 548 DLKTSINRKAE 558
K + +
Sbjct: 188 IEKLVLKNELR 198
>gnl|CDD|35680 KOG0459, KOG0459, KOG0459, Polypeptide release factor 3
[Translation, ribosomal structure and biogenesis].
Length = 501
Score = 46.1 bits (109), Expect = 4e-05
Identities = 53/184 (28%), Positives = 76/184 (41%), Gaps = 22/184 (11%)
Query: 430 KNITFLDTPGHAAFYEMRARGARVTDIAVLVLAA-------DEEIMPQAIESINHAKAAD 482
K T LD PGH +F GA D+AVLV++A E Q E AK A
Sbjct: 157 KRFTILDAPGHKSFVPNMIGGASQADLAVLVISARKGEFETGFEKGGQTREHAMLAKTAG 216
Query: 483 VS-IIVAINKIDKLGADPQKVRMSLLKHDV--FVESMGG----DILDVEISAKNNLNLDK 535
V +IV INK+D + R K + F+ +G D V +S N+
Sbjct: 217 VKHLIVLINKMDDPTVNWSNERYEECKEKLQPFLRKLGFNPKPDKHFVPVSGLTGANVKD 276
Query: 536 LLDAI------LLQAEMLDLKTSINRKAEGIVVEGKLDRGR--GPVVTVLVQKGTLSKGN 587
D++ + E LD + R G + ++ + G VV V+ G++ KG
Sbjct: 277 RTDSVCPWYKGPIFLEYLDELPHLERILNGPIRCPVANKYKDMGTVVGGKVESGSIKKGQ 336
Query: 588 ILVV 591
LVV
Sbjct: 337 QLVV 340
>gnl|CDD|133279 cd01878, HflX, 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 = 44.3 bits (106), Expect = 2e-04
Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 11/62 (17%)
Query: 479 KAADVSIIVAINKIDKLGADPQKVRMSLLKHDVFVESMGGDILDVEISAKNNLNLDKLLD 538
A D+ +I+ +NKID L + + R+ + D V ISAK LD+LL+
Sbjct: 150 GAEDIPMILVLNKIDLLDDEELEERLEAGRPDA-----------VFISAKTGEGLDELLE 198
Query: 539 AI 540
AI
Sbjct: 199 AI 200
>gnl|CDD|133278 cd01876, YihA_EngB, The YihA (EngB) subfamily. This 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 = 43.6 bits (104), Expect = 2e-04
Identities = 32/168 (19%), Positives = 63/168 (37%), Gaps = 34/168 (20%)
Query: 395 GKTSLLDAI--RKADVAKGEIGGITQHIGAYQVAYQGKNITFLDTPGHAAFY-------E 445
GK+SL++A+ RK + G TQ I + V +D PG Y E
Sbjct: 11 GKSSLINALTNRKKLARTSKTPGKTQLINFFNV---NDKFRLVDLPG----YGYAKVSKE 63
Query: 446 MRARGARVTD----------IAVLVLAADEEIMPQAIESINHAKAADVSIIVAINKIDKL 495
++ + ++ + VL++ + +E ++ + + +V + K DKL
Sbjct: 64 VKEKWGKLIEEYLENRENLKGVVLLIDSRHGPTEIDLEMLDWLEELGIPFLVVLTKADKL 123
Query: 496 GADPQKVRMSLLKHDVFVESMGGDILDVEI---SAKNNLNLDKLLDAI 540
+ +K + + +D I S+ +D+L I
Sbjct: 124 KKSELAKALKEIK-----KELKLFEIDPPIILFSSLKGQGIDELRALI 166
>gnl|CDD|32720 COG2895, CysN, GTPases - Sulfate adenylate transferase subunit 1
[Inorganic ion transport and metabolism].
Length = 431
Score = 43.3 bits (102), Expect = 3e-04
Identities = 39/176 (22%), Positives = 70/176 (39%), Gaps = 41/176 (23%)
Query: 390 GHVDHGKTSL---------------LDAIRKADVAKGEIG------------------GI 416
G VD GK++L L ++ + KG G GI
Sbjct: 13 GSVDDGKSTLIGRLLYDTKAIYEDQLASLERDSKRKGTQGEKIDLALLVDGLEAEREQGI 72
Query: 417 TQHIGAYQVAYQGKNITFLDTPGHAAFYEMRARGARVTDIAVLVLAADEEIMPQAIESIN 476
T + + + + DTPGH + A GA D+A+L++ A + ++ Q +
Sbjct: 73 TIDVAYRYFSTEKRKFIIADTPGHEQYTRNMATGASTADLAILLVDARKGVLEQ---TRR 129
Query: 477 HAKAADV----SIIVAINKIDKLGADPQKVRMSLLKHDVFVESMGG-DILDVEISA 527
H+ A + ++VA+NK+D + + + + F +G D+ + ISA
Sbjct: 130 HSFIASLLGIRHVVVAVNKMDLVDYSEEVFEAIVADYLAFAAQLGLKDVRFIPISA 185
>gnl|CDD|133294 cd01894, EngA1, EngA1 subfamily. This 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 = 43.2 bits (103), Expect = 3e-04
Identities = 29/130 (22%), Positives = 54/130 (41%), Gaps = 24/130 (18%)
Query: 423 YQVAYQGKNITFLDTPGHAAFYE-----MRA---RGARVTDIAVLVLAADEEIMPQAIES 474
+ + G+ +DT G E +R D+ + V+ E + P E
Sbjct: 38 GEAEWGGREFILIDTGGIEPDDEGISKEIREQAELAIEEADVILFVVDGREGLTPADEEI 97
Query: 475 INHAKAADVSIIVAINKIDKLGADPQKVRMSLLKHDVFVE--SMG-GDILDVEISAKNNL 531
+ + + +I+ +NK+D ++ + D E S+G G+ + ISA++
Sbjct: 98 AKYLRKSKKPVILVVNKVD-----------NIKEEDEAAEFYSLGFGEP--IPISAEHGR 144
Query: 532 NLDKLLDAIL 541
+ LLDAIL
Sbjct: 145 GIGDLLDAIL 154
>gnl|CDD|133281 cd01881, Obg_like, 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 = 176
Score = 42.9 bits (102), Expect = 4e-04
Identities = 41/179 (22%), Positives = 68/179 (37%), Gaps = 47/179 (26%)
Query: 395 GKTSLLDAIRKADVAKGEIGG-----ITQHIGAYQVAYQGKNITFLDTPG---HAAFYEM 446
GK++LL+A+ A ++ + ++G +V G I D PG A+
Sbjct: 8 GKSTLLNALTNAKP---KVANYPFTTLEPNLGVVEVPD-GARIQVADIPGLIEGAS---- 59
Query: 447 RARG--------ARVTDIAVLVL--AADEEIMP----QAIESINH----AKAADVS---- 484
RG R D + V+ + D++I + E +N +
Sbjct: 60 EGRGLGNQFLAHIRRADAILHVVDASEDDDIGGVDPLEDYEILNAELKLYDLETILGLLT 119
Query: 485 ---IIVAINKIDKLGADPQKVRMSLLKHDVFVESMGGDILDVEISAKNNLNLDKLLDAI 540
+I +NKID A+ L + V ++ V ISAK LD+L+ AI
Sbjct: 120 AKPVIYVLNKIDLDDAEE------LEEELVRELALEEGAEVVPISAKTEEGLDELIRAI 172
>gnl|CDD|32410 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 42.6 bits (100), Expect = 5e-04
Identities = 39/177 (22%), Positives = 71/177 (40%), Gaps = 22/177 (12%)
Query: 381 IRPPVVTIMGHVDHGKTSLL-----------DAIRKADVAKG-EIGGITQHIGAYQVAYQ 428
+ + ++G V GKT+ + +A + KG + G+ ++ +
Sbjct: 8 MIETKIVVIGPVGAGKTTFVRALSDKPLVITEADASSVSGKGKRPTTVAMDFGSIEL-DE 66
Query: 429 GKNITFLDTPGHAAFYEMRARGARVTDIAVLVLAADEEIMPQAIESINHAKA-ADVSIIV 487
+ TPG F M +R A++++ + I A E I+ + + ++V
Sbjct: 67 DTGVHLFGTPGQERFKFMWEILSRGAVGAIVLVDSSRPITFHAEEIIDFLTSRNPIPVVV 126
Query: 488 AINKIDKLGAD-PQKVRMSLLKHDVFVESMGGDILDVEISAKNNLNLDKLLDAILLQ 543
AINK D A P+K+R +L + V +EI A LD +LL+
Sbjct: 127 AINKQDLFDALPPEKIREALKLELLSVPV-------IEIDATEGEGARDQLDVLLLK 176
>gnl|CDD|145992 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 = 42.6 bits (101), Expect = 5e-04
Identities = 19/70 (27%), Positives = 36/70 (51%), Gaps = 3/70 (4%)
Query: 805 GNVAGCKVSEGKVERGSGVRLIRNSTVIYEGKLKTLKRFKDEVSEVHAGQDCGMAFE--K 862
G VA +V G +++G V + N T +G++ +L+ F ++ E AG + G+
Sbjct: 1 GTVATGRVESGTLKKGDKVVIGPNGT-GKKGRVTSLEMFHGDLREAVAGANAGIILAGIG 59
Query: 863 YDNIQAGDMI 872
+I+ GD +
Sbjct: 60 LKDIKRGDTL 69
Score = 35.7 bits (83), Expect = 0.058
Identities = 19/71 (26%), Positives = 34/71 (47%), Gaps = 8/71 (11%)
Query: 571 GPVVTVLVQKGTLSKGNILVVG----DQWGKIRALFNDRG---QGISKAVPSMPIEVLGL 623
G V T V+ GTL KG+ +V+G + G++ +L G + ++ A + + +GL
Sbjct: 1 GTVATGRVESGTLKKGDKVVIGPNGTGKKGRVTSLEMFHGDLREAVAGANAGIILAGIGL 60
Query: 624 QGMPMAGDKFG 634
+ GD
Sbjct: 61 KD-IKRGDTLT 70
>gnl|CDD|34855 COG5258, GTPBP1, GTPase [General function prediction only].
Length = 527
Score = 41.4 bits (97), Expect = 0.001
Identities = 67/300 (22%), Positives = 106/300 (35%), Gaps = 71/300 (23%)
Query: 357 VKRVLESDIEVGIFDVADSESDLDIRPPVVTIMGHVDHGKTSLLDAIRK----------- 405
V+ +D V V + V GHVDHGK++L+ +
Sbjct: 92 VRVHEGTDGYVAEVLVRRKTEEAPEHVLVGV-AGHVDHGKSTLVGVLVTGRLDDGDGATR 150
Query: 406 --ADVAKGEI-GGITQHIGAYQVAYQG-----------------------KNITFLDTPG 439
DV K E+ G++ I + K ++F+DT G
Sbjct: 151 SYLDVQKHEVERGLSADISLRVYGFDDGKVVRLKNPLDEAEKAAVVKRADKLVSFVDTVG 210
Query: 440 HAAFYEMRARG--ARVTDIAVLVLAADEEIMPQAIESINHAKAADVSIIVAINKIDKLGA 497
H + RG + D +LV+AAD+ + E + A A ++ +IV + KID +
Sbjct: 211 HEPWLRTTIRGLLGQKVDYGLLVVAADDGVTKMTKEHLGIALAMELPVIVVVTKIDMVPD 270
Query: 498 DP-QKVR---MSLLK------------HDVFVESMGGDILD-----VEISAKNNLNLDKL 536
D Q V +LLK DV + + S+ LD L
Sbjct: 271 DRFQGVVEEISALLKRVGRIPLIVKDTDDVVLAAKAMKAGRGVVPIFYTSSVTGEGLDLL 330
Query: 537 LDAILLQAEMLDLKTSINRKAEG----IVVEGKLDRGRGPVVTVLVQKGTLSKGNILVVG 592
+ LL L EG + + G G VV+ V+ G L G+ +++G
Sbjct: 331 DEFFLL------LPKRRRWDDEGPFLMYIDKIYSVTGVGTVVSGSVKSGILHVGDTVLLG 384
>gnl|CDD|133347 cd04147, Ras_dva, 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 = 198
Score = 41.3 bits (97), Expect = 0.001
Identities = 37/131 (28%), Positives = 54/131 (41%), Gaps = 9/131 (6%)
Query: 419 HIGAYQVAYQGKNITFLDTPGHAAFYEMRARGARVTDIAVLVLAADEEIMPQAIES---- 474
H Y+V + LDT G +F MR + +D LV A D+ + +E
Sbjct: 36 HRKEYEVGGVSLTLDILDTSGSYSFPAMRKLSIQNSDAFALVYAVDDPESFEEVERLREE 95
Query: 475 INHAKA-ADVSIIVAINKIDKLGADPQKVRMSLLKHDVFVESMGGDILDVEISAKNNLNL 533
I K V I+V NK D L + Q L + + VE SAK+N N+
Sbjct: 96 ILEVKEDKFVPIVVVGNKADSLEEERQVPAKDALS----TVELDWNCGFVETSAKDNENV 151
Query: 534 DKLLDAILLQA 544
++ +L QA
Sbjct: 152 LEVFKELLRQA 162
>gnl|CDD|32443 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 40.7 bits (95), Expect = 0.002
Identities = 44/198 (22%), Positives = 79/198 (39%), Gaps = 36/198 (18%)
Query: 384 PVVTIMGHVDHGKTSLLDAIRKADVA--------------KGEIGGITQHIGAYQVAYQG 429
P+V ++G+ + GK++L +A+ ADV + E+G + + V +
Sbjct: 193 PLVALVGYTNAGKSTLFNALTGADVYVADQLFATLDPTTRRIELGDGRKVLLTDTVGF-- 250
Query: 430 KNITFLDTPGHAAFYEMRARGARVTDIAVLVL-AADEEIMPQA---IESINHAKAADVSI 485
I L P AF + D+ + V+ A+D EI+ + + + A ++ I
Sbjct: 251 --IRDLPHPLVEAFKSTLEE-VKEADLLLHVVDASDPEILEKLEAVEDVLAEIGADEIPI 307
Query: 486 IVAINKIDKLGADPQKVRMSLLKHDVFVESMGGDILDVEISAKNNLNLDKLLDAI--LLQ 543
I+ +NKID L + + + V ISAK LD L + I LL
Sbjct: 308 ILVLNKIDLLEDEEILAELERGSPNP-----------VFISAKTGEGLDLLRERIIELLS 356
Query: 544 AEMLDLKTSINRKAEGIV 561
++ + G +
Sbjct: 357 GLRTEVTLELPYTDAGRL 374
>gnl|CDD|35679 KOG0458, KOG0458, KOG0458, Elongation factor 1 alpha [Translation,
ribosomal structure and biogenesis].
Length = 603
Score = 40.0 bits (93), Expect = 0.003
Identities = 34/133 (25%), Positives = 51/133 (38%), Gaps = 12/133 (9%)
Query: 415 GITQHIGAYQVAYQGKNITFLDTPGHAAFYEMRARGARVTDIAVLVLAADEEIMPQAIES 474
G+T + + K +T +D PGH F GA D+AVLV+ A +
Sbjct: 240 GVTMDVKTTWFESKSKIVTLIDAPGHKDFIPNMISGASQADVAVLVVDASTGEFESGFDP 299
Query: 475 IN----HAKAADV----SIIVAINKIDKLGADPQKVRMSLLKHDVFVESMGG----DILD 522
HA +IVAINK+D + + K F++ G +
Sbjct: 300 GGQTREHALLLRSLGISQLIVAINKMDLVSWSQDRFEEIKNKLSSFLKESCGFKESSVKF 359
Query: 523 VEISAKNNLNLDK 535
+ IS + NL K
Sbjct: 360 IPISGLSGENLIK 372
>gnl|CDD|35690 KOG0469, KOG0469, KOG0469, Elongation factor 2 [Translation,
ribosomal structure and biogenesis].
Length = 842
Score = 40.0 bits (93), Expect = 0.003
Identities = 30/141 (21%), Positives = 59/141 (41%), Gaps = 32/141 (22%)
Query: 386 VTIMGHVDHGKTSLLDA-IRKADVAKGEIGGITQHIGA-------------------YQV 425
++++ HVDHGK++L D+ ++KA + G T+ +++
Sbjct: 22 MSVIAHVDHGKSTLTDSLVQKAGIISAAKAGETRFTDTRKDEQERGITIKSTAISLFFEM 81
Query: 426 ------AYQGKN------ITFLDTPGHAAFYEMRARGARVTDIAVLVLAADEEIMPQAIE 473
+ + I +D+PGH F RVTD A++V+ + Q
Sbjct: 82 SDDDLKFIKQEGDGNGFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCVSGVCVQTET 141
Query: 474 SINHAKAADVSIIVAINKIDK 494
+ A A + ++ +NK+D+
Sbjct: 142 VLRQAIAERIKPVLVMNKMDR 162
>gnl|CDD|35687 KOG0466, KOG0466, KOG0466, Translation initiation factor 2, gamma
subunit (eIF-2gamma; GTPase) [Translation, ribosomal
structure and biogenesis].
Length = 466
Score = 39.5 bits (92), Expect = 0.004
Identities = 34/121 (28%), Positives = 60/121 (49%), Gaps = 17/121 (14%)
Query: 430 KNITFLDTPGHAAFYEMRARGARVTDIAVLVLAADEEI-MPQAIESINHAKAADV----S 484
++++F+D PGH GA V D A+L++A +E PQ E H A ++
Sbjct: 125 RHVSFVDCPGHDILMATMLNGAAVMDAALLLIAGNESCPQPQTSE---HLAAVEIMKLKH 181
Query: 485 IIVAINKIDKLGADPQKVRMSLLKHDVFVESMGGDILD----VEISAKNNLNLDKLLDAI 540
II+ NKID + K +L +H+ + + G + + + ISA+ N+D + + I
Sbjct: 182 IIILQNKIDLI-----KESQALEQHEQIQKFIQGTVAEGAPIIPISAQLKYNIDVVCEYI 236
Query: 541 L 541
+
Sbjct: 237 V 237
>gnl|CDD|133366 cd04166, CysN_ATPS, 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 = 208
Score = 38.6 bits (91), Expect = 0.007
Identities = 34/153 (22%), Positives = 55/153 (35%), Gaps = 56/153 (36%)
Query: 390 GHVDHGKTSL---------------LDAI--RKADVAKGEIG--------------GITQ 418
G VD GK++L L A+ + + GIT
Sbjct: 6 GSVDDGKSTLIGRLLYDSKSIFEDQLAALESKSCGTGGEPLDLALLVDGLQAEREQGIT- 64
Query: 419 HIGAYQVAYQGKNITF---------LDTPGHAAFYEMRARGARVTDIAVLVLAADEEIMP 469
I VAY F DTPGH + GA D+A+L++ A + ++
Sbjct: 65 -I---DVAY----RYFSTPKRKFIIADTPGHEQYTRNMVTGASTADLAILLVDARKGVLE 116
Query: 470 QAIESINHAKAADV----SIIVAINKIDKLGAD 498
Q + H+ + ++VA+NK+D +
Sbjct: 117 Q---TRRHSYILSLLGIRHVVVAVNKMDLVDYS 146
>gnl|CDD|133359 cd04159, Arl10_like, 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 = 38.8 bits (91), Expect = 0.007
Identities = 42/164 (25%), Positives = 63/164 (38%), Gaps = 22/164 (13%)
Query: 386 VTIMGHVDHGKTSLLDAIRKADVAKGEIGGITQHIGAYQVAYQGKNITFLDTPGHAAFYE 445
+T++G + GKT+L++ I ++ I T +V + D G F
Sbjct: 2 ITLVGLQNSGKTTLVNVIAGGQFSEDTIP--TVGFNMRKVTKGNVTLKVWDLGGQPRFRS 59
Query: 446 MRARGARVTDIAVLVL-AADEEIMPQAIES----INHAKAADVSIIVAINKIDKLGADPQ 500
M R R + V V+ AAD + A + + ++V NK D GA
Sbjct: 60 MWERYCRGVNAIVYVVDAADRTALEAAKNELHDLLEKPSLEGIPLLVLGNKNDLPGA--- 116
Query: 501 KVRMSLLKHDVFVESMG-GDILDVE-----ISAKNNLNLDKLLD 538
L D +E M I D E IS K N+D +LD
Sbjct: 117 ------LSVDELIEQMNLKSITDREVSCYSISCKEKTNIDIVLD 154
>gnl|CDD|133364 cd04164, trmE, 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 = 157
Score = 38.6 bits (91), Expect = 0.008
Identities = 21/87 (24%), Positives = 32/87 (36%), Gaps = 15/87 (17%)
Query: 455 DIAVLVLAADEEIMPQAIESINHAKAADVSIIVAINKIDKLGADPQKVRMSLLKHDVFVE 514
D+ + V+ D + AD IIV +NK D L ++
Sbjct: 82 DLVLFVI--DASRGLDEEDLEILELPADKPIIVVLNKSDLLPDSELLSLLAGKPI----- 134
Query: 515 SMGGDILDVEISAKNNLNLDKLLDAIL 541
+ ISAK LD+L +A+L
Sbjct: 135 --------IAISAKTGEGLDELKEALL 153
>gnl|CDD|35298 KOG0075, KOG0075, KOG0075, GTP-binding ADP-ribosylation factor-like
protein [General function prediction only].
Length = 186
Score = 38.4 bits (89), Expect = 0.009
Identities = 43/173 (24%), Positives = 69/173 (39%), Gaps = 22/173 (12%)
Query: 386 VTIMGHVDHGKTSLLDAIRKADVAKGEIGGITQHIGAYQVAYQGKNITFLDTPGHAAFYE 445
++++G + GKT+L++ I + E T +V I D G F
Sbjct: 23 LSLVGLQNSGKTTLVNVIARGQYL--EDMIPTVGFNMRKVTKGNVTIKLWDLGGQPRFRS 80
Query: 446 MRARGARVTDIAVLVL-AADEEIMPQAIESIN----HAKAADVSIIVAINKIDKLGADPQ 500
M R R V V+ AAD + + + ++ + ++V NKID GA
Sbjct: 81 MWERYCRGVSAIVYVVDAADPDKLEASRSELHDLLDKPSLTGIPLLVLGNKIDLPGA--- 137
Query: 501 KVRMSLLKHDVFVESMG-GDILDVE-----ISAKNNLNLDKLLDAILLQAEML 547
L +E MG I D E IS K +N+D LD ++ ++ L
Sbjct: 138 ------LSKIALIERMGLSSITDREVCCFSISCKEKVNIDITLDWLIEHSKSL 184
>gnl|CDD|30719 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 37.9 bits (88), Expect = 0.013
Identities = 40/171 (23%), Positives = 75/171 (43%), Gaps = 19/171 (11%)
Query: 384 PVVTIMGHVDHGKTSLLDAIRKADVAKGEIGGITQHIGAYQVAYQGKNITFLDTPGHAAF 443
V ++G+ + GKT+L +A+ A+ G G+T ++ Y+G I +D PG
Sbjct: 4 LTVALVGNPNVGKTTLFNALTGANQKVGNWPGVTVEKKEGKLKYKGHEIEIVDLPG---T 60
Query: 444 YEMRARGA--RVT-------DIAVLVLAADEEIMPQAIESINHAKAADVSIIVAINKIDK 494
Y + A +V ++V D + + + + +I+A+N ID+
Sbjct: 61 YSLTAYSEDEKVARDFLLEGKPDLIVNVVDATNLERNLYLTLQLLELGIPMILALNMIDE 120
Query: 495 LGADPQKVRMSLLKHDVFVESMGGDILDVEISAKNNLNLDKLLDAILLQAE 545
A + +R+ + K + +G + V AK L++L AI+ AE
Sbjct: 121 --AKKRGIRIDIEK---LSKLLGVPV--VPTVAKRGEGLEELKRAIIELAE 164
>gnl|CDD|33396 COG3596, COG3596, Predicted GTPase [General function prediction
only].
Length = 296
Score = 37.6 bits (87), Expect = 0.016
Identities = 25/138 (18%), Positives = 54/138 (39%), Gaps = 10/138 (7%)
Query: 368 GIFDVADSESDLDIRPPVVTIMGHVDHGKTSLLDAIRKADVAKGEIGGITQHIGAYQVAY 427
I + + P V +MG GK+SL++A+ + +V + G+ I
Sbjct: 24 RILEQLRMLQLTEKEPVNVLLMGATGAGKSSLINALFQGEVKEVSKVGVGTDITTRLRLS 83
Query: 428 Q-GKNITFLDTPGHAAFYEMRARGARV-------TDIAVLVLAADEEIMPQAIESINH-- 477
G+N+ DTPG + A ++ D+ + ++ AD+ + + +
Sbjct: 84 YDGENLVLWDTPGLGDGKDKDAEHRQLYRDYLPKLDLVLWLIKADDRALGTDEDFLRDVI 143
Query: 478 AKAADVSIIVAINKIDKL 495
D ++ + + D+
Sbjct: 144 ILGLDKRVLFVVTQADRA 161
>gnl|CDD|57926 cd01855, YqeH, YqeH. 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 = 190
Score = 36.8 bits (85), Expect = 0.025
Identities = 18/68 (26%), Positives = 34/68 (50%), Gaps = 7/68 (10%)
Query: 477 HAKAADVSIIVAINKIDKLGADPQKVRMSLLKHDVFVES---MGGDILDVE-ISAKNNLN 532
+ +I+ NKID L P+ + +K+ + ++ +G DV ISAK
Sbjct: 56 RLFGGNNPVILVGNKIDLL---PKDKNLVRIKNWLRAKAAAGLGLKPKDVILISAKKGWG 112
Query: 533 LDKLLDAI 540
+++L++AI
Sbjct: 113 VEELINAI 120
>gnl|CDD|35615 KOG0394, KOG0394, KOG0394, Ras-related GTPase [General function
prediction only].
Length = 210
Score = 36.9 bits (85), Expect = 0.025
Identities = 43/173 (24%), Positives = 68/173 (39%), Gaps = 21/173 (12%)
Query: 386 VTIMGHVDHGKTSLLDAI---RKADVAKGEIGGITQHIGAYQVAYQGKNITFLDTPGHAA 442
V I+G GKTSL++ + + K IG QV + + DT G
Sbjct: 12 VIILGDSGVGKTSLMNQYVNKKFSQQYKATIGADFLT-KEVQVDDRSVTLQIWDTAGQER 70
Query: 443 FYEMRARGARVTDIAVLVLAADEEIMPQAIESINH-----AKAADVS------IIVAINK 491
F + R D VLV + P++ E++ + A ++ NK
Sbjct: 71 FQSLGVAFYRGADCCVLVYDVNN---PKSFENLENWRKEFLIQASPQDPETFPFVILGNK 127
Query: 492 IDKLGADPQKVRMSLLKHDVFVESMGGDILDVEISAKNNLNLDKLLDAILLQA 544
ID G ++V K + +S G +I E SAK N+D+ + I +A
Sbjct: 128 IDVDGGKSRQVSEK--KAQTWCKSKG-NIPYFETSAKEATNVDEAFEEIARRA 177
>gnl|CDD|57927 cd01856, YlqF, YlqF. 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 a
phylogenetically diverse array of bacteria (including
gram-positive bacteria, proteobacteria, Synechocystis,
Borrelia, and Thermotoga) and in all eukaryotes..
Length = 171
Score = 36.7 bits (85), Expect = 0.026
Identities = 24/87 (27%), Positives = 42/87 (48%), Gaps = 4/87 (4%)
Query: 354 GNTVKRVLESDIEVGIFDVADSESDLDIRPPVVTIMGHVDHGKTSLLDAIRKADVAK-GE 412
G VK++L++ ++ L R ++G + GK++L++ +R VAK G
Sbjct: 86 GKGVKKLLKAAKKLLKDIEKLKAKGLLPRGIRAMVVGIPNVGKSTLINRLRGKKVAKVGN 145
Query: 413 IGGITQHIGAYQVAYQGKNITFLDTPG 439
G+T+ I ++ I LDTPG
Sbjct: 146 KPGVTKGIQWIKI---SPGIYLLDTPG 169
>gnl|CDD|36358 KOG1143, KOG1143, KOG1143, Predicted translation elongation factor
[Translation, ribosomal structure and biogenesis].
Length = 591
Score = 36.5 bits (84), Expect = 0.036
Identities = 35/166 (21%), Positives = 68/166 (40%), Gaps = 40/166 (24%)
Query: 365 IEVGIFDVADSESDLDIRPPVVTIMGHVDHGKTSLLDAIRKADV---------------- 408
+EV + V DS+ +++R V ++G D GK++LL + + ++
Sbjct: 152 VEVLVRKVPDSQQFIEVR---VAVLGGCDVGKSTLLGVLTQGELDNGNGRARLNIFRHPH 208
Query: 409 ------------------AKGEIGGITQHIGAYQVAYQG-KNITFLDTPGHAAFYEMRAR 449
+G++ Q++ A ++ + K +TF+D GHA + +
Sbjct: 209 EIQSGRTSSISNEVLGFDNRGKVVNYAQNMTAEEIVEKSSKLVTFIDLAGHAKYQKTTIH 268
Query: 450 G--ARVTDIAVLVLAADEEIMPQAIESINHAKAADVSIIVAINKID 493
G A LV++AD I E + A ++ V + K+D
Sbjct: 269 GLTGYTPHFACLVVSADRGITWTTREHLGLIAALNIPFFVLVTKMD 314
Score = 28.8 bits (64), Expect = 6.8
Identities = 22/102 (21%), Positives = 44/102 (43%), Gaps = 4/102 (3%)
Query: 767 YDLLDSIKDSMSELLSPEIRETFLGNA---EVLEVFAVTKLGNVAGCKVSEGKVERGSGV 823
LL + + +S + E R + +V E++ V +G V G +SEG++ G+ V
Sbjct: 376 LRLLRTFLNCLSPAGTAEERIQLVQLPAEFQVDEIYNVPHVGQVVGGMLSEGQLHEGADV 435
Query: 824 RL-IRNSTVIYEGKLKTLKRFKDEVSEVHAGQDCGMAFEKYD 864
+ + + +++R + V AGQ ++ D
Sbjct: 436 LVGPMKDGTFEKITVGSIRRNRQACRVVRAGQAASLSLNDPD 477
>gnl|CDD|36405 KOG1191, KOG1191, KOG1191, Mitochondrial GTPase [Translation,
ribosomal structure and biogenesis].
Length = 531
Score = 35.3 bits (81), Expect = 0.071
Identities = 45/223 (20%), Positives = 80/223 (35%), Gaps = 28/223 (12%)
Query: 343 ADLSEIIANEFGNTVKRVLESDIEVGIFDVADSESDLDIRPPVVTIMGHVDHGKTSLLDA 402
+ + E L +V E + + I+G + GK+SLL+A
Sbjct: 228 EEERPLEEIETVEIFIESLSLLDDVLSHLNKADEIERLQSGLQIAIVGRPNVGKSSLLNA 287
Query: 403 IRKADVA-KGEIGGITQHIGAYQVAYQGKNITFLDTPG--------HAAFYEMRAR-GAR 452
+ + D + + G T+ QV G + DT G A RAR
Sbjct: 288 LSREDRSIVSPVPGTTRDAIEAQVTVNGVPVRLSDTAGIREESNDGIEALGIERARKRIE 347
Query: 453 VTDIAVLVLAADEEIMPQAIE------------SINHAKAADVSIIVAINKIDKLGADPQ 500
D+ +LV+ A+E ++ + K II+ NK D + P+
Sbjct: 348 RADVILLVVDAEESDTESDLKIARILETEGVGLVVIVNKMEKQRIILVANKSDLVSKIPE 407
Query: 501 KVRMSLLKHDVFVESMGGDILD--VEISAKNNLNLDKLLDAIL 541
++ + V+ + G + VE+S ++L A+L
Sbjct: 408 MTKIPV----VYPSAEGRSVFPIVVEVSCTTKEGCERLSTALL 446
>gnl|CDD|35313 KOG0090, KOG0090, KOG0090, Signal recognition particle receptor,
beta subunit (small G protein superfamily)
[Intracellular trafficking, secretion, and vesicular
transport].
Length = 238
Score = 34.9 bits (80), Expect = 0.093
Identities = 35/182 (19%), Positives = 60/182 (32%), Gaps = 17/182 (9%)
Query: 383 PPVVTIMGHVDHGKTSLLDAIRKADVAKGEIGGITQHIGAYQVAYQGKNITFLDTPGHAA 442
V ++G D GKTSL + +G + I + Y+ +N+T +D PGH+
Sbjct: 38 QNAVLLVGLSDSGKTSLFTQLITGSH-RGTVTSIEPNEATYR--LGSENVTLVDLPGHSR 94
Query: 443 ----FYEMRARGARVTDIAVLV--LAADEEIMPQA-----IESINHAKAADVSIIVAINK 491
E I +V + + A I + K +++A NK
Sbjct: 95 LRRKLLEYLKHNYSAKAIVFVVDSATFLKNVRDVAEFLYDILLDSRVKKNKPPVLIACNK 154
Query: 492 IDKLGADPQKVRMSLLK---HDVFVESMGGDILDVEISAKNNLNLDKLLDAILLQAEMLD 548
D A + L+ H + + E AK+ + D E
Sbjct: 155 QDLFTAKTAEKIRQQLEKEIHKLRESRSALRSISDEDIAKDFTLGKEGEDFKFSHLEDQK 214
Query: 549 LK 550
+
Sbjct: 215 VT 216
>gnl|CDD|133254 cd00878, Arf_Arl, 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 = 34.9 bits (81), Expect = 0.11
Identities = 31/155 (20%), Positives = 55/155 (35%), Gaps = 23/155 (14%)
Query: 395 GKTSLLDAIRKADVAKGEIGGITQHIGAYQVAYQGKNITFLDTPGHAAFYEMRARGARVT 454
GKT++L ++ +V T V Y+ + T D G + T
Sbjct: 11 GKTTILYKLKLGEVVTTIP---TIGFNVETVEYKNVSFTVWDVGGQDKIRPLWKHYYENT 67
Query: 455 DIAVLVL-AADEEIMPQAIESI----NHAKAADVSIIVAINKIDKLGADPQKV------R 503
+ + V+ ++D E + +A E + N + V +++ NK D GA
Sbjct: 68 NGIIFVVDSSDRERIEEAKEELHKLLNEEELKGVPLLIFANKQDLPGALSVSELIEKLGL 127
Query: 504 MSLLKHDVFVESMGGDILDVEISAKNNLNLDKLLD 538
+L ++ SA LD+ LD
Sbjct: 128 EKILGRRWHIQP---------CSAVTGDGLDEGLD 153
>gnl|CDD|133343 cd04143, Rhes_like, Rhes_like subfamily. 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 = 34.7 bits (80), Expect = 0.12
Identities = 35/130 (26%), Positives = 58/130 (44%), Gaps = 25/130 (19%)
Query: 426 AYQGKNITFLDTPGHAAFYEMRARGARVTDIAVLVLAAD------------EEIMPQAIE 473
YQ + LDT G+ F MR D+ +LV + D E+I+
Sbjct: 47 VYQ---LDILDTSGNHPFPAMRRLSILTGDVFILVFSLDNRESFEEVCRLREQILETKSC 103
Query: 474 SINHAK-AADVSIIVAINKIDKLGADPQKVRMSLLKHDVFVESMGGDILDV--EISAKNN 530
N K + +++ NK D+ P++V+ + +V + +GGD E+SAK N
Sbjct: 104 LKNKTKENVKIPMVICGNKADR--DFPREVQ----RDEV-EQLVGGDENCAYFEVSAKKN 156
Query: 531 LNLDKLLDAI 540
NLD++ A+
Sbjct: 157 SNLDEMFRAL 166
>gnl|CDD|133298 cd01898, Obg, Obg subfamily. 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 = 34.7 bits (81), Expect = 0.13
Identities = 40/176 (22%), Positives = 68/176 (38%), Gaps = 49/176 (27%)
Query: 395 GKTSLLDAIRKADVAKGEIGG-----ITQHIGAYQVAYQGKNITFLDTPG---------- 439
GK++LL AI A K +I + ++G +V G++ D PG
Sbjct: 12 GKSTLLSAISNA---KPKIADYPFTTLVPNLGVVRV-DDGRSFVVADIPGLIEGASEGKG 67
Query: 440 -------HAAFYEMRARGARVTDIAVLV-LAADEEIMPQAIESINH------AKAADVSI 485
H R R + ++ L+ D++ + + ++I + + +
Sbjct: 68 LGHRFLRHIE----RTRL-----LLHVIDLSGDDDPV-EDYKTIRNELELYNPELLEKPR 117
Query: 486 IVAINKIDKLGADPQKVRMSLLKHDVFVESMGGDILDVEISAKNNLNLDKLLDAIL 541
IV +NKID L + LLK + E G + ISA LD+LL +
Sbjct: 118 IVVLNKIDLLDEEE---LFELLKELLK-ELWGKPV--FPISALTGEGLDELLRKLA 167
>gnl|CDD|35385 KOG0163, KOG0163, KOG0163, Myosin class VI heavy chain
[Cytoskeleton].
Length = 1259
Score = 33.5 bits (76), Expect = 0.24
Identities = 29/153 (18%), Positives = 61/153 (39%), Gaps = 1/153 (0%)
Query: 116 EIESRRRALHEAQVREEELRKRLEQQSLEQPSQESSIDLPEVCDSQQVPEQVLEDPCKEK 175
E E +RR E + REEE +KR + + + E + + +++ ++ E KE
Sbjct: 934 EAERKRREAEEKRRREEEEKKRAKAEMETKRKAEEEQRKAQEEEERRLALELQEQLAKEA 993
Query: 176 DLEIKDVDVGTEVESSVILSHDMGDSDSSSVVNNKFRESSSDASSNRGKSRGGAGKYASV 235
+ E K + + L+ + +SD V ++ + ++ + +V
Sbjct: 994 EEEAKRQNQLEQERRDHELALRLANSDGGQVEDSPPVIRALVNDASPMGPNKMLIRSENV 1053
Query: 236 NSSKPVTRNKVGDDDK-KYKKVRIAVAADVDEE 267
+ + + D K KY ++R + D E
Sbjct: 1054 RAQQAALGKQKYDLSKWKYAELRDTINTSCDIE 1086
>gnl|CDD|34868 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 33.5 bits (76), Expect = 0.26
Identities = 53/313 (16%), Positives = 111/313 (35%), Gaps = 32/313 (10%)
Query: 78 SSQDLSQAKAKGNFRRASRSDKVSSQKNDSSFAGLSQGEIESRRRALHEAQVREEELRKR 137
+ +DL + + K N + A+ ++ K D + A + E V ++ +
Sbjct: 3912 NEEDLLETEQKSNEQSAANNESDLVSKEDDNKALEDKDRQEKEDEEEMSDDVGIDDEIQP 3971
Query: 138 LEQQSLEQPSQE-SSIDLPEVCDSQQVPEQVLEDPCKEKDLEIKDVDVGTE--------- 187
Q++ QP E +DLPE + V +D DLE D++ E
Sbjct: 3972 DIQENNSQPPPENEDLDLPEDLKLDEKEGDVSKD----SDLEDMDMEAADENKEEADAEK 4027
Query: 188 ---------VESSVILSHDMGDSDSSSVVNNKFRES----SSDASSNRGKSRGGAGKYAS 234
+E + L D+ D S + + + + + N + G
Sbjct: 4028 DEPMQDEDPLEENNTLDEDIQQDDFSDLAEDDEKMNEDGFEENVQENEESTEDGVKSDEE 4087
Query: 235 VNSSKPVTRNKVGDDDKKYKKVRIAVAADVDEEGGASRGRSLSAMRRRQEKFRRN-QQQE 293
+ + V ++ D+ K +A+ DEE + ++ R N
Sbjct: 4088 LEQGE-VPEDQAIDNHPKMDAKSTFASAEADEENTDKGIVGENEELGEEDGVRGNGTADG 4146
Query: 294 KREKISREIVVPETITIQELSQRMSERSADVIKFLMKEGQIMKPGDVIDADLSEIIANEF 353
+ E++ + P+ + R + D ++ + +I + D+ ++ +EF
Sbjct: 4147 EFEQVQEDTSTPK--EAMSEADRQYQSLGDHLREWQQANRIHEWEDLTESQSQAFDDSEF 4204
Query: 354 GNTVKRVLESDIE 366
+ VK E D++
Sbjct: 4205 MH-VKEDEEEDLQ 4216
>gnl|CDD|35300 KOG0077, KOG0077, KOG0077, Vesicle coat complex COPII, GTPase
subunit SAR1 [Intracellular trafficking, secretion, and
vesicular transport].
Length = 193
Score = 33.4 bits (76), Expect = 0.31
Identities = 27/112 (24%), Positives = 45/112 (40%), Gaps = 16/112 (14%)
Query: 395 GKTSLLDAIRKADVAKGEIGGITQHIGAYQVAYQGKNITFLDTPGHAAFYEMRARGAR-- 452
GKT+LL ++ + + T H + +++ G T D GH R +
Sbjct: 32 GKTTLLHMLKDDRLGQHVP---TLHPTSEELSIGGMTFTTFDLGGHLQ----ARRVWKDY 84
Query: 453 ---VTDIAVLVLAADEEIMPQAIES----INHAKAADVSIIVAINKIDKLGA 497
V I LV A D+E ++ + ++ A V ++ NKID A
Sbjct: 85 FPQVDAIVYLVDAYDQERFAESKKELDALLSDESLATVPFLILGNKIDIPYA 136
>gnl|CDD|146992 pfam04615, Utp14, Utp14 protein. This protein is found to be part
of a large ribonucleoprotein complex containing the U3
snoRNA. Depletion of the Utp proteins impedes production
of the 18S rRNA, indicating that they are part of the
active pre-rRNA processing complex. This large RNP
complex has been termed the small subunit (SSU)
processome.
Length = 731
Score = 33.1 bits (76), Expect = 0.32
Identities = 37/193 (19%), Positives = 73/193 (37%), Gaps = 16/193 (8%)
Query: 121 RRALHEAQVREEELRKRLEQQSLEQPSQESSIDLPEVCDSQQVPEQVLEDPCKEKDLEIK 180
R AL E + EELR+++E +S+ + ++ D E + + E+P + K
Sbjct: 305 RAALEEQLRQGEELRRKIEGKSVSEEDEDEDSDSEEEDEDDDEDDDDGENPWMLRKKLGK 364
Query: 181 DVDVGTEVESSVILSHD-MGDSDSSSVVNNK------------FRESSSDASSNRGKSRG 227
+ + E+S +LS M +++ N + + K
Sbjct: 365 LKEGEDDEENSGLLSMKFMQRAEARRKEENDAEIEELRRELEGEESGDEEENEEPEKKNV 424
Query: 228 GAGKYASVNSSKPV---TRNKVGDDDKKYKKVRIAVAADVDEEGGASRGRSLSAMRRRQE 284
G K+ N K K ++ K KK DEE + + +R E
Sbjct: 425 GRRKFGPENLEKEAESKKLKKENKNEFKEKKSSDEEEELEDEEEDKVKEVVNKLLLKRSE 484
Query: 285 KFRRNQQQEKREK 297
K ++ +++E+ ++
Sbjct: 485 KAQKEEEEEELDE 497
>gnl|CDD|37213 KOG2002, KOG2002, KOG2002, TPR-containing nuclear phosphoprotein that
regulates K(+) uptake [Inorganic ion transport and
metabolism].
Length = 1018
Score = 33.0 bits (75), Expect = 0.41
Identities = 49/231 (21%), Positives = 83/231 (35%), Gaps = 33/231 (14%)
Query: 61 KVSVFRKSSRVIESSSDSSQDL-SQAKAKGNFRRASRSD-KVSSQKNDSSFAGLSQGEI- 117
K R S VI + +DL QA +A D + K + L + E+
Sbjct: 797 KNGDKRISKTVIAQEAQLCKDLLKQALEHV--AQAQEEDEEERRAKQEKEEEALIEKELE 854
Query: 118 ESRRRALHEAQVREEELRKRLEQQSLEQPSQESSIDLPEV------------CDSQQVPE 165
E+RR+ E RE+ ++R E + + ++ E DS E
Sbjct: 855 EARRKEEEEKARREKLEKQREEYRERTK-EILKLPEIEEEKKKSGGGGRKRGDDSDSDGE 913
Query: 166 QVLEDPCKEKDL-------EIKDVDVGTEVESSVILSHDMGDSDSSSVVNNKFRESSSDA 218
+ K+KD + + +E + S + S ++ +++ SD+
Sbjct: 914 RKKGGKRKKKDKKKRKRKPKKDSKEKLSESDRRKPKSKAFISTSERS-DDDVVKKAESDS 972
Query: 219 SSNRGKSRGGAGKYASVNSSKPVTRNKVGDDDKKYKKVRIAVAADVDEEGG 269
+ SR AS S +P+ + D D+ KK R D DEE
Sbjct: 973 DDDSQDSRE-----ASEESDRPIESD--SDSDETSKKDRNKELNDSDEESE 1016
>gnl|CDD|35616 KOG0395, KOG0395, KOG0395, Ras-related GTPase [General function
prediction only].
Length = 196
Score = 32.7 bits (74), Expect = 0.48
Identities = 41/142 (28%), Positives = 54/142 (38%), Gaps = 20/142 (14%)
Query: 434 FLDTPGHAAFYEMRARGARVTDIAVLVLAADE----EIMPQAIESINHAKAAD-VSIIVA 488
LDT G F MR R D +LV + + E Q E I K D V II+
Sbjct: 55 ILDTAGQEEFSAMRDLYIRNGDGFLLVYSITDRSSFEEAKQLREQILRVKGRDDVPIILV 114
Query: 489 INKIDKLGADPQKVRMSLLKHDVFVESMGGDILDVEISAKNNLNLDKLLDAILLQAEMLD 548
NK D ++V K S G +E SAK N N+D++ +
Sbjct: 115 GNKCD--LERERQVSEEEGKA--LARSWG--CAFIETSAKLNYNVDEVFY---------E 159
Query: 549 LKTSINRKAEGIVVEGKLDRGR 570
L I EG + KL G+
Sbjct: 160 LVREIRLPREGSLKGRKLSSGK 181
>gnl|CDD|39860 KOG4661, KOG4661, KOG4661, Hsp27-ERE-TATA-binding protein/Scaffold
attachment factor (SAF-B) [Transcription].
Length = 940
Score = 32.5 bits (73), Expect = 0.56
Identities = 26/101 (25%), Positives = 49/101 (48%), Gaps = 1/101 (0%)
Query: 49 TRKRRSYVQGEEKVSVFRKSSRVIESSSDSSQDLSQAKAKGNFRRASRSDKVSSQKNDSS 108
+R +S +G+E+ V KS S +SQD + ++K R++ +K + D
Sbjct: 555 SRSTKSGSRGKERTVVMDKSKGDPVISVKTSQDSKERRSKSQDRKSRSREKRRERSFDKR 614
Query: 109 FAGLSQGEIESRRRALHEAQVREEELRKRLEQQSLEQPSQE 149
+ E E R+R + E + RE+ + +E++ LE+ E
Sbjct: 615 KEERRRREAEERQR-IREEREREQRRKAAVEREELERLKAE 654
>gnl|CDD|37709 KOG2498, KOG2498, KOG2498, IK cytokine down-regulator of HLA class
II [Signal transduction mechanisms].
Length = 544
Score = 32.3 bits (73), Expect = 0.57
Identities = 36/242 (14%), Positives = 77/242 (31%), Gaps = 24/242 (9%)
Query: 49 TRKRRSYVQGEEKVSVFRKSSRVIESSSDSSQDLSQAKAKGNFRRASRSDKVSSQKNDSS 108
R Y + E+K + R+ + + + +A +R + + K D
Sbjct: 47 HEMPREYKEDEDKAARSREKKKALYGKLKKQHIEKEDEAALKYRDRAAERRDGVNK-DYE 105
Query: 109 FAGLSQGEIESRRRALHEAQVREEELRKRLEQQSLEQPSQESSIDLPEVCDSQQVPEQVL 168
L E + R++L Q+S L + D + +
Sbjct: 106 ETELPSTAQYRAVGPDAEKDKDQAIKRRQLIQESKFLGGDMEHTHLVKGLDYALLQKVRS 165
Query: 169 EDPCKEKDLEIKDVDVGTEVESSVILSHDMGDSDSSSVVNNKFRESSSDASSNRGKSRGG 228
E K+ + E + ++ + + S D + + R S + R
Sbjct: 166 EIAAKDDEEE-ELMEKPVDEKKS--------AEDPEEKIEAELRLGESGKVLKKKLGRNV 216
Query: 229 AGKYASVNSSKPVTRNKVGDDDKKYKKVRIAVAADVDEEGGASR-----GRSLSAMRRRQ 283
+ +NK + ++ + R+A +D+E + GRS + +Q
Sbjct: 217 YRV---------LFKNKEDERNELFAPGRMAYVVILDDEVLETDIPTTLGRSKLDLPTKQ 267
Query: 284 EK 285
E+
Sbjct: 268 EE 269
>gnl|CDD|35900 KOG0681, KOG0681, KOG0681, Actin-related protein - Arp5p
[Cytoskeleton].
Length = 645
Score = 32.3 bits (73), Expect = 0.57
Identities = 18/58 (31%), Positives = 28/58 (48%)
Query: 118 ESRRRALHEAQVREEELRKRLEQQSLEQPSQESSIDLPEVCDSQQVPEQVLEDPCKEK 175
+R A+ E ++LE + Q QES++DL + VP ++ ED KEK
Sbjct: 293 ALKRVEKINARENRREDEQQLESYNKAQGEQESNLDLEQKFPLLNVPAELDEDQLKEK 350
>gnl|CDD|31281 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 32.2 bits (73), Expect = 0.60
Identities = 15/62 (24%), Positives = 25/62 (40%)
Query: 378 DLDIRPPVVTIMGHVDHGKTSLLDAIRKADVAKGEIGGITQHIGAYQVAYQGKNITFLDT 437
+D P + + G+ + GK+SL+ + A T+ I I +DT
Sbjct: 163 AIDPDLPTIVVAGYPNVGKSSLVRKLTTAKPEVAPYPFTTKGIHVGHFERGYLRIQVIDT 222
Query: 438 PG 439
PG
Sbjct: 223 PG 224
>gnl|CDD|133296 cd01896, 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 = 32.1 bits (74), Expect = 0.61
Identities = 16/64 (25%), Positives = 24/64 (37%), Gaps = 16/64 (25%)
Query: 486 IVAINKIDKLGADPQKVRMSLLKHDVFVESMGGDILDVEISAKNNLNLDKLLDAILLQAE 545
+ NKID + + + V ISA+ LNLD+L + I +
Sbjct: 180 LYVYNKIDLISIEELDLLARQPNS-------------VVISAEKGLNLDELKERIW---D 223
Query: 546 MLDL 549
L L
Sbjct: 224 KLGL 227
>gnl|CDD|36247 KOG1029, KOG1029, KOG1029, Endocytic adaptor protein intersectin
[Signal transduction mechanisms, Intracellular
trafficking, secretion, and vesicular transport].
Length = 1118
Score = 32.0 bits (72), Expect = 0.65
Identities = 15/36 (41%), Positives = 23/36 (63%)
Query: 114 QGEIESRRRALHEAQVREEELRKRLEQQSLEQPSQE 149
Q E+E RR+AL E Q RE E ++ E++ E+ +E
Sbjct: 326 QAELERRRQALEEQQQREREEVEQKEREEEEKKERE 361
>gnl|CDD|48380 cd03116, MobB, Molybdenum is an essential trace element in the form
of molybdenum cofactor (Moco) which is associated with
the metabolism of nitrogen, carbon and sulfur by redox
active enzymes. In E. coli, the synthesis of Moco
involves genes from several loci: moa, mob, mod, moe and
mog. The mob locus contains mobA and mobB genes. MobB
catalyzes the attachment of the guanine dinucleotide to
molybdopterin..
Length = 159
Score = 32.1 bits (73), Expect = 0.68
Identities = 19/75 (25%), Positives = 33/75 (44%), Gaps = 10/75 (13%)
Query: 383 PPVVTIMGHVDHGKTSLLDAIRKADVAKGEIGGITQHIGAYQVAYQGKNITFLDTPGHAA 442
V+ +G+ GKT+LL+ + A A+G + + + +I DTPG +
Sbjct: 1 MKVIGFVGYSGSGKTTLLEKLIPALSARG------LRVAVIKHDHHDFDI---DTPGKDS 51
Query: 443 FYEMRARGARVTDIA 457
Y R GA ++
Sbjct: 52 -YRHREAGAEEVLVS 65
>gnl|CDD|38818 KOG3612, KOG3612, KOG3612, PHD Zn-finger protein [General function
prediction only].
Length = 588
Score = 32.0 bits (72), Expect = 0.77
Identities = 51/254 (20%), Positives = 89/254 (35%), Gaps = 20/254 (7%)
Query: 84 QAKAKGNFRRASRSDKVSSQKNDSSFAGLSQGEIES---RRRALHEAQVREEELRKRLEQ 140
A AK S D + Q N S F G S EI R+ + + + K Q
Sbjct: 273 GAAAKYTPLTPSPMDLLDLQTNPSVFVGQSIREIRRCPLCYRSSNTLSLGDTWFTKPCLQ 332
Query: 141 QSLEQPSQESSIDLPEVCDSQQVPEQVLEDPCKEKDLEIKDVDVGTEVESSVILSHDMGD 200
+ P+ ++ S P +V P +E IK S L +
Sbjct: 333 RHELAPAPQAG--------SSPWPAKVPVSP-REP---IKYDVRFVGGTHSRALIEERDV 380
Query: 201 SDSSSVVNNKFRESSSDASSNRGKSRGGAGKYASVNSSKPVTRNKVGDD--DKKYKKVRI 258
+ S S+ + S K + A ++ S + + K K I
Sbjct: 381 TSSDSIPMSPITPRGPSVLSAAIKLTQVSKMLADLHYSTQLGGVHADPTVVEDKMKDAII 440
Query: 259 AVAADVDEEGGASRGRSLSA-MRRRQEKFRRNQQQEKREKISREIVVPETITIQELSQRM 317
+ + SR RSL A + +++F QQ +RE + + + E+ + +
Sbjct: 441 DLQESTLSDYSGSRERSLVAATEKLRQEFEELQQTSRRE--LPVPLRNFELEMAEMRKTL 498
Query: 318 SERSADVIKFLMKE 331
++ A+ IK +K+
Sbjct: 499 EQKHAENIKEEIKK 512
>gnl|CDD|31356 COG1162, COG1162, Predicted GTPases [General function prediction
only].
Length = 301
Score = 31.8 bits (72), Expect = 0.91
Identities = 22/95 (23%), Positives = 44/95 (46%), Gaps = 7/95 (7%)
Query: 447 RARGARVTDIAVLVLAADEEIMPQAIES-INHAKAADVSIIVAINKIDKLGADPQKVRMS 505
R A ++V D + ++ + A+A + ++ +NKID L + V+
Sbjct: 74 RPPVANNDQAIIVVSLVDPDFNTNLLDRYLVLAEAGGIEPVIVLNKIDLLDDEEAAVKEL 133
Query: 506 LLKHDVFVESMGGDILDVEISAKNNLNLDKLLDAI 540
L ++ E +G +L +SAKN L++L + +
Sbjct: 134 LREY----EDIGYPVL--FVSAKNGDGLEELAELL 162
>gnl|CDD|36273 KOG1055, KOG1055, KOG1055, GABA-B ion channel receptor subunit
GABABR1 and related subunits, G-protein coupled receptor
superfamily [Inorganic ion transport and metabolism,
Amino acid transport and metabolism, Signal transduction
mechanisms].
Length = 865
Score = 31.5 bits (71), Expect = 0.92
Identities = 25/144 (17%), Positives = 52/144 (36%), Gaps = 27/144 (18%)
Query: 80 QDLSQAKAKGNFRRASRSDKVSSQKNDSSFAGLSQGEIESRRRALHEAQVREEELRKRLE 139
Q S+A+ +S ++ ++ L + E R+ + E + R EL+ +
Sbjct: 736 QWASEAQRNMKTGPSSSVNENEEERLR-----LLKKENRRLRKKIMEKEERLSELKHQ-- 788
Query: 140 QQSLEQPSQESSIDLPEVCDSQQVPEQVLEDPCKEKDLEIKDVDVGTEVESSVIL----- 194
L+ +++ ++P +SQ P + + D+ T++ S+ L
Sbjct: 789 ---LQPRPRKTITEIP--GNSQ--LRSRRHKPSPTELVVYHDITSLTDITPSLSLQRGNH 841
Query: 195 --------SHDMGDSDSSSVVNNK 210
S G S S + K
Sbjct: 842 PPEPPPRDSPVDGSSVSPVGLLTK 865
>gnl|CDD|35301 KOG0078, KOG0078, KOG0078, GTP-binding protein SEC4, small G
protein superfamily, and related Ras family GTP-binding
proteins [Signal transduction mechanisms, Intracellular
trafficking, secretion, and vesicular transport].
Length = 207
Score = 31.7 bits (72), Expect = 0.92
Identities = 47/190 (24%), Positives = 74/190 (38%), Gaps = 20/190 (10%)
Query: 386 VTIMGHVDHGKTSLLDAIRKADVAKGEI--GGITQHIGAYQVAYQGKNITF--LDTPGHA 441
+ ++G GKT LL I GI I ++ GK I DT G
Sbjct: 15 LLLIGDSGVGKTCLLLRFSDDSFNTSFISTIGIDFKIKTIEL--DGKKIKLQIWDTAGQE 72
Query: 442 AFYEMRARGARVTDIAVLVL-AADE---EIMPQAIESINHAKAADVSIIVAINKIDKLGA 497
F + R +LV +E E + I++I+ + DV I+ NK D
Sbjct: 73 RFRTITTAYYRGAMGILLVYDITNEKSFENIRNWIKNIDEHASDDVVKILVGNKCDL--E 130
Query: 498 DPQKVRMSLLKHDVFVESMGGDILDVEISAKNNLNLDK----LLDAILLQAEMLDLKTSI 553
+ ++V + + G I E SAK N N+++ L IL + E +L+ S
Sbjct: 131 EKRQVSKE--RGEALAREYG--IKFFETSAKTNFNIEEAFLSLARDILQKLEDAELEASN 186
Query: 554 NRKAEGIVVE 563
N K + +
Sbjct: 187 NSKIRPLDIN 196
>gnl|CDD|39796 KOG4596, KOG4596, KOG4596, Uncharacterized conserved protein
[Function unknown].
Length = 1936
Score = 31.6 bits (71), Expect = 0.93
Identities = 27/125 (21%), Positives = 44/125 (35%), Gaps = 9/125 (7%)
Query: 35 QGANQGRARSVVVETRKRRSYVQGEEKVSVFRKSSRVIESSSDSSQDLSQAKAKGNFRRA 94
QG NQ + S+ E VQ + R++E D LS + +
Sbjct: 1655 QGRNQ-ISSSIRREENVESREVQIRRCEQLVD---RIVEEPIDLKMALSTDICEEERIKK 1710
Query: 95 SRSDKVSSQKNDSSFAG--LSQGEIESRRRALHEAQVREEELRKRLEQQSLEQPSQESSI 152
R + S + ++ G S G I R+ + + L+Q + E SI
Sbjct: 1711 DRIREKSCEAAENVKFGGKRSAGCI---RQGGGPPPKLGRFISAKDLPVPLQQQNDEDSI 1767
Query: 153 DLPEV 157
+ EV
Sbjct: 1768 NAEEV 1772
>gnl|CDD|39393 KOG4191, KOG4191, KOG4191, Histone acetyltransferases
PCAF/SAGA/ADA, subunit TADA3L/NGG1 [Chromatin structure
and dynamics].
Length = 516
Score = 30.4 bits (68), Expect = 2.1
Identities = 26/157 (16%), Positives = 53/157 (33%), Gaps = 14/157 (8%)
Query: 161 QQVPEQVLEDPCKEKDLEIKDVDVGTEVESSVILSHDMGDSDSSSVVNNKFRESSSDASS 220
++ + E P + V VE ++ S + S ES +D +S
Sbjct: 306 LRLSSALHEQPEDGLPFALTQRAVQEFVEENISSSMENSPIPDMSGK-----ESGADGAS 360
Query: 221 NRGKSRGGAGKYASVNSSKPVTRNKVGDDDKKYKKVRIAVAADVDEEGGASRGRSLSAMR 280
+++ N V K + K + + + D D L+ +R
Sbjct: 361 TSPRNQ---------NKPFSVPHTKSLESRLKEELIAQGLLEDEDRPASDDDDEVLAELR 411
Query: 281 RRQEKFRRNQQQEKREKISREIVVPETITIQELSQRM 317
+ Q + + +++K + PE + QE Q +
Sbjct: 412 KLQAELKAVSAHNRKKKHDLLRLAPEEMARQEFQQVL 448
>gnl|CDD|133005 cd02511, Beta4Glucosyltransferase, UDP-glucose LOS-beta-1,4
glucosyltransferase is required for biosynthesis of
lipooligosaccharide. UDP-glucose: lipooligosaccharide
(LOS) beta-1-4-glucosyltransferase catalyzes the
addition of the first residue, glucose, of the
lacto-N-neotetrase structure to HepI of the LOS inner
core. LOS is the major constituent of the outer leaflet
of the outer membrane of gram-positive bacteria. It
consists of a short oligosaccharide chain of variable
composition (alpha chain) attached to a branched inner
core which is lined in turn to lipid A. Beta 1,4
glucosyltransferase is required to attach the alpha
chain to the inner core.
Length = 229
Score = 30.3 bits (69), Expect = 2.5
Identities = 10/36 (27%), Positives = 16/36 (44%)
Query: 458 VLVLAADEEIMPQAIESINHAKAADVSIIVAINKID 493
VL L ADE + P+ + I A D + + +
Sbjct: 75 VLSLDADERLTPELADEILALLATDDYDGYYVPRRN 110
>gnl|CDD|58094 cd03703, aeIF5B_II, aeIF5B_II: This family represents the domain II
of archeal and eukaryotic aeIF5B. aeIF5B is a homologue
of prokaryotic Initiation Factor 2 (IF2). 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 joining of
60S subunits. 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 of EF1A, eEF1A and aeIF2gamma..
Length = 110
Score = 30.1 bits (68), Expect = 2.7
Identities = 18/50 (36%), Positives = 28/50 (56%), Gaps = 4/50 (8%)
Query: 557 AEGIVVEGKLDRGRGPVVTVLVQKGTLSKGNILVVGDQWG----KIRALF 602
+G V+E K + G G + V++ GTL +G+ +VV G K+RAL
Sbjct: 1 LQGTVLEVKEEEGLGTTIDVILYDGTLREGDTIVVCGLNGPIVTKVRALL 50
>gnl|CDD|147703 pfam05695, DUF825, Plant protein of unknown function (DUF825).
This family consists of several plant proteins greater
than 1000 residues in length. The function of this
family is unknown.
Length = 1170
Score = 29.9 bits (67), Expect = 3.1
Identities = 12/31 (38%), Positives = 14/31 (45%)
Query: 763 YKIIYDLLDSIKDSMSELLSPEIRETFLGNA 793
Y I +L + M L PE E FLGN
Sbjct: 203 YSPISELFTEDEKYMINNLFPEEMERFLGNF 233
>gnl|CDD|133365 cd04165, GTPBP1_like, GTPBP1-like. 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 = 29.5 bits (67), Expect = 3.6
Identities = 41/195 (21%), Positives = 71/195 (36%), Gaps = 54/195 (27%)
Query: 386 VTIMGHVDHGKTSLLDAI--------------------------RKADVAKGEIG----- 414
V ++G+VD GK++LL + R + V+ +G
Sbjct: 2 VAVVGNVDAGKSTLLGVLTQGELDNGRGKARLNLFRHKHEVESGRTSSVSNEILGFDSDG 61
Query: 415 -------GITQHIGAYQVAYQGKNITFLDTPGHAAFYEMRARG--ARVTDIAVLVLAADE 465
K +TF+D GH + + G D A+LV+AA+
Sbjct: 62 EVVNYPDNHLSESDIEICEKSSKLVTFIDLAGHERYLKTTLFGLTGYAPDYAMLVVAANA 121
Query: 466 EIMPQAIESINHAKAADVSIIVAINKID--------KLGADPQKVRMS--LLKHDVFVES 515
I+ E + A A ++ + V + KID + D +++ + K V V+S
Sbjct: 122 GIIGMTKEHLGLALALNIPVFVVVTKIDLAPANILQETLKDLKRILKVPGVRKLPVPVKS 181
Query: 516 MGGDILDVEISAKNN 530
DV ++A N
Sbjct: 182 DD----DVVLAASNF 192
>gnl|CDD|30425 COG0076, GadB, Glutamate decarboxylase and related PLP-dependent
proteins [Amino acid transport and metabolism].
Length = 460
Score = 29.6 bits (66), Expect = 3.9
Identities = 21/91 (23%), Positives = 38/91 (41%), Gaps = 7/91 (7%)
Query: 353 FGNTVKRVLESDIEVGIFDVADSESDLDIRPPVVTIMGHVDHGKTSLLDAIRKADVAKGE 412
G + +D + + + ++ + I VV G D G ++ + AD+A+
Sbjct: 179 LGLRRVPTVPTDYRIDVDALEEAIDENTIGGVVVGTAGTTDTGSIDDIEEL--ADIAEEY 236
Query: 413 IGGITQHIGAYQVAYQGKNITFLDTPGHAAF 443
GI H+ A A+ G + FL+ G F
Sbjct: 237 --GIWLHVDA---AFGGFLLPFLEPDGRWDF 262
>gnl|CDD|110105 pfam01080, Presenilin, Presenilin. Mutations in presenilin-1 are a
major cause of early onset Alzheimer's disease. It has
been found that presenilin-1 binds to beta-catenin
in-vivo. This family also contains SPE proteins from
C.elegans.
Length = 403
Score = 29.4 bits (66), Expect = 4.2
Identities = 26/120 (21%), Positives = 41/120 (34%), Gaps = 15/120 (12%)
Query: 46 VVETRKRRSYVQGEEKVSVFRKSSRVIESSSDSSQDLSQAKAKGNFRRASRSDKVSSQKN 105
+VET + R E SS V+ + S+Q+ + RR S+S +
Sbjct: 202 LVETAQER----NEPIFPALIYSSTVVVLTVGSNQEETNEGTPSTIRRTSKSTR------ 251
Query: 106 DSSFAGLSQGEIESRRRALHEAQVREEELRKRLEQQSLEQPSQESSIDLPEVCDSQQVPE 165
+ + + L + E S E SQ S PE D+ + PE
Sbjct: 252 ----SAANPDSAPTSHSTLELPEKSSTPELSDDESDSSETESQSDSSLAPE-EDAAEQPE 306
>gnl|CDD|31357 COG1163, DRG, Predicted GTPase [General function prediction only].
Length = 365
Score = 29.4 bits (66), Expect = 4.5
Identities = 25/97 (25%), Positives = 39/97 (40%), Gaps = 9/97 (9%)
Query: 386 VTIMGHVDHGKTSLLDAIRKADVAKGEIGGITQHIGAYQVAYQGKNITFLDTPG-HAAFY 444
V ++G GK++LL+ + + T + Y+G I LD PG
Sbjct: 66 VALVGFPSVGKSTLLNKLTNTKSEVADYPFTTLEPVPGMLEYKGAQIQLLDLPGIIEGAS 125
Query: 445 EMRARG------ARVTDIAVLVLAADEEIMPQAIESI 475
R RG AR D+ ++VL E+ P + I
Sbjct: 126 SGRGRGRQVLSVARNADLIIIVLDVFED--PHHRDII 160
>gnl|CDD|37850 KOG2639, KOG2639, KOG2639, Sodium sulfate symporter and related
arsenite permeases [Inorganic ion transport and
metabolism].
Length = 685
Score = 29.5 bits (66), Expect = 4.6
Identities = 13/73 (17%), Positives = 28/73 (38%)
Query: 96 RSDKVSSQKNDSSFAGLSQGEIESRRRALHEAQVREEELRKRLEQQSLEQPSQESSIDLP 155
+ + + + + S+ E RR + + R LR+RL P++ L
Sbjct: 396 KHEIHVWRLAAAQVSPASKEEENVRRTLSAKIRARARSLRERLPTSCNSNPAENYFNTLA 455
Query: 156 EVCDSQQVPEQVL 168
E+ ++ + L
Sbjct: 456 ELQAKNRIRNKTL 468
>gnl|CDD|147076 pfam04732, Filament_head, Intermediate filament head (DNA
binding) region. This family represents the N-terminal
head region of intermediate filaments. Intermediate
filament heads bind DNA. Vimentin heads are able to
alter nuclear architecture and chromatin distribution,
and the liberation of heads by HIV-1 protease liberates
may play an important role in HIV-1 associated
cytopathogenesis and carcinogenesis. Phosphorylation of
the head region can affect filament stability. The head
has been shown to interaction with the rod domain of
the same protein.
Length = 89
Score = 29.0 bits (65), Expect = 5.7
Identities = 25/79 (31%), Positives = 36/79 (45%), Gaps = 3/79 (3%)
Query: 19 TLKTSSLGVGHSSFQNQGANQGRARSVVVETRKRRSYVQGEEKVSVFRKSSRVIESSSDS 78
T +SS G SS ++ ++ R+RSV R S K S ++SS S S
Sbjct: 14 TRSSSSRSSGGSSGRSSSSSGFRSRSVS---RSSSSSPSPSLKSSYRKRSSSAPPSLSSD 70
Query: 79 SQDLSQAKAKGNFRRASRS 97
S D S A A N + +R+
Sbjct: 71 SLDFSLADALNNEFKITRT 89
>gnl|CDD|57924 cd01849, YlqF_related_GTPase, YlqF-related GTPases. These proteins
are found in bacteria, eukaryotes, and archaea. They
all exhibit a circular permutation of the GTPase
signature motifs so that the order of the conserved G
box motifs is G4-G5-G1-G2-G3, with G4 and G5 being
permuted from the C-terminal region of proteins in the
Ras superfamily to the N-terminus of YlqF-related
GTPases..
Length = 155
Score = 28.8 bits (64), Expect = 6.8
Identities = 17/59 (28%), Positives = 28/59 (47%), Gaps = 4/59 (6%)
Query: 382 RPPVVTIMGHVDHGKTSLLDAIRKADVAK-GEIGGITQHIGAYQVAYQGKNITFLDTPG 439
+ V ++G+ + GK+S+++A+ K G + G T Q I LDTPG
Sbjct: 99 KSITVGVIGYPNVGKSSVINALLNKLKLKVGNVPGTTTSQ---QEVKLDNKIKLLDTPG 154
>gnl|CDD|35275 KOG0052, KOG0052, KOG0052, Translation elongation factor EF-1
alpha/Tu [Translation, ribosomal structure and
biogenesis].
Length = 391
Score = 28.8 bits (64), Expect = 7.5
Identities = 28/106 (26%), Positives = 42/106 (39%), Gaps = 28/106 (26%)
Query: 386 VTIMGHVDHGKTS----LLDAIRK----------ADVAKGEI--------------GGIT 417
+ ++GHVD GK++ I K A++ KG GIT
Sbjct: 10 IVVIGHVDSGKSTTTGYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERERGIT 69
Query: 418 QHIGAYQVAYQGKNITFLDTPGHAAFYEMRARGARVTDIAVLVLAA 463
I ++ +T +D PGH F + G D AVL++AA
Sbjct: 70 IDIALWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAA 115
>gnl|CDD|35889 KOG0670, KOG0670, KOG0670, U4/U6-associated splicing factor PRP4
[RNA processing and modification].
Length = 752
Score = 28.5 bits (63), Expect = 7.5
Identities = 38/207 (18%), Positives = 73/207 (35%), Gaps = 19/207 (9%)
Query: 95 SRSDKVSSQKNDSSFAGLSQGEIESRRRALHEAQVREEELRKRLEQQSLEQPSQESSIDL 154
R +V S K SS S E+ R+ + E++ K+ + ++
Sbjct: 2 ERDSEVKSDKGTSSSEKSSSSEVNRRKTDRSRSGSDEKKGHKK------SKKEKKDKKHK 55
Query: 155 PEVCDSQQVPEQVLEDPCKEKDLEIKDVDVGTEVESSVILSHDMGDSDSSSVVNNKFRES 214
++V + ++ P K++ LE V T+ S + + N R
Sbjct: 56 KHHDREKEVHHENVDSPTKKRTLE----PVDTKGNESKRKESKESSRNEEDEIRNPDRRE 111
Query: 215 SSDASSNRGKSRGGAGKYASVNSSKPVTRNKVGDDDKKYKKVRIAVAADVDEEGGASRGR 274
S + R K + + D D++ + D EG RGR
Sbjct: 112 RSKSPERR---DRELRKRRDAERRELSKERRSIDRDREDNR------RDPRHEGNRRRGR 162
Query: 275 SLSAMRRRQEKFRRNQQQEKREKISRE 301
S R + + R++++E+R + R+
Sbjct: 163 SRRRFRNNRRERDRDKRRERRHRRDRD 189
>gnl|CDD|36699 KOG1486, KOG1486, KOG1486, GTP-binding protein DRG2 (ODN
superfamily) [Signal transduction mechanisms].
Length = 364
Score = 28.7 bits (64), Expect = 7.6
Identities = 32/103 (31%), Positives = 46/103 (44%), Gaps = 17/103 (16%)
Query: 370 FDVADSESDLDIRPPVVTIMGHVDHGKTSLLDAIR--KADVAKGEIGGITQHIGAYQVAY 427
F+V S D R V ++G GK++LL I ++ A E +T G + Y
Sbjct: 55 FEVLKSG---DAR---VALIGFPSVGKSTLLSKITSTHSEAASYEFTTLTCIPGV--IHY 106
Query: 428 QGKNITFLDTPG-HAAFYEMRARG------ARVTDIAVLVLAA 463
G NI LD PG + + RG AR D+ ++VL A
Sbjct: 107 NGANIQLLDLPGIIEGASQGKGRGRQVIAVARTADLILMVLDA 149
>gnl|CDD|143815 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 28.7 bits (65), Expect = 7.7
Identities = 29/128 (22%), Positives = 46/128 (35%), Gaps = 29/128 (22%)
Query: 395 GKTSLLDAIRKADVAKGEIGGI--TQHIGAYQVAYQGKNITFLDTPGHAAFYEMRARGAR 452
GKT++L + GEI T V Y+ T D G R
Sbjct: 26 GKTTILYKL-----KLGEIVTTIPTIGFNVETVTYKNVKFTVWDVGGQ--------ESLR 72
Query: 453 ---------VTDIAVLVLAADEEIMPQAIES----INHAKAADVSIIVAINKIDKLGA-D 498
+ +V +AD + + +A E +N + AD +++ NK D GA
Sbjct: 73 PLWRNYFPNTDAVIFVVDSADRDRIEEAKEELHALLNEEELADAPLLILANKQDLPGAMS 132
Query: 499 PQKVRMSL 506
++R L
Sbjct: 133 EAEIRELL 140
>gnl|CDD|133252 cd00876, Ras, Ras family. The Ras family of the Ras superfamily
includes classical N-Ras, H-Ras, and K-Ras, as well as
R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG, Rin/Rit, RSR1,
RRP22, Ras2, Ras-dva, and RGK proteins. Ras proteins
regulate cell growth, proliferation and differentiation.
Ras is activated by guanine nucleotide exchange factors
(GEFs) that release GDP and allow GTP binding. Many
RasGEFs have been identified. These are sequestered in
the cytosol until activation by growth factors triggers
recruitment to the plasma membrane or Golgi, where the
GEF colocalizes with Ras. Active GTP-bound Ras
interacts with several effector proteins: among the best
characterized are the Raf kinases, phosphatidylinositol
3-kinase (PI3K), RalGEFs and NORE/MST1. 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 = 160
Score = 28.7 bits (65), Expect = 7.7
Identities = 28/131 (21%), Positives = 46/131 (35%), Gaps = 35/131 (26%)
Query: 431 NITFLDTPGHAAFYEMRARGARVTDIAVLVLAADEEIMPQAIESINHAKA---------- 480
+ LDT G F MR R D +LV + + ES K
Sbjct: 48 TLDILDTAGQEEFSAMRDLYIRQGDGFILVYSITDR------ESFEEIKGYREQILRVKD 101
Query: 481 -ADVSIIVAINKIDKLGADPQKVRMSLLKHDVFVESMGGDILD------VEISAKNNLNL 533
D+ I++ NK D L + G + +E SAK+N+N+
Sbjct: 102 DEDIPIVLVGNKCD------------LENERQVSKEEGKALAKEWGCPFIETSAKDNINI 149
Query: 534 DKLLDAILLQA 544
D++ ++ +
Sbjct: 150 DEVFKLLVREI 160
>gnl|CDD|176210 cd08248, RTN4I1, Human Reticulon 4 Interacting Protein 1. Human
Reticulon 4 Interacting Protein 1 is a member of the
medium chain dehydrogenase/ reductase (MDR) family.
Riticulons are endoplasmic reticulum associated proteins
involved in membrane trafficking and neuroendocrine
secretion. The MDR/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES.
Length = 350
Score = 28.7 bits (65), Expect = 8.1
Identities = 18/80 (22%), Positives = 29/80 (36%), Gaps = 8/80 (10%)
Query: 658 MARRLGSHSALEKLVKNANISSKMKEFPVIIKGDVQGSVEAIVDSLGALK-NSEVCLSI- 715
M G L K K + EFP+ + D G V I + + + EV ++
Sbjct: 48 MRSGYGRT-LLNKKRKPQSCKYSGIEFPLTLGRDCSGVVVDIGSGVKSFEIGDEVWGAVP 106
Query: 716 -----VHSSVGAINETDVSL 730
H+ + E +VS
Sbjct: 107 PWSQGTHAEYVVVPENEVSK 126
>gnl|CDD|133250 cd00154, Rab, Rab family. 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 = 28.6 bits (65), Expect = 8.5
Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 6/59 (10%)
Query: 482 DVSIIVAINKIDKLGADPQKVRMSLLKHDVFVESMGGDILDVEISAKNNLNLDKLLDAI 540
++ II+ NKID D ++V + + +L E SAK N+++L ++
Sbjct: 105 NIPIILVGNKIDL--EDQRQV----STEEAQQFAKENGLLFFETSAKTGENVEELFQSL 157
>gnl|CDD|173857 cd08492, PBP2_NikA_DppA_OppA_like_15, 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 = 484
Score = 28.3 bits (64), Expect = 8.6
Identities = 18/75 (24%), Positives = 25/75 (33%), Gaps = 9/75 (12%)
Query: 401 DAIRKADVAKGEIGGITQHIGAYQVAYQ----GKNITFLDTPGHAAFYEMRARGARVTDI 456
++R + G++ IT I G I TPG + D+
Sbjct: 209 ASVRVGALQSGQVDVITD-IPPQDEKQLAADGGPVIETRPTPGVPYSLYLNTTRPPFDDV 267
Query: 457 AV---LVLAAD-EEI 467
V L LA D E I
Sbjct: 268 RVRQALQLAIDREAI 282
>gnl|CDD|58088 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 = 28.5 bits (64), Expect = 9.3
Identities = 16/83 (19%), Positives = 37/83 (44%), Gaps = 13/83 (15%)
Query: 794 EVLEVFAVTKLGNVAGCKVSEGKVERGSGVRLI-----RNSTVIYEGKLKTLKRFKDEVS 848
+ +VF++ G V ++ G ++ G V ++ +TV ++ F+ +
Sbjct: 4 PIEDVFSIPGRGTVVTGRIERGTIKVGDEVEIVGFGETLKTTVT------GIEMFRKTLD 57
Query: 849 EVHAGQDCGMAFE--KYDNIQAG 869
E AG + G+ K ++++ G
Sbjct: 58 EAEAGDNVGVLLRGVKREDVERG 80
>gnl|CDD|31949 COG1763, MobB, Molybdopterin-guanine dinucleotide biosynthesis
protein [Coenzyme metabolism].
Length = 161
Score = 28.4 bits (63), Expect = 9.7
Identities = 19/107 (17%), Positives = 43/107 (40%), Gaps = 13/107 (12%)
Query: 383 PPVVTIMGHVDHGKTSLLDAIRKADVAKGEIGGITQHIG-AYQVAYQGKNITFLDTPGHA 441
++ I+G+ + GKT+L++ + + A+G +H + + GK DT
Sbjct: 2 MKILGIVGYKNSGKTTLIEKLVRKLKARGYRVATVKHAHHDFDLDKPGK-----DT---- 52
Query: 442 AFYEMRARGARVTDIAV-LVLAADEEIMPQAIESINHAKAADVSIIV 487
Y R GA +A A + ++++ + +++
Sbjct: 53 --YRHRKAGADQVVVASDHRTALMTRTPDRDLDAVLSRLDPLLDLVL 97
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.313 0.130 0.346
Gapped
Lambda K H
0.267 0.0585 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 9,467,721
Number of extensions: 501547
Number of successful extensions: 1710
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1587
Number of HSP's successfully gapped: 207
Length of query: 884
Length of database: 6,263,737
Length adjustment: 102
Effective length of query: 782
Effective length of database: 4,059,619
Effective search space: 3174622058
Effective search space used: 3174622058
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 62 (28.0 bits)