RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11993
(630 letters)
>gnl|CDD|237875 PRK14974, PRK14974, cell division protein FtsY; Provisional.
Length = 336
Score = 268 bits (687), Expect = 1e-84
Identities = 137/362 (37%), Positives = 208/362 (57%), Gaps = 35/362 (9%)
Query: 268 KMVGGIKDLEVESSSEEESSDDEEDVRAETSHVSAKKANGKANKGMFSLFRGLVGSKNLT 327
K+ ++ +E + EEE E + E KK G F + +
Sbjct: 8 KLSKFVEKVEEKIEEEEEEEAPEAEEEEEEEDEEEKKEK----PGFFDKAK----ITEIK 59
Query: 328 KSDMKPILEKMKDHLIAKNVAADIAVKLCDSVALKLEGKVLGTFESVANTVKSTLTDALV 387
+ D++ +LE+++ L+ +VA ++A ++ +S+ KL GK + E V VK+ L +AL+
Sbjct: 60 EKDIEDLLEELELELLESDVALEVAEEILESLKEKLVGKKVKRGEDVEEIVKNALKEALL 119
Query: 388 QILSPKRRVDILRDALEAKKQGRPFVMAFCGVNGVGKSTNLAKICFWLIENNLNVLIAAC 447
++LS D++ E K +G+P V+ F GVNG GK+T +AK+ ++L +N +V+IAA
Sbjct: 120 EVLSVGDLFDLIE---EIKSKGKPVVIVFVGVNGTGKTTTIAKLAYYLKKNGFSVVIAAG 176
Query: 448 DTFRAGAVEQLRTHVRHLCSLHPAAKHGGREMVQLFEKGYGKDPAEIAFRAISHARDMHI 507
DTFRAGA+EQL H L V++ + YG DPA +A+ AI HA+ I
Sbjct: 177 DTFRAGAIEQLEEHAERL-------------GVKVIKHKYGADPAAVAYDAIEHAKARGI 223
Query: 508 DVVLIDTAGRMQDNEPLMRALAKLVKVNQPDLLLFVGEALVGNEAVDQLVKFNNAMADHS 567
DVVLIDTAGRM + LM L K+V+V +PDL++FVG+AL GN+AV+Q +FN A+
Sbjct: 224 DVVLIDTAGRMHTDANLMDELKKIVRVTKPDLVIFVGDALAGNDAVEQAREFNEAVG--- 280
Query: 568 LSDNPHLIDGIVLTKFDTIDDKVGAAISMTYITGQPIVFVGTGQTYTDLKSLNAKAVVNA 627
IDG++LTK D D K GAA+S+ Y+ G+PI+F+G GQ Y DL + V+
Sbjct: 281 -------IDGVILTKVDA-DAKGGAALSIAYVIGKPILFLGVGQGYDDLIPFDPDWFVDK 332
Query: 628 LM 629
L+
Sbjct: 333 LL 334
>gnl|CDD|223626 COG0552, FtsY, Signal recognition particle GTPase [Intracellular
trafficking and secretion].
Length = 340
Score = 262 bits (673), Expect = 2e-82
Identities = 124/359 (34%), Positives = 186/359 (51%), Gaps = 38/359 (10%)
Query: 279 ESSSEEESSDDEEDVRAETSHVSAKKA-NGKANKGMFSLFRGLVGSKNLTKSDMKPILEK 337
E +E+E ++E++ + K K K +GL K + + + +LE+
Sbjct: 13 ELEAEKEKIEEEDEEEEKEGWFERLKQGLSKTKKNFGKGIKGL-FLKKIKEKLDEDLLEE 71
Query: 338 MKDHLIAKNVAADIAVKLCDSVALKLEGKVLGTFESVANTVKSTLTDALVQILSPKRRVD 397
+++ LI +V + A ++ + + K EGK + TVK L +AL++IL P VD
Sbjct: 72 LEELLIEADVGVETAEEIIEELR-KREGKKKKIKDE--ETVKEALREALIEILRP---VD 125
Query: 398 ILRDALEAKKQGRPFVMAFCGVNGVGKSTNLAKICFWLIENNLNVLIAACDTFRAGAVEQ 457
+ LE K+ +PFV+ F GVNGVGK+T +AK+ +L + +VL+AA DTFRA A+EQ
Sbjct: 126 KVDLPLEIPKEKKPFVILFVGVNGVGKTTTIAKLAKYLKQQGKSVLLAAGDTFRAAAIEQ 185
Query: 458 LRTHVRHLCSLHPAAKHGGREMVQLFEKGYGKDPAEIAFRAISHARDMHIDVVLIDTAGR 517
L R V + G DPA +AF AI A+ IDVVLIDTAGR
Sbjct: 186 LEVWGE-------------RLGVPVISGKEGADPAAVAFDAIQAAKARGIDVVLIDTAGR 232
Query: 518 MQDNEPLMRALAKLVKVNQPDL------LLFVGEALVGNEAVDQLVKFNNAMADHSLSDN 571
+ + + LM L K+V+V + D +L V +A G A+ Q FN A+
Sbjct: 233 LHNKKNLMDELKKIVRVIKKDDPDAPHEILLVLDATTGQNALSQAKIFNEAVG------- 285
Query: 572 PHLIDGIVLTKFDTIDDKVGAAISMTYITGQPIVFVGTGQTYTDLKSLNAKAVVNALMK 630
+DGI+LTK D K G +S+ Y G PI F+G G+ Y DL+ +A+ V+AL+
Sbjct: 286 ---LDGIILTKLDG-TAKGGIILSIAYELGIPIKFIGVGEGYDDLRPFDAEWFVDALLG 340
>gnl|CDD|217884 pfam04086, SRP-alpha_N, Signal recognition particle, alpha subunit,
N-terminal. SRP is a complex of six distinct
polypeptides and a 7S RNA that is essential for
transferring nascent polypeptide chains that are
destined for export from the cell to the translocation
apparatus of the endoplasmic reticulum (ER) membrane.
SRP binds hydrophobic signal sequences as they emerge
from the ribosome, and arrests translation.
Length = 272
Score = 240 bits (613), Expect = 9e-75
Identities = 107/272 (39%), Positives = 145/272 (53%), Gaps = 14/272 (5%)
Query: 26 TPSLNALIKSVILQERGGNQVFEHNGLVLKHKLDNEFDLVFVVGFQKILQLSYVDKLLDD 85
T +N+LI+ V L+ER GN F+ + LK KLDNEF LVFVV +QKIL LSY+DKLLDD
Sbjct: 1 TSPVNSLIRDVFLEERSGNPSFKKDSYTLKWKLDNEFGLVFVVVYQKILHLSYIDKLLDD 60
Query: 86 VHLEFRDKYKNEL--GSDMHLYDYDFESTYNVLLKEAEEWSKVQACIPKQMRTFEESSKS 143
V FRD YKN+L YD +F+ ++ L+E E+ SK QA PK MRTFEES KS
Sbjct: 61 VRTIFRDLYKNQLRQEKARTTYDEEFDEYFDQQLRELEKESKKQAKSPKAMRTFEESKKS 120
Query: 144 KKTIASMIIDKNKKEEKSVPSKKKGKAVETKVEPVTPPSPVQNGDA---GIEEDIIMINR 200
KKT+ SMI K K+ +KK + T E +P + + ++ R
Sbjct: 121 KKTVDSMIERKPKEPGLKRKQRKKAQESATSPESSPSSTPNSSRPSTPHLLKAKEGPSRR 180
Query: 201 QKLAMKMGSPKNKTKPKTPK---ANAKEGKKPRIWELSGDQRDLSTLEYTKDKPSDSNAL 257
K A K+ S + K+PK A K GKK R W+L GD+ D + L+Y+ +D NA
Sbjct: 181 AKKAAKLSSTASSGDEKSPKSKAAPKKAGKKMRKWDLDGDEDDDAVLDYSAPDANDENAD 240
Query: 258 N------ITPDTHLVGKMVGGIKDLEVESSSE 283
+ ++ G M G L++
Sbjct: 241 APEDVEEVDQESWGRGTMKGDFVLLDLGDEVH 272
>gnl|CDD|239389 cd03115, SRP, The signal recognition particle (SRP) mediates the
transport to or across the plasma membrane in bacteria
and the endoplasmic reticulum in eukaryotes. SRP
recognizes N-terminal sighnal sequences of newly
synthesized polypeptides at the ribosome. The
SRP-polypeptide complex is then targeted to the membrane
by an interaction between SRP and its cognated receptor
(SR). In mammals, SRP consists of six protein subunits
and a 7SL RNA. One of these subunits is a 54 kd protein
(SRP54), which is a GTP-binding protein that interacts
with the signal sequence when it emerges from the
ribosome. SRP54 is a multidomain protein that consists
of an N-terminal domain, followed by a central G
(GTPase) domain and a C-terminal M domain.
Length = 173
Score = 234 bits (599), Expect = 5e-74
Identities = 81/197 (41%), Positives = 116/197 (58%), Gaps = 24/197 (12%)
Query: 412 FVMAFCGVNGVGKSTNLAKICFWLIENNLNVLIAACDTFRAGAVEQLRTHVRHLCSLHPA 471
V+ G+ GVGK+T AK+ +L + VL+ A DT+R A+EQLR
Sbjct: 1 TVILLVGLQGVGKTTTAAKLALYLKKKGKKVLLVAADTYRPAAIEQLRVLGE-------- 52
Query: 472 AKHGGREMVQLFEKGYGKDPAEIAFRAISHARDMHIDVVLIDTAGRMQDNEPLMRALAKL 531
+ V +FE+G GKDP IA RAI HAR+ + DVV++DTAGR+Q +E LM L K+
Sbjct: 53 -----QVGVPVFEEGEGKDPVSIAKRAIEHAREENFDVVIVDTAGRLQIDENLMEELKKI 107
Query: 532 VKVNQPDLLLFVGEALVGNEAVDQLVKFNNAMADHSLSDNPHLIDGIVLTKFDTIDDKVG 591
+V +PD +L V +A+ G +AV+Q FN A+ I G++LTK D D + G
Sbjct: 108 KRVVKPDEVLLVVDAMTGQDAVNQAKAFNEALG----------ITGVILTKLDG-DARGG 156
Query: 592 AAISMTYITGQPIVFVG 608
AA+S+ +TG+PI F+G
Sbjct: 157 AALSIRAVTGKPIKFIG 173
>gnl|CDD|214940 smart00962, SRP54, SRP54-type protein, GTPase domain. This entry
represents the GTPase domain of the 54 kDa SRP54
component, a GTP-binding protein that interacts with the
signal sequence when it emerges from the ribosome. SRP54
of the signal recognition particle has a three-domain
structure: an N-terminal helical bundle domain, a GTPase
domain, and the M-domain that binds the 7s RNA and also
binds the signal sequence. The extreme C-terminal region
is glycine-rich and lower in complexity and poorly
conserved between species. The GTPase domain is
evolutionary related to P-loop NTPase domains found in a
variety of other proteins.
Length = 197
Score = 235 bits (602), Expect = 5e-74
Identities = 85/222 (38%), Positives = 117/222 (52%), Gaps = 27/222 (12%)
Query: 411 PFVMAFCGVNGVGKSTNLAKICFWLIENN-LNVLIAACDTFRAGAVEQLRTHVRHLCSLH 469
P V+ G NGVGK+T +AK+ L VL+ A DTFRA AVEQL+T+
Sbjct: 1 PGVILLVGPNGVGKTTTIAKLAARLKLKGGKKVLLVAADTFRAAAVEQLKTY-------- 52
Query: 470 PAAKHGGREM-VQLFEKGYGKDPAEIAFRAISHARDMHIDVVLIDTAGRMQDNEPLMRAL 528
+ V G G DP +A A+ A+ DVVLIDTAGR+ ++E LM L
Sbjct: 53 ------AEILGVVPVAGGEGADPVAVAKDAVELAKARGYDVVLIDTAGRLHNDENLMEEL 106
Query: 529 AKLVKVNQPDLLLFVGEALVGNEAVDQLVKFNNAMADHSLSDNPHLIDGIVLTKFDTIDD 588
K+ +V +PD +L V +A G +AV+Q FN A + GI+LTK D
Sbjct: 107 KKIKRVIKPDEVLLVSDATTGQDAVEQAKAFNEA----------LGLTGIILTKLD-GTA 155
Query: 589 KVGAAISMTYITGQPIVFVGTGQTYTDLKSLNAKAVVNALMK 630
K GAA+S+ TG PI F+GTG+ DL+ + + V+ L+
Sbjct: 156 KGGAALSIAAETGLPIKFIGTGEKVPDLEPFDPERFVSRLLG 197
>gnl|CDD|232804 TIGR00064, ftsY, signal recognition particle-docking protein FtsY.
There is a weak division between FtsY and SRP54; both
are GTPases. In E.coli, ftsY is an essential gene
located in an operon with cell division genes ftsE and
ftsX, but its apparent function is as the signal
recognition particle docking protein [Protein fate,
Protein and peptide secretion and trafficking].
Length = 272
Score = 208 bits (531), Expect = 1e-62
Identities = 99/301 (32%), Positives = 152/301 (50%), Gaps = 41/301 (13%)
Query: 334 ILEKMKDHLIAKNVAADIAVKLCDSVALKLEGKVLGTFESVANTVKSTLTDALVQILSPK 393
E++++ L+ +V ++ K+ +++ +L+GK + E + +K L + L +
Sbjct: 6 FFEELEEILLESDVGYEVVEKIIEALKKELKGKKVKDAELLKEILKEYLKEILKET---- 61
Query: 394 RRVDILRDALEAKKQGRPFVMAFCGVNGVGKSTNLAKICFWLIENNLNVLIAACDTFRAG 453
D ++ +P V+ F GVNGVGK+T +AK+ L + +VL+AA DTFRA
Sbjct: 62 -------DLELIVEENKPNVILFVGVNGVGKTTTIAKLANKLKKQGKSVLLAAGDTFRAA 114
Query: 454 AVEQLRTHVRHLCSLHPAAKHGGREMVQLFEKGYGKDPAEIAFRAISHARDMHIDVVLID 513
A+EQL R V + ++ G DPA +AF AI A+ +IDVVLID
Sbjct: 115 AIEQLEE-------------WAKRLGVDVIKQKEGADPAAVAFDAIQKAKARNIDVVLID 161
Query: 514 TAGRMQDNEPLMRALAKLVKV------NQPDLLLFVGEALVGNEAVDQLVKFNNAMADHS 567
TAGR+Q+ LM L K+ +V + PD +L V +A G A++Q FN A+
Sbjct: 162 TAGRLQNKVNLMDELKKIKRVIKKVDKDAPDEVLLVLDATTGQNALEQAKVFNEAVG--- 218
Query: 568 LSDNPHLIDGIVLTKFDTIDDKVGAAISMTYITGQPIVFVGTGQTYTDLKSLNAKAVVNA 627
+ GI+LTK D K G +S+ Y PI F+G G+ DL +A V A
Sbjct: 219 -------LTGIILTKLDG-TAKGGIILSIAYELKLPIKFIGVGEKIDDLAPFDADWFVEA 270
Query: 628 L 628
L
Sbjct: 271 L 271
>gnl|CDD|215925 pfam00448, SRP54, SRP54-type protein, GTPase domain. This family
includes relatives of the G-domain of the SRP54 family
of proteins.
Length = 196
Score = 198 bits (507), Expect = 3e-60
Identities = 83/219 (37%), Positives = 122/219 (55%), Gaps = 24/219 (10%)
Query: 411 PFVMAFCGVNGVGKSTNLAKICFWLIENNLNVLIAACDTFRAGAVEQLRTHVRHLCSLHP 470
P V+ G+ G GK+T +AK+ +L + VL+ A DTFRA A+EQL+ L
Sbjct: 1 PNVILLVGLQGSGKTTTIAKLAAYLKKQGKKVLLVAADTFRAAAIEQLKQLAERL----- 55
Query: 471 AAKHGGREMVQLFEKGYGKDPAEIAFRAISHARDMHIDVVLIDTAGRMQDNEPLMRALAK 530
V +F G G DPA +AF A+ A+ + DVVL+DTAGR+Q+++ LM L K
Sbjct: 56 --------GVPVFGSGTGSDPAAVAFDAVEKAKAENYDVVLVDTAGRLQNDKNLMDELKK 107
Query: 531 LVKVNQPDLLLFVGEALVGNEAVDQLVKFNNAMADHSLSDNPHLIDGIVLTKFDTIDDKV 590
+ +V PD +L V +A G A++Q FN A+ I G++LTK D D K
Sbjct: 108 IKRVIAPDEVLLVLDATTGQNALNQAKAFNEAVG----------ITGVILTKLDG-DAKG 156
Query: 591 GAAISMTYITGQPIVFVGTGQTYTDLKSLNAKAVVNALM 629
GAA+S+ TG+PI F+G G+ DL+ + + V+ L+
Sbjct: 157 GAALSIAAETGKPIKFIGVGEKIDDLEPFDPERFVSRLL 195
>gnl|CDD|236686 PRK10416, PRK10416, signal recognition particle-docking protein
FtsY; Provisional.
Length = 318
Score = 174 bits (445), Expect = 1e-49
Identities = 101/335 (30%), Positives = 158/335 (47%), Gaps = 47/335 (14%)
Query: 303 KKANGKANKGMFSLFRGLVGSKNLTKSDMKPILEKMKDHLIAKNVAADIAVKLCDSVALK 362
KK K + GL K + + +LE++++ LI +V + ++ + + +
Sbjct: 21 KKGLSKTRENFGEGINGLFAKKKIDED----LLEELEELLIEADVGVETTEEIIEELRER 76
Query: 363 LEGKVLGTFESVANTVKSTLTDALVQILSPKRRVDILRDALEAKKQGRPFVMAFCGVNGV 422
++ K L E +K L + L +IL P + + + +PFV+ GVNGV
Sbjct: 77 VKRKNLKDPE----ELKELLKEELAEILEPVEKPLNIEE-------KKPFVILVVGVNGV 125
Query: 423 GKSTNLAKICFWLIENNLNVLIAACDTFRAGAVEQLRTHVRHLCSLHPAAKHGGREMVQL 482
GK+T + K+ VL+AA DTFRA A+EQL+ G R V +
Sbjct: 126 GKTTTIGKLAHKYKAQGKKVLLAAGDTFRAAAIEQLQV-------------WGERVGVPV 172
Query: 483 FEKGYGKDPAEIAFRAISHARDMHIDVVLIDTAGRMQDNEPLMRALAKLVKV------NQ 536
+ G DPA +AF AI A+ IDV++IDTAGR+ + LM L K+ +V +
Sbjct: 173 IAQKEGADPASVAFDAIQAAKARGIDVLIIDTAGRLHNKTNLMEELKKIKRVIKKADPDA 232
Query: 537 PDLLLFVGEALVGNEAVDQLVKFNNAMADHSLSDNPHLIDGIVLTKFD-TIDDKVGAAIS 595
P +L V +A G A+ Q F+ A + GI+LTK D T K G +
Sbjct: 233 PHEVLLVLDATTGQNALSQAKAFHEA-VG---------LTGIILTKLDGT--AKGGVVFA 280
Query: 596 MTYITGQPIVFVGTGQTYTDLKSLNAKAVVNALMK 630
+ G PI F+G G+ DL+ +A+ V+AL+
Sbjct: 281 IADELGIPIKFIGVGEGIDDLQPFDAEEFVDALLG 315
>gnl|CDD|223615 COG0541, Ffh, Signal recognition particle GTPase [Intracellular
trafficking and secretion].
Length = 451
Score = 170 bits (432), Expect = 1e-46
Identities = 93/316 (29%), Positives = 153/316 (48%), Gaps = 33/316 (10%)
Query: 315 SLFRGLVGSKNLTKSDMKPILEKMKDHLIAKNVAADIAVKLCDSVALK-LEGKVLGTFES 373
+ + L G +T+ D+K L +++ L+ +V + + + L +V +
Sbjct: 11 NALKKLRGKGRITEKDVKEALREIRRALLEADVNLKVVKDFIKRIKERALGEEVPKGL-T 69
Query: 374 VANTVKSTLTDALVQILSPKRRVDILRDALEAKKQGRPFVMAFCGVNGVGKSTNLAKICF 433
+ + LV++L + L K+ P V+ G+ G GK+T K+
Sbjct: 70 PGQQFIKIVYEELVKLLGGENS------ELNLAKK-PPTVILMVGLQGSGKTTTAGKLAK 122
Query: 434 WLIENNLNVLIAACDTFRAGAVEQLRTHVRHLCSLHPAAKHGGREMVQLFEKGYGKDPAE 493
+L + VL+ A DT+R A+EQL+ A+ G V F G KDP E
Sbjct: 123 YLKKKGKKVLLVAADTYRPAAIEQLKQ----------LAEQVG---VPFFGSGTEKDPVE 169
Query: 494 IAFRAISHARDMHIDVVLIDTAGRMQDNEPLMRALAKLVKVNQPDLLLFVGEALVGNEAV 553
IA A+ A++ DVV++DTAGR+ +E LM L ++ +V PD L V +A++G +AV
Sbjct: 170 IAKAALEKAKEEGYDVVIVDTAGRLHIDEELMDELKEIKEVINPDETLLVVDAMIGQDAV 229
Query: 554 DQLVKFNNAMADHSLSDNPHLIDGIVLTKFDTIDDKVGAAISMTYITGQPIVFVGTGQTY 613
+ FN A+ I G++LTK D D + GAA+S ITG+PI F+GTG+
Sbjct: 230 NTAKAFNEALG----------ITGVILTKLDG-DARGGAALSARAITGKPIKFIGTGEKI 278
Query: 614 TDLKSLNAKAVVNALM 629
DL+ + + ++
Sbjct: 279 DDLEPFHPDRFASRIL 294
>gnl|CDD|233210 TIGR00959, ffh, signal recognition particle protein. This model
represents Ffh (Fifty-Four Homolog), the protein
component that forms the bacterial (and organellar)
signal recognition particle together with a 4.5S RNA.
Ffh is a GTPase homologous to eukaryotic SRP54 and also
to the GTPase FtsY (TIGR00064) that is the receptor for
the signal recognition particle [Protein fate, Protein
and peptide secretion and trafficking].
Length = 428
Score = 168 bits (428), Expect = 3e-46
Identities = 93/315 (29%), Positives = 158/315 (50%), Gaps = 34/315 (10%)
Query: 317 FRGLVGSKNLTKSDMKPILEKMKDHLIAKNVAADIAVKLCDSVALK-LEGKVLGTFESVA 375
F+ L G +T+ ++K L +++ L+ +V + V K L +VL + S
Sbjct: 12 FKKLSGRGTITEKNIKEALREIRLALLEADVNLQVVKDFIKKVKEKALGQEVLKSL-SPG 70
Query: 376 NTVKSTLTDALVQILSPKRRVDILRDALEAKKQGRPFVMAFCGVNGVGKSTNLAKICFWL 435
+ + LV IL + + + P V+ G+ G GK+T K+ ++L
Sbjct: 71 QQFIKIVHEELVAILGGENA-SL------NLAKKPPTVILMVGLQGSGKTTTCGKLAYYL 123
Query: 436 IE-NNLNVLIAACDTFRAGAVEQLRTHVRHLCSLHPAAKHGGREMVQLFEKGYGKDPAEI 494
+ VL+ ACD +R A+EQL+ G + V +F G G+ P EI
Sbjct: 124 KKKQGKKVLLVACDLYRPAAIEQLKVL-------------GQQVGVPVFALGKGQSPVEI 170
Query: 495 AFRAISHARDMHIDVVLIDTAGRMQDNEPLMRALAKLVKVNQPDLLLFVGEALVGNEAVD 554
A RA+ +A++ DVV++DTAGR+Q +E LM LA + ++ PD +L V +A+ G +AV+
Sbjct: 171 ARRALEYAKENGFDVVIVDTAGRLQIDEELMEELAAIKEILNPDEILLVVDAMTGQDAVN 230
Query: 555 QLVKFNNAMADHSLSDNPHLIDGIVLTKFDTIDDKVGAAISMTYITGQPIVFVGTGQTYT 614
FN + + G+VLTK D D + GAA+S+ +TG+PI F+G G+
Sbjct: 231 TAKTFNERLG----------LTGVVLTKLDG-DARGGAALSVRSVTGKPIKFIGVGEKID 279
Query: 615 DLKSLNAKAVVNALM 629
DL+ + + + + ++
Sbjct: 280 DLEPFHPERMASRIL 294
>gnl|CDD|236780 PRK10867, PRK10867, signal recognition particle protein;
Provisional.
Length = 433
Score = 150 bits (383), Expect = 7e-40
Identities = 82/234 (35%), Positives = 124/234 (52%), Gaps = 32/234 (13%)
Query: 384 DALVQILSPKRRVDILRDALEAKKQGRPFVMAFCGVNGVGKSTNLAKICFWLIEN-NLNV 442
D LV+IL + ++ L AK P V+ G+ G GK+T K+ +L + V
Sbjct: 80 DELVEILGGENS-EL---NLAAKP---PTVIMMVGLQGAGKTTTAGKLAKYLKKKKKKKV 132
Query: 443 LIAACDTFRAGAVEQLRTHVRHLCSLHPAAKHGGREMVQLFEKGYGKDPAEIAFRAISHA 502
L+ A D +R A+EQL+T L G + V +F G G+DP +IA A+ A
Sbjct: 133 LLVAADVYRPAAIEQLKT-------L------GEQIGVPVFPSGDGQDPVDIAKAALEEA 179
Query: 503 RDMHIDVVLIDTAGRMQDNEPLMRALAKLVKVNQPDLLLFVGEALVGNEAVDQLVKFNNA 562
++ DVV++DTAGR+ +E LM L + PD +L V +A+ G +AV+ FN A
Sbjct: 180 KENGYDVVIVDTAGRLHIDEELMDELKAIKAAVNPDEILLVVDAMTGQDAVNTAKAFNEA 239
Query: 563 MADHSLSDNPHLIDGIVLTKFDTIDDKVGAAISMTYITGQPIVFVGTGQTYTDL 616
+ + G++LTK D D + GAA+S+ +TG+PI F+GTG+ DL
Sbjct: 240 LG----------LTGVILTKLDG-DARGGAALSIRAVTGKPIKFIGTGEKLDDL 282
>gnl|CDD|179118 PRK00771, PRK00771, signal recognition particle protein Srp54;
Provisional.
Length = 437
Score = 117 bits (296), Expect = 3e-28
Identities = 64/220 (29%), Positives = 105/220 (47%), Gaps = 26/220 (11%)
Query: 410 RPFVMAFCGVNGVGKSTNLAKICFWLIENNLNVLIAACDTFRAGAVEQLRTHVRHLCSLH 469
+P + G+ G GK+T AK+ + + L V + A DT+R A +QL+ L
Sbjct: 94 KPQTIMLVGLQGSGKTTTAAKLARYFKKKGLKVGLVAADTYRPAAYDQLKQ----LAE-- 147
Query: 470 PAAKHGGREMVQLFEKGYGKDPAEIAFRAISHARDMHIDVVLIDTAGRMQDNEPLMRALA 529
+ V + KD EIA + + DV+++DTAGR E L+ +
Sbjct: 148 -------KIGVPFYGDPDNKDAVEIAKEGLEKFKKA--DVIIVDTAGRHALEEDLIEEMK 198
Query: 530 KLVKVNQPDLLLFVGEALVGNEAVDQLVKFNNAMADHSLSDNPHLIDGIVLTKFDTIDDK 589
++ + +PD +L V +A +G +A +Q F+ A+ I GI++TK D K
Sbjct: 199 EIKEAVKPDEVLLVIDATIGQQAKNQAKAFHEAVG----------IGGIIITKLDG-TAK 247
Query: 590 VGAAISMTYITGQPIVFVGTGQTYTDLKSLNAKAVVNALM 629
G A+S TG PI F+GTG+ DL+ + ++ L+
Sbjct: 248 GGGALSAVAETGAPIKFIGTGEKIDDLERFDPDRFISRLL 287
>gnl|CDD|130492 TIGR01425, SRP54_euk, signal recognition particle protein SRP54.
This model represents examples from the eukaryotic
cytosol of the signal recognition particle protein
component, SRP54. This GTP-binding protein is a
component of the eukaryotic signal recognition particle,
along with several other protein subunits and a 7S RNA.
Some species, including Arabidopsis, have several
closely related forms. The extreme C-terminal region is
glycine-rich and lower in complexity, poorly conserved
between species, and excluded from this model.
Length = 429
Score = 94.5 bits (235), Expect = 1e-20
Identities = 56/223 (25%), Positives = 105/223 (47%), Gaps = 24/223 (10%)
Query: 407 KQGRPFVMAFCGVNGVGKSTNLAKICFWLIENNLNVLIAACDTFRAGAVEQLRTHVRHLC 466
K+G+ V+ F G+ G GK+T K+ ++ + DTFRAGA +QL+ +
Sbjct: 96 KKGKQNVIMFVGLQGSGKTTTCTKLAYYYQRKGFKPCLVCADTFRAGAFDQLKQN----- 150
Query: 467 SLHPAAKHGGREMVQLFEKGYGKDPAEIAFRAISHARDMHIDVVLIDTAGRMQDNEPLMR 526
A K + + DP +IA + + + D++++DT+GR + + L
Sbjct: 151 ----ATKAR----IPFYGSYTESDPVKIASEGVEKFKKENFDIIIVDTSGRHKQEDSLFE 202
Query: 527 ALAKLVKVNQPDLLLFVGEALVGNEAVDQLVKFNNAMADHSLSDNPHLIDGIVLTKFDTI 586
+ ++ + QPD ++FV + +G A Q F +++ + +++TK D
Sbjct: 203 EMLQVAEAIQPDNIIFVMDGSIGQAAEAQAKAFKDSVD----------VGSVIITKLDG- 251
Query: 587 DDKVGAAISMTYITGQPIVFVGTGQTYTDLKSLNAKAVVNALM 629
K G A+S T PI+F+GTG+ D + + ++ L+
Sbjct: 252 HAKGGGALSAVAATKSPIIFIGTGEHIDDFEIFKTQPFISKLL 294
>gnl|CDD|224337 COG1419, FlhF, Flagellar GTP-binding protein [Cell motility and
secretion].
Length = 407
Score = 82.8 bits (205), Expect = 7e-17
Identities = 63/216 (29%), Positives = 94/216 (43%), Gaps = 44/216 (20%)
Query: 407 KQGRPFVMAFCGVNGVGKSTNLAKIC--FWLIENNLNVLIAACDTFRAGAVEQLRTHVRH 464
+Q R V+A G GVGK+T LAK+ + +++ V I DT+R GAVEQL+T+
Sbjct: 201 EQKR--VIALVGPTGVGKTTTLAKLAARYVMLKKKKKVAIITTDTYRIGAVEQLKTYADI 258
Query: 465 L-CSLHPAAKHGGREMVQLFEKGYGKDPAEIAFRAISHARDMHIDVVLIDTAGRMQDNEP 523
+ L P E+A AI RD DV+L+DTAGR Q ++
Sbjct: 259 MGVPLEVV-----------------YSPKELA-EAIEALRD--CDVILVDTAGRSQYDKE 298
Query: 524 LMRALAKLVKVNQPDLLLFV----GEALVGNEAVDQLVKFNNAMADHSLSDNPHLIDGIV 579
+ L +L+ V+ + V + E + Q F IDG++
Sbjct: 299 KIEELKELIDVSHSIEVYLVLSATTKYEDLKEIIKQFSLFP--------------IDGLI 344
Query: 580 LTKFDTIDDKVGAAISMTYITGQPIVFVGTGQTYTD 615
TK D +G S+ Y T P+ +V GQ +
Sbjct: 345 FTKLDET-TSLGNLFSLMYETRLPVSYVTNGQRVPE 379
>gnl|CDD|234232 TIGR03499, FlhF, flagellar biosynthetic protein FlhF. [Cellular
processes, Chemotaxis and motility].
Length = 283
Score = 74.7 bits (184), Expect = 9e-15
Identities = 50/186 (26%), Positives = 77/186 (41%), Gaps = 45/186 (24%)
Query: 334 ILEKMKDHLIAKNVAADIAVKLCDSVALKLEGKVLGTFESVANTVKSTLTDALVQILSPK 393
+LE++ + +++ +A ++ KL + E ++ L +
Sbjct: 140 LLERLLEAGVSEELARELLEKLPE----------DLDAEDAWRWLREALEG---MLPVKP 186
Query: 394 RRVDILRDALEAKKQGRPFVMAFCGVNGVGKSTNLAKIC--FWLIENNLNVLIAACDTFR 451
IL R V+A G GVGK+T LAK+ F L V + DT+R
Sbjct: 187 EEDPILE---------RGGVIALVGPTGVGKTTTLAKLAARFVLEHGKKKVALITTDTYR 237
Query: 452 AGAVEQLRTHVRHL-CSLHPAAKHGGREMVQLFEKGYGKDPAEIAFRAISHARDMHIDVV 510
GAVEQL+T+ L + A +DP E+A A+ RD D++
Sbjct: 238 IGAVEQLKTYAEILGVPVKVA-----------------RDPKELA-EALDRLRDK--DLI 277
Query: 511 LIDTAG 516
LIDTAG
Sbjct: 278 LIDTAG 283
>gnl|CDD|235570 PRK05703, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 424
Score = 74.5 bits (184), Expect = 4e-14
Identities = 95/366 (25%), Positives = 149/366 (40%), Gaps = 61/366 (16%)
Query: 274 KDLEVESSSEEESSDDEEDVRAETSHVSAKKANGKANKGMFSLFRGLVGSKNLTKSDMKP 333
L+ E++ E + E+ + A + K + L L KNL + +
Sbjct: 93 ALLQAENALPEWKKELEKPSEPKEEEPKAAAESKVVQKELDELRDELKELKNLLEDQLSG 152
Query: 334 ILEK-MKDHLIAKNVAADIAVKLCDSVALKLEGKVLGTFESVANTVKSTLTDALVQILSP 392
+ + A+ L +A KL +L T L + L ++ P
Sbjct: 153 LRQVERIPPEFAELYKRLKRSGLSPEIAEKLLKLLLEHMPPRERTAWRYLLELLANMI-P 211
Query: 393 KRRVDILRDALEAKKQGRPFVMAFCGVNGVGKSTNLAKIC--FWLIENNLNVLIAACDTF 450
R DIL KQG V+A G GVGK+T LAK+ + L+ V + DT+
Sbjct: 212 VRVEDIL-------KQGG--VVALVGPTGVGKTTTLAKLAARYALLYGKKKVALITLDTY 262
Query: 451 RAGAVEQLRTHVRHL-CSLHPAAKHGGREMVQLFEKGYGKDPAEIAFRAISHARDMHIDV 509
R GAVEQL+T+ + + + DP E+A +A+ RD DV
Sbjct: 263 RIGAVEQLKTYAKIMGIPVEVV-----------------YDPKELA-KALEQLRDC--DV 302
Query: 510 VLIDTAGRMQDNEPLMRALAKLVKVNQPDLLLFVGEALVGNEAVDQLV-----KFNNAMA 564
+LIDTAGR Q ++ L+ L L++ + G LV K +
Sbjct: 303 ILIDTAGRSQRDKRLIEELKALIEFS-------------GEPIDVYLVLSATTK-YEDLK 348
Query: 565 D--HSLSDNPHLIDGIVLTKFD-TIDDKVGAAISMTYITGQPIVFVGTGQTY-TDLKSLN 620
D S P +DG++ TK D T +G+ +S+ +G PI ++ GQ D+K N
Sbjct: 349 DIYKHFSRLP--LDGLIFTKLDET--SSLGSILSLLIESGLPISYLTNGQRVPDDIKVAN 404
Query: 621 AKAVVN 626
+ +V
Sbjct: 405 PEELVR 410
>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only detects
a fraction of this vast family. The poorly conserved
N-terminal helix is missing from the alignment.
Length = 148
Score = 57.8 bits (139), Expect = 6e-10
Identities = 21/140 (15%), Positives = 38/140 (27%), Gaps = 19/140 (13%)
Query: 410 RPFVMAFCGVNGVGKSTNLAKICFWLIENNLNVLIAACDTFRAGAVEQLRTHVRHLCSLH 469
V+ G G GK+T + L V+ + ++QL +
Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVG----- 55
Query: 470 PAAKHGGREMVQLFEKGYGKDPAEIAFRAISHARDMHIDVVLIDTAGRMQDNEPLMRALA 529
K A++ AR + DV+++D + D E L
Sbjct: 56 --------------GKKASGSGELRLRLALALARKLKPDVLILDEITSLLDAEQEALLLL 101
Query: 530 KLVKVNQPDLLLFVGEALVG 549
L ++
Sbjct: 102 LEELRLLLLLKSEKNLTVIL 121
>gnl|CDD|183704 PRK12726, PRK12726, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 407
Score = 60.1 bits (145), Expect = 1e-09
Identities = 66/246 (26%), Positives = 110/246 (44%), Gaps = 35/246 (14%)
Query: 371 FESVANTVKSTLTDALVQILSPKRRVDILRDALEAKKQGRPFVMAFCGVNGVGKSTNLAK 430
F+ V +TD V LS K V+ D+ + +++ G GVGK+T L K
Sbjct: 172 FKQVETAHLDDITDWFVPYLSGKLAVE---DSFDLSNHR---IISLIGQTGVGKTTTLVK 225
Query: 431 ICFWLIENNLNVLIAACDTFRAGAVEQLRTHVRHLCSLHPAAKHGGREMVQLFEKGYGKD 490
+ + L++ N V DTFR+GAVEQ + + L V+L
Sbjct: 226 LGWQLLKQNRTVGFITTDTFRSGAVEQFQGYADKL-------------DVELI---VATS 269
Query: 491 PAEIAFRAISHARDMH-IDVVLIDTAGRMQDNEPLMRALAKLVKVNQPDLLLFVGEALVG 549
PAE+ A+ + ++ +D +LIDT GR E + ++ V PDL F + G
Sbjct: 270 PAELE-EAVQYMTYVNCVDHILIDTVGRNYLAEESVSEISAYTDVVHPDLTCFTFSS--G 326
Query: 550 NEAVDQLVKFNNAMADHSLSDNPHLIDGIVLTKFDTIDDKVGAAISMTYITGQPIVFVGT 609
++ D + L++ P IDG ++TK D ++G ++ T P++++
Sbjct: 327 MKSADVMTILPK------LAEIP--IDGFIITKMDET-TRIGDLYTVMQETNLPVLYMTD 377
Query: 610 GQTYTD 615
GQ T+
Sbjct: 378 GQNITE 383
>gnl|CDD|237182 PRK12727, PRK12727, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 559
Score = 55.0 bits (132), Expect = 7e-08
Identities = 64/219 (29%), Positives = 95/219 (43%), Gaps = 40/219 (18%)
Query: 413 VMAFCGVNGVGKSTNLAKICFWLIENNL--NVLIAACDTFRAGAVEQLRTHVRHL-CSLH 469
V+A G G GK+T +AK+ + +V + DT R G EQL ++ R L ++H
Sbjct: 352 VIALVGPTGAGKTTTIAKLAQRFAAQHAPRDVALVTTDTQRVGGREQLHSYGRQLGIAVH 411
Query: 470 PAAKHGGREMVQLFEKGYGKDPAEIAFRAISHARDMHIDVVLIDTAGRMQDNEPLMRALA 529
A ++ L E+ RD + VLIDTAG Q + L L
Sbjct: 412 EA--DSAESLLDLLER----------------LRDYKL--VLIDTAGMGQRDRALAAQLN 451
Query: 530 KLVKVNQ-PDLLLFVGEALVGNEAVDQLV-KFNNAMADHSLSDNPHLIDGIVLTKFDTID 587
L Q LL+ A + +D++V +F +A P G+VLTK D
Sbjct: 452 WLRAARQVTSLLVLPANAHFSD--LDEVVRRFAHA--------KPQ---GVVLTKLDET- 497
Query: 588 DKVGAAISMTYITGQPIVFVGTGQTY-TDLKSLNAKAVV 625
+ G+A+S+ PI +V GQ DL NA ++V
Sbjct: 498 GRFGSALSVVVDHQMPITWVTDGQRVPDDLHRANAASLV 536
>gnl|CDD|237802 PRK14723, flhF, flagellar biosynthesis regulator FlhF; Provisional.
Length = 767
Score = 54.4 bits (131), Expect = 1e-07
Identities = 66/223 (29%), Positives = 97/223 (43%), Gaps = 37/223 (16%)
Query: 394 RRVDILRDALEAKKQGRPFVMAFCGVNGVGKSTNLAKIC--FWLIENNLNVLIAACDTFR 451
+ +LRD QG V+A G GVGK+T AK+ E + + D+FR
Sbjct: 170 THLPVLRDEDALLAQGG--VLALVGPTGVGKTTTTAKLAARCVAREGADQLALLTTDSFR 227
Query: 452 AGAVEQLRTHVRHL-CSLHPAAKHGGREMVQLFEKGYGKDPAEIAFRAISHARDMHIDVV 510
GA+EQLR + R L +H KD A++ F A++ D H+ V
Sbjct: 228 IGALEQLRIYGRILGVPVHAV-----------------KDAADLRF-ALAALGDKHL--V 267
Query: 511 LIDTAGRMQDNEPLMRALAKLVKVNQPDLLLFVGEALVGNEAV--DQLVKFNNAMADHSL 568
LIDT G Q + + +A L V +P V L+ N A D L + +A +
Sbjct: 268 LIDTVGMSQRDRNVSEQIAMLCGVGRP-----VRRLLLLNAASHGDTLNEVVHAYRHGAG 322
Query: 569 SDNPHLIDGIVLTKFDTIDDKVGAAISMTYITGQPIVFVGTGQ 611
D +DG ++TK D +G A+ P+ +V TGQ
Sbjct: 323 ED----VDGCIITKLDEA-THLGPALDTVIRHRLPVHYVSTGQ 360
>gnl|CDD|173185 PRK14722, flhF, flagellar biosynthesis regulator FlhF; Provisional.
Length = 374
Score = 52.4 bits (125), Expect = 3e-07
Identities = 72/281 (25%), Positives = 117/281 (41%), Gaps = 38/281 (13%)
Query: 333 PILEKMKDHLIAKNVAADIAVKLCDSVALKLEGKVLGTFESVANTVKSTLTDALVQILSP 392
P+ + +L A +A + + D++ EG+ T ++ A+ +S L L + S
Sbjct: 74 PVHGALTKYLFAAGFSAQLVRMIVDNLP---EGEGYDTLDAAADWAQSVLAANLPVLDS- 129
Query: 393 KRRVDILRDALEAKKQGRPFVMAFCGVNGVGKSTNLAKICFWLIE--NNLNVLIAACDTF 450
DAL R V A G GVGK+T AK+ + V + D++
Sbjct: 130 -------EDAL----MERGGVFALMGPTGVGKTTTTAKLAARCVMRFGASKVALLTTDSY 178
Query: 451 RAGAVEQLRTHVRHLCSLHPAAKHGGREMVQLFEKGYGKDPAEIAFRAISHARDMHIDVV 510
R G EQLR + L A K GG +QL A++ R+ H+ V
Sbjct: 179 RIGGHEQLRIFGKILGVPVHAVKDGGD--LQL---------------ALAELRNKHM--V 219
Query: 511 LIDTAGRMQDNEPLMRALAKLVKVNQPDLLLFVGEALVGNEAVDQLVKFNNAMADHSLSD 570
LIDT G Q + + +A L + P L + A + ++++V+ + A +
Sbjct: 220 LIDTIGMSQRDRTVSDQIAMLHGADTPVQRLLLLNATSHGDTLNEVVQAYRSAAGQPKAA 279
Query: 571 NPHLIDGIVLTKFDTIDDKVGAAISMTYITGQPIVFVGTGQ 611
P L G +LTK D + +G + P+ +V TGQ
Sbjct: 280 LPDLA-GCILTKLDEASN-LGGVLDTVIRYKLPVHYVSTGQ 318
>gnl|CDD|75717 PRK06731, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 270
Score = 51.7 bits (123), Expect = 4e-07
Identities = 50/200 (25%), Positives = 91/200 (45%), Gaps = 31/200 (15%)
Query: 414 MAFCGVNGVGKSTNLAKICFWLIENNLNVLIAACDTFRAGAVEQLRTHVRHLCSLHPAAK 473
+A G GVGK+T LAK+ + V D R G V+QL+ +V+ +
Sbjct: 78 IALIGPTGVGKTTTLAKMAWQFHGKKKTVGFITTDHSRIGTVQQLQDYVKTI-------- 129
Query: 474 HGGREMVQLFEKGYGKDPAEIAFRAISHAR-DMHIDVVLIDTAGRMQDNEPLMRALAKLV 532
G E++ + +D A + RA+++ + + +D +LIDTAG+ + + + +
Sbjct: 130 --GFEVIAV------RDEAAMT-RALTYFKEEARVDYILIDTAGKNYRASETVEEMIETM 180
Query: 533 KVNQPDLL-LFVGEALVGNEAVDQLVKFNNAMADHSLSDNPHLIDGIVLTKFDTIDDKVG 591
+PD + L + ++ + ++ + F + IDGIV TKFD G
Sbjct: 181 GQVEPDYICLTLSASMKSKDMIEIITNFKDIH-----------IDGIVFTKFDETASS-G 228
Query: 592 AAISMTYITGQPIVFVGTGQ 611
+ + ++ PIV + GQ
Sbjct: 229 ELLKIPAVSSAPIVLMTDGQ 248
>gnl|CDD|183360 PRK11889, flhF, flagellar biosynthesis regulator FlhF; Provisional.
Length = 436
Score = 52.8 bits (126), Expect = 4e-07
Identities = 50/200 (25%), Positives = 91/200 (45%), Gaps = 31/200 (15%)
Query: 414 MAFCGVNGVGKSTNLAKICFWLIENNLNVLIAACDTFRAGAVEQLRTHVRHLCSLHPAAK 473
+A G GVGK+T LAK+ + V D R G V+QL+ +V+ +
Sbjct: 244 IALIGPTGVGKTTTLAKMAWQFHGKKKTVGFITTDHSRIGTVQQLQDYVKTI-------- 295
Query: 474 HGGREMVQLFEKGYGKDPAEIAFRAISHAR-DMHIDVVLIDTAGRMQDNEPLMRALAKLV 532
G E++ + +D A + RA+++ + + +D +LIDTAG+ + + + +
Sbjct: 296 --GFEVIAV------RDEAAMT-RALTYFKEEARVDYILIDTAGKNYRASETVEEMIETM 346
Query: 533 KVNQPD-LLLFVGEALVGNEAVDQLVKFNNAMADHSLSDNPHLIDGIVLTKFDTIDDKVG 591
+PD + L + ++ + ++ + F + IDGIV TKFD G
Sbjct: 347 GQVEPDYICLTLSASMKSKDMIEIITNFKDIH-----------IDGIVFTKFDETASS-G 394
Query: 592 AAISMTYITGQPIVFVGTGQ 611
+ + ++ PIV + GQ
Sbjct: 395 ELLKIPAVSSAPIVLMTDGQ 414
>gnl|CDD|214941 smart00963, SRP54_N, SRP54-type protein, helical bundle domain.
This entry represents the N-terminal helical bundle
domain of the 54 kDa SRP54 component, a GTP-binding
protein that interacts with the signal sequence when it
emerges from the ribosome. SRP54 of the signal
recognition particle has a three-domain structure: an
N-terminal helical bundle domain, a GTPase domain, and
the M-domain that binds the 7s RNA and also binds the
signal sequence. The extreme C-terminal region is
glycine-rich and lower in complexity and poorly
conserved between species.
Length = 77
Score = 44.1 bits (105), Expect = 7e-06
Identities = 21/78 (26%), Positives = 42/78 (53%), Gaps = 1/78 (1%)
Query: 313 MFSLFRGLVGSKNLTKSDMKPILEKMKDHLIAKNVAADIAVKLCDSVALKLEGKVLGTFE 372
+ L+G LT+ D + +LE++++ L+ +V ++ ++ + V K +G+VL
Sbjct: 1 LSKALGKLLGELFLTEKDDEELLEELEEALLEADVGVEVVKEIIERVKEKAKGEVLKGL- 59
Query: 373 SVANTVKSTLTDALVQIL 390
+ VK L + LV+IL
Sbjct: 60 TPKQEVKKILKEELVKIL 77
>gnl|CDD|234368 TIGR03835, termin_org_DnaJ, terminal organelle assembly protein
TopJ. This model describes TopJ (MG_200, CbpA), a DnaJ
homolog and probable assembly protein of the Mycoplasma
terminal organelle. The terminal organelle is involved
in both cytadherence and gliding motility [Cellular
processes, Chemotaxis and motility].
Length = 871
Score = 39.4 bits (91), Expect = 0.006
Identities = 40/214 (18%), Positives = 80/214 (37%), Gaps = 11/214 (5%)
Query: 105 YDYDFESTYNVLLKEAEEWSKVQACIPKQMRTFEESSKSKKTIASMIIDKNKKEEKSVPS 164
+D + E + E W + P+ + + I+S ++ +E P
Sbjct: 216 FDENGEWIWKGYFDEDGNWVWTRELEPQDDSEDDYVIPDAEIISSPTLEVTAPKEVEQPL 275
Query: 165 KKKGKAVETKVE--PVTPPSPVQNG--------DAGIEEDIIMINRQKLAMKMGSPKNKT 214
+ + ET E P P Q ++ +EE++ IN+ A++ S T
Sbjct: 276 QPEPVDEETVAETKAEEEPQPTQTVETKPTSAPESTVEENLPEINQPTQAVQPTSETIST 335
Query: 215 KPKTPKANAKEGKKPRIWELSGDQRDLSTLEYTKDKPSDSNALNITPDTHLVGKMVGGIK 274
P P K + +I E + +E K +D +N L ++V +
Sbjct: 336 TPVEPTDQLKPKEVDQIQE-ELKKTKEIEVEELPTKKNDLVEINFDDLEELKFELVQTNQ 394
Query: 275 DLEVESSSEEESSDDEEDVRAETSHVSAKKANGK 308
+ E E + E ++D + D +++ K+ + K
Sbjct: 395 EKEPEKAVENWATDYQLDEPTQSNIDWYKQEDPK 428
>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the AAA
superfamily.
Length = 154
Score = 37.6 bits (87), Expect = 0.006
Identities = 23/119 (19%), Positives = 40/119 (33%), Gaps = 2/119 (1%)
Query: 394 RRVDILRDALEAKKQGRPFVMAFCGVNGVGKSTNLAKICFWLIENNLNVLIAACDTFRAG 453
++ L DAL + G P + G +G GK++ L ++ L+ A + A
Sbjct: 7 EELERLLDALRRARSGGPPSVLLTGPSGTGKTSLLRELLEGLLVAAGKCDQAERNPPYA- 65
Query: 454 AVEQLRTHVRHLCSLHPAAKHGGREMVQLFEKGYGKDPAEIAFRAISHARDMHIDVVLI 512
+ LR +R L A RE L G + +++
Sbjct: 66 FSQALRELLRQLLRELAAELLLLRE-ALLAALGAELIEGLQDLVELLERLLARARPLVL 123
>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional.
Length = 1388
Score = 38.9 bits (91), Expect = 0.009
Identities = 29/162 (17%), Positives = 47/162 (29%), Gaps = 16/162 (9%)
Query: 131 PKQMRTFEESSKSKKTIASMIIDKNKKEEKSVPSKKKGKAVETKVEPVTPPSPVQNGDAG 190
+ + S S+ D +K+ + K+ + P P NG +
Sbjct: 1242 RLKSKKNNSSKSSEDNDEFSSDDLSKEGKPKNAPKRVSAVQYSPPPPSKRPDGESNGGSK 1301
Query: 191 IEEDIIMINRQKLAMKMGSPKNKTKPKTPKANAKEGKKPRIWELSGDQRDLSTLEYTKDK 250
++ GS K K + KK S +
Sbjct: 1302 PSSPT---KKKVKKRLEGSLAALKKKKKSEKKTARKKK-------------SKTRVKQAS 1345
Query: 251 PSDSNALNITPDTHLVGKMVGGIKDLEVESSSEEESSDDEED 292
S S+ L P D EV+ S +E+ DDE+D
Sbjct: 1346 ASQSSRLLRRPRKKKSDSSSEDDDDSEVDDSEDEDDEDDEDD 1387
>gnl|CDD|217266 pfam02881, SRP54_N, SRP54-type protein, helical bundle domain.
Length = 77
Score = 34.9 bits (81), Expect = 0.012
Identities = 13/72 (18%), Positives = 30/72 (41%)
Query: 311 KGMFSLFRGLVGSKNLTKSDMKPILEKMKDHLIAKNVAADIAVKLCDSVALKLEGKVLGT 370
S G + L + + +LE++++ L+ +V + K+ + + + K L
Sbjct: 6 SKTRSKLGGKIKDLFLGEKKIDELLEELEEALLEADVGVETTEKIIERLKELVGRKGLSD 65
Query: 371 FESVANTVKSTL 382
E + +K L
Sbjct: 66 PEEIKKALKEEL 77
>gnl|CDD|238941 cd01983, Fer4_NifH, The Fer4_NifH superfamily contains a variety of
proteins which share a common ATP-binding domain.
Functionally, proteins in this superfamily use the
energy from hydrolysis of NTP to transfer electron or
ion.
Length = 99
Score = 35.1 bits (81), Expect = 0.016
Identities = 15/96 (15%), Positives = 28/96 (29%), Gaps = 12/96 (12%)
Query: 413 VMAFCGVNGVGKSTNLAKICFWLIENNLNVLI------------AACDTFRAGAVEQLRT 460
V+ G GVGK+T A + L + VL+
Sbjct: 1 VIVVTGKGGVGKTTLAANLAAALAKRGKRVLLIDDYVLIDTPPGLGLLVLLCLLALLAAD 60
Query: 461 HVRHLCSLHPAAKHGGREMVQLFEKGYGKDPAEIAF 496
V + + A G R + ++ + + +
Sbjct: 61 LVIIVTTPEALAVLGARRLTEVVLELAIEGLRPVGV 96
>gnl|CDD|129833 TIGR00750, lao, LAO/AO transport system ATPase. In E. coli,
mutation of this kinase blocks phosphorylation of two
transporter system periplasmic binding proteins and
consequently inhibits those transporters. This kinase is
also found in Gram-positive bacteria, archaea, and the
roundworm C. elegans. It may have a more general, but
still unknown function. Mutations have also been found
that do not phosphorylate the periplasmic binding
proteins, yet still allow transport. The ATPase activity
of this protein seems to be necessary, however
[Transport and binding proteins, Amino acids, peptides
and amines, Regulatory functions, Protein interactions].
Length = 300
Score = 37.1 bits (86), Expect = 0.019
Identities = 44/192 (22%), Positives = 66/192 (34%), Gaps = 44/192 (22%)
Query: 379 KSTLTDALVQILSPKRRVDILRDALEAKKQGRPFVMAFCGVNGVGKSTNLAKICFWLIEN 438
+ L A+ + + L D + G + G G GKST L + L
Sbjct: 3 RRALARAITLVENRHPEAKELLDRIMPY-TGNAHRVGITGTPGAGKSTLLEALGMELRRR 61
Query: 439 NLNVLIAACD---TFRAGAVEQLRTHVRHLCSLHPAA---------KHGG-----REMVQ 481
L V + A D F G++ RT ++ L + P A GG RE+V
Sbjct: 62 GLRVAVIAVDPSSPFTGGSILGDRTRMQRL-ATDPGAFIRSMPTRGHLGGLSQATRELVL 120
Query: 482 LFEK-GYGKDPAEIAFRAISHARDMHIDVVLIDTAGRMQDNEPLMRALAKLVKVNQPDLL 540
L + GY DV++++T G Q + V V P
Sbjct: 121 LLDAAGY--------------------DVIIVETVGVGQSEVDIANMADTFVLVTIPGT- 159
Query: 541 LFVGEALVGNEA 552
G+ L G +A
Sbjct: 160 ---GDDLQGIKA 168
>gnl|CDD|183703 PRK12724, PRK12724, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 432
Score = 37.3 bits (86), Expect = 0.024
Identities = 44/188 (23%), Positives = 77/188 (40%), Gaps = 23/188 (12%)
Query: 277 EVESSSEEESSDDEEDVRAETSHVSAKKANGKANKGMFSLFRGLVGSKNLTKSDMKPILE 336
E ES+ E S + E+V E S + L + +S+ I+
Sbjct: 103 EKESAIYEIESFELEEVITEPERPVG-----------LSFEKELFEKNSFLESE-TTIVR 150
Query: 337 KMKD----HLIAKNVAADIAVKLCDSVALKLEGKVLGTFESVANTVKSTLTDALVQILSP 392
K KD L + V ++ + +A KLE ++ V +T+ V L
Sbjct: 151 KEKDSPLQRLGERLVREGMSQSYVEEMASKLEERL----SPVDQGRNHNVTERAVTYL-- 204
Query: 393 KRRVDILRDALEAKKQGRPFVMAFCGVNGVGKSTNLAKICF-WLIENNLNVLIAACDTFR 451
+ RV + D + + V+ F G G GK+T++AK+ + + +V + D +R
Sbjct: 205 EERVSVDSDLFSGTGKNQRKVVFFVGPTGSGKTTSIAKLAAKYFLHMGKSVSLYTTDNYR 264
Query: 452 AGAVEQLR 459
A+EQL+
Sbjct: 265 IAAIEQLK 272
>gnl|CDD|112137 pfam03308, ArgK, ArgK protein. The ArgK protein acts as an ATPase
enzyme and as a kinase, and phosphorylates periplasmic
binding proteins involved in the LAO (lysine, arginine,
ornithine)/AO transport systems.
Length = 267
Score = 35.0 bits (81), Expect = 0.086
Identities = 37/148 (25%), Positives = 56/148 (37%), Gaps = 40/148 (27%)
Query: 386 LVQILSPKRRVDILRDALEAKKQGRPFVMAFCGVNGVGKSTNLAKICFWLIENNLNVLIA 445
LV+ P+ R +LR + GR + GV G GKST + + L V +
Sbjct: 7 LVESRRPEARE-LLRRLMP--LTGRAHRVGITGVPGAGKSTLIEALGMELRRRGHRVAVL 63
Query: 446 ACD---TFRAGAVEQLRTHVRHLCSLHPAA---------KHGG-----REMVQLFEKGYG 488
A D F G++ RT ++ L ++ P A GG RE + L + G
Sbjct: 64 AVDPSSPFTGGSILGDRTRMQRL-AVDPGAFIRSSPSRGALGGLSRATREAILLLD-AAG 121
Query: 489 KDPAEIAFRAISHARDMHIDVVLIDTAG 516
DV++I+T G
Sbjct: 122 ------------------FDVIIIETVG 131
>gnl|CDD|233595 TIGR01845, outer_NodT, efflux transporter, outer membrane factor
(OMF) lipoprotein, NodT family. Members of This model
comprise a subfamily of the Outer Membrane Factor (TCDB
1.B.17) porins. OMF proteins operate in conjunction with
a primary transporter of the RND, MFS, ABC, or PET
systems, and a MFP (membrane fusion protein) to tranport
substrates across membranes. The complex thus formed
allows transport (export) of various solutes (heavy
metal cations; drugs, oligosaccharides, proteins, etc.)
across the two envelopes of the Gram-negative bacterial
cell envelope in a single energy-coupled step. Current
data suggest that the OMF (and not the MFP) is largely
responsible for the formation of both the trans-outer
membrane and trans-periplasmic channels. The roles
played by the MFP have yet to be determined [Cellular
processes, Detoxification, Transport and binding
proteins, Porins].
Length = 454
Score = 35.5 bits (82), Expect = 0.090
Identities = 26/132 (19%), Positives = 46/132 (34%), Gaps = 28/132 (21%)
Query: 290 EEDVRAETSHVSAKKAN-----------GKANKGMFSLFRGLVGSKNLTKSDMKPILE-- 336
E + A + + KA G + + LF G ++ + PI +
Sbjct: 284 ERRLAAANAQIGVAKAAFFPSITLSASIGLSASQLSRLFDGGSRFWSIGPALALPIFDGG 343
Query: 337 KMKDHLIAKNVAADIAVKLCDSVALKLEGKVLGTFESVANTVKSTLTDALVQILSPKRRV 396
++ L + D AV VL F+ VA+ + + A RR+
Sbjct: 344 SLRAALDSAKATYDAAVAQY-------RQTVLTAFQEVADALVALQALA--------RRL 388
Query: 397 DILRDALEAKKQ 408
D R A+E ++
Sbjct: 389 DAQRQAVEQAQE 400
>gnl|CDD|226691 COG4240, COG4240, Predicted kinase [General function prediction
only].
Length = 300
Score = 34.5 bits (79), Expect = 0.14
Identities = 18/61 (29%), Positives = 27/61 (44%), Gaps = 1/61 (1%)
Query: 400 RDALEAKKQGRPFVMAFCGVNGVGKSTNLAKICFWLIENNL-NVLIAACDTFRAGAVEQL 458
+ A A+++GRP ++ G G GKST A I L L + D ++L
Sbjct: 39 KIAPWAQERGRPLIVGISGPQGSGKSTLSALIVRLLAAKGLERTATLSLDDLYLTHADRL 98
Query: 459 R 459
R
Sbjct: 99 R 99
>gnl|CDD|235904 PRK06995, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 484
Score = 34.2 bits (79), Expect = 0.23
Identities = 56/222 (25%), Positives = 82/222 (36%), Gaps = 74/222 (33%)
Query: 413 VMAFCGVNGVGKSTNLAKICFWLIENNLNVLIAAC--------------DTFRAGAVEQL 458
V A G GVGK+T AK L A C D++R G EQL
Sbjct: 258 VFALMGPTGVGKTTTTAK------------LAARCVMRHGASKVALLTTDSYRIGGHEQL 305
Query: 459 RTHVRHL-CSLHPAAKHGGREMVQLFEKGYGKDPAEIAFRAISHARDMHIDVVLIDTAGR 517
R + + L +H KD A++ A+S R+ HI VLIDT G
Sbjct: 306 RIYGKILGVPVHAV-----------------KDAADLRL-ALSELRNKHI--VLIDTIGM 345
Query: 518 MQDNEPLMRALAKLVKVNQPDLLLFVGEALVGNEAVDQLVKFNNAMADHSLSD------N 571
Q + + +A L P V +L+ N +L++
Sbjct: 346 SQRDRMVSEQIAMLHGAGAP---------------VKRLLLLNATSHGDTLNEVVQAYRG 390
Query: 572 PHLIDGIVLTKFDTIDDKVGAAISM-TYITGQ-PIVFVGTGQ 611
P L G +LTK +D+ ++ I + P+ +V GQ
Sbjct: 391 PGL-AGCILTK---LDEAASLGGALDVVIRYKLPLHYVSNGQ 428
>gnl|CDD|183702 PRK12723, PRK12723, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 388
Score = 33.7 bits (77), Expect = 0.25
Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 4/58 (6%)
Query: 408 QGRPFVMAFCGVNGVGKSTNLAKIC----FWLIENNLNVLIAACDTFRAGAVEQLRTH 461
+ V G GVGK+T +AK+ + +LN+ I D +R GA +Q++T+
Sbjct: 171 NLKKRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQIQTY 228
>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional.
Length = 509
Score = 33.8 bits (78), Expect = 0.29
Identities = 26/180 (14%), Positives = 56/180 (31%), Gaps = 7/180 (3%)
Query: 134 MRTFEESSKSKKTIASMIIDKNKKEEKSVPSKKKGKAVETKVEPVTPPSPVQNGDAGIEE 193
E +++ + + K + + ++ +A+E+K + V +G+ +
Sbjct: 5 STKAELAAEEEAKKKLKKLAAKSKSKGFITKEEIKEALESKKKTPEQIDQVLIFLSGMVK 64
Query: 194 DIIMINRQKLAMKMGSPKNK---TKPKTPKANAKEGKKPRIWELSGDQRDLSTLEYTKDK 250
D + K K K K E + E L Y KD
Sbjct: 65 DTDDATESDIPKKKTKTAAKAAAAKAPAKKKLKDELDSSKKAEKKNALDKDDDLNYVKDI 124
Query: 251 PSDSNALNITPDTHLVGKMVGGI----KDLEVESSSEEESSDDEEDVRAETSHVSAKKAN 306
+ A + D I D + + +++ DDE++ + E + +
Sbjct: 125 DVLNQADDDDDDDDDDDLDDDDIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKELEKLSDD 184
>gnl|CDD|173184 PRK14721, flhF, flagellar biosynthesis regulator FlhF; Provisional.
Length = 420
Score = 33.4 bits (76), Expect = 0.36
Identities = 53/224 (23%), Positives = 93/224 (41%), Gaps = 39/224 (17%)
Query: 413 VMAFCGVNGVGKSTNLAKICFWLI--ENNLNVLIAACDTFRAGAVEQLRTHVRHL-CSLH 469
V A G GVGK+T AK+ + V + D++R G EQLR + + L S+
Sbjct: 193 VYALIGPTGVGKTTTTAKLAARAVIRHGADKVALLTTDSYRIGGHEQLRIYGKLLGVSVR 252
Query: 470 PAAKHGGREMVQLFEKGYGKDPAEIAFRAISHARDMHIDVVLIDTAGRMQDNEPLMRALA 529
KD A++ + R H+ VLIDT G Q ++ L +A
Sbjct: 253 SI-----------------KDIADLQL-MLHELRGKHM--VLIDTVGMSQRDQMLAEQIA 292
Query: 530 KLVKVNQPDLLLFVGEALVGNEAVDQLVKFNNAMADHSLSDNPHLIDGIVLTKFDTIDDK 589
L + L + A + +D+++ + H I G ++TK +D+
Sbjct: 293 MLSQCGTQVKHLLLLNATSSGDTLDEVIS----------AYQGHGIHGCIITK---VDEA 339
Query: 590 VGAAISMTYITGQPIV--FVGTGQTY-TDLKSLNAKAVVNALMK 630
I++ + + +V +V GQ DL N++ +++ + K
Sbjct: 340 ASLGIALDAVIRRKLVLHYVTNGQKVPEDLHEANSRYLLHRIFK 383
>gnl|CDD|220271 pfam09507, CDC27, DNA polymerase subunit Cdc27. This protein forms
the C subunit of DNA polymerase delta. It carries the
essential residues for binding to the Pol1 subunit of
polymerase alpha, from residues 293-332, which are
characterized by the motif D--G--VT, referred to as the
DPIM motif. The first 160 residues of the protein form
the minimal domain for binding to the B subunit, Cdc1,
of polymerase delta, the final 10 C-terminal residues,
362-372, being the DNA sliding clamp, PCNA, binding
motif.
Length = 427
Score = 32.5 bits (74), Expect = 0.76
Identities = 22/104 (21%), Positives = 35/104 (33%), Gaps = 3/104 (2%)
Query: 127 QACIPKQMRTFEESSKSKKTIASMIIDKNKKEEKSVPSKKKGKAVETKVEPVTPPSPVQN 186
+ SSK K+I S + K K +K+ + K+ K E T
Sbjct: 151 SPALKPTANGKRPSSKPPKSIMSPEV-KVKSAKKTQDTSKETTTE--KTEGKTSVKAASL 207
Query: 187 GDAGIEEDIIMINRQKLAMKMGSPKNKTKPKTPKANAKEGKKPR 230
++ IM + K K K + T K ++E R
Sbjct: 208 KRNPPKKSNIMSSFFKKKTKEKKEKKEASESTVKEESEEESGKR 251
>gnl|CDD|206727 cd04164, trmE, trmE is a tRNA modification GTPase. TrmE (MnmE,
ThdF, MSS1) is a 3-domain protein found in bacteria and
eukaryotes. It controls modification of the uridine at
the wobble position (U34) of tRNAs that read codons
ending with A or G in the mixed codon family boxes. TrmE
contains a GTPase domain that forms a canonical Ras-like
fold. It functions a molecular switch GTPase, and
apparently uses a conformational change associated with
GTP hydrolysis to promote the tRNA modification
reaction, in which the conserved cysteine in the
C-terminal domain is thought to function as a catalytic
residue. In bacteria that are able to survive in
extremely low pH conditions, TrmE regulates
glutamate-dependent acid resistance.
Length = 159
Score = 31.3 bits (72), Expect = 0.79
Identities = 28/112 (25%), Positives = 47/112 (41%), Gaps = 25/112 (22%)
Query: 504 DMHID---VVLIDTAG-RMQDN----EPLMRALAKLVKVNQPDLLLFVGEALVGNEAVDQ 555
++ + V LIDTAG R ++ + RA + + DL+L V +A G + D
Sbjct: 45 EIDLGGIPVRLIDTAGLRETEDEIEKIGIERAREAI---EEADLVLLVVDASEGLDEEDL 101
Query: 556 LVKFNNAMADHSLSDNPHLIDGIVLTKFDTIDDKVGAAISMTYITGQPIVFV 607
L +I +VL K D + D G + + G+PI+ +
Sbjct: 102 --------EILELPAKKPVI--VVLNKSDLLSDAEGISE----LNGKPIIAI 139
>gnl|CDD|183452 PRK12337, PRK12337, 2-phosphoglycerate kinase; Provisional.
Length = 475
Score = 32.1 bits (73), Expect = 0.89
Identities = 22/86 (25%), Positives = 38/86 (44%), Gaps = 7/86 (8%)
Query: 342 LIAKNVAADIAVKLCDSVALKLEGKVLGTFESVANTVKSTLTDALVQILSPK--RRVDIL 399
L+A +A D+A +L L G + ++ + L++ + RR +L
Sbjct: 189 LMAAGLAPDVARRLARETERDLRR--SGDRVVRRDQLRRKVEALLLEEAGEEVARRYRLL 246
Query: 400 RDALEAKKQGRPFVMAFCGVNGVGKS 425
R ++ RP + GV+GVGKS
Sbjct: 247 R---SIRRPPRPLHVLIGGVSGVGKS 269
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 31.8 bits (73), Expect = 1.2
Identities = 15/75 (20%), Positives = 27/75 (36%)
Query: 140 SSKSKKTIASMIIDKNKKEEKSVPSKKKGKAVETKVEPVTPPSPVQNGDAGIEEDIIMIN 199
SK I++K +K+ + +KK KA K + + + EE+
Sbjct: 404 GSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAE 463
Query: 200 RQKLAMKMGSPKNKT 214
+K + K T
Sbjct: 464 EEKEEEEEKKKKQAT 478
>gnl|CDD|187777 cd09646, Cas7_I-E, CRISPR/Cas system-associated RAMP superfamily
protein Cas7. CRISPR (Clustered Regularly Interspaced
Short Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Cas7 is a RAMP superfamily protein; Subunit of the
Cascade complex; also known as Cse4/CasC family.
Length = 325
Score = 31.3 bits (71), Expect = 1.5
Identities = 27/149 (18%), Positives = 47/149 (31%), Gaps = 24/149 (16%)
Query: 190 GIEEDIIMINRQKLAMKMGSPKNKTKPKTPKANAKE-----GKKPRIW-ELSGDQRDLST 243
G +EDI + K+A + K K +A E + E +
Sbjct: 78 GYDEDIAEPDAAKIAYGLKKASGKKSDKLLLLSAPEAAWVARYAAELADEFDAAAAADAV 137
Query: 244 LEYTKDKPS--DSNALNITP---DTHLVGKMVGGIKDLEVE---------SSSEEESSDD 289
+ DK D A + D L G+M+ + + V+ + E D
Sbjct: 138 ADKELDKNFKEDLAAARLPQGGVDIALFGRMLASLPEANVDAAVQVAHAFTVHAVEVEVD 197
Query: 290 ----EEDVRAETSHVSAKKANGKANKGMF 314
+D++ E S + + G F
Sbjct: 198 FFTAVDDLKKEEDSGSGHMGETEFSSGTF 226
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 29.9 bits (68), Expect = 1.6
Identities = 20/134 (14%), Positives = 44/134 (32%), Gaps = 23/134 (17%)
Query: 413 VMAFCGVNGVGKSTNLAKICFWLIENNLNVLIAACDTFRAGAVEQLRTHVRHLCSLHPAA 472
+ G +G GK+T L + L N + + G + L + L P +
Sbjct: 6 IGVLTGESGSGKTTLLRR----LARQLPNRRVVYVEAPSLGTPKDLLRKILRALGL-PLS 60
Query: 473 KHGGREMVQLFEKGYGKDPAEIAFRAISHARDMHIDVVLIDTAGRMQDNEPLMRALAKLV 532
E+++ + +++ID A + + L L
Sbjct: 61 GGTTAELLEAILD---------------ALKRRGRPLLIIDEAQHLSLE--ALEELRDLY 103
Query: 533 KVNQPDL-LLFVGE 545
+++ + ++ VG
Sbjct: 104 DLSEKGIQVILVGT 117
>gnl|CDD|221803 pfam12846, AAA_10, AAA-like domain. This family of domains contain
a P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins.
Length = 316
Score = 30.9 bits (70), Expect = 1.8
Identities = 10/31 (32%), Positives = 15/31 (48%)
Query: 414 MAFCGVNGVGKSTNLAKICFWLIENNLNVLI 444
M G +G GKST L + L+ V++
Sbjct: 4 MLIVGPSGSGKSTLLKLLALRLLARGGRVIV 34
>gnl|CDD|238835 cd01672, TMPK, Thymidine monophosphate kinase (TMPK), also known as
thymidylate kinase, catalyzes the phosphorylation of
thymidine monophosphate (TMP) to thymidine diphosphate
(TDP) utilizing ATP as its preferred phophoryl donor.
TMPK represents the rate-limiting step in either de novo
or salvage biosynthesis of thymidine triphosphate (TTP).
Length = 200
Score = 30.7 bits (70), Expect = 1.9
Identities = 8/29 (27%), Positives = 14/29 (48%)
Query: 415 AFCGVNGVGKSTNLAKICFWLIENNLNVL 443
F G++G GK+T + + L V+
Sbjct: 4 VFEGIDGAGKTTLIELLAERLEARGYEVV 32
>gnl|CDD|223998 COG1072, CoaA, Panthothenate kinase [Coenzyme metabolism].
Length = 283
Score = 30.7 bits (70), Expect = 2.2
Identities = 13/40 (32%), Positives = 19/40 (47%)
Query: 387 VQILSPKRRVDILRDALEAKKQGRPFVMAFCGVNGVGKST 426
+ + + +R L L Q RPF++ G VGKST
Sbjct: 58 LYVEARERLFAELLRFLGTNNQQRPFIIGIAGSVAVGKST 97
>gnl|CDD|237312 PRK13236, PRK13236, nitrogenase reductase; Reviewed.
Length = 296
Score = 30.8 bits (69), Expect = 2.2
Identities = 22/71 (30%), Positives = 32/71 (45%), Gaps = 1/71 (1%)
Query: 414 MAFCGVNGVGKSTNLAKICFWLIENNLNVLIAACDTFRAGAVEQLRTHVRHLCSLHPAAK 473
+AF G G+GKST + E +LI CD +A + + LH AA+
Sbjct: 9 IAFYGKGGIGKSTTSQNTLAAMAEMGQRILIVGCDP-KADSTRLMLHSKAQTTVLHLAAE 67
Query: 474 HGGREMVQLFE 484
G E ++L E
Sbjct: 68 RGAVEDLELHE 78
>gnl|CDD|206646 cd00880, Era_like, E. coli Ras-like protein (Era)-like GTPase. The
Era (E. coli Ras-like protein)-like family includes
several distinct subfamilies (TrmE/ThdF, FeoB, YihA
(EngB), Era, and EngA/YfgK) that generally show sequence
conservation in the region between the Walker A and B
motifs (G1 and G3 box motifs), to the exclusion of other
GTPases. TrmE is ubiquitous in bacteria and is a
widespread mitochondrial protein in eukaryotes, but is
absent from archaea. The yeast member of TrmE family,
MSS1, is involved in mitochondrial translation;
bacterial members are often present in
translation-related operons. FeoB represents an unusual
adaptation of GTPases for high-affinity iron (II)
transport. YihA (EngB) family of GTPases is typified by
the E. coli YihA, which is an essential protein involved
in cell division control. Era is characterized by a
distinct derivative of the KH domain (the pseudo-KH
domain) which is located C-terminal to the GTPase
domain. EngA and its orthologs are composed of two
GTPase domains and, since the sequences of the two
domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family.
Length = 161
Score = 29.9 bits (68), Expect = 2.3
Identities = 23/107 (21%), Positives = 38/107 (35%), Gaps = 16/107 (14%)
Query: 507 IDVVLIDTAG--RMQDNEPLMRALAKLVKVNQPDLLLFVGEALVGNEAVDQLVKFNNAMA 564
VVLIDT G A+ V ++ DL+L V ++ V++ K
Sbjct: 46 GPVVLIDTPGLDEEGGLGRERVEEARQV-ADRADLVLLVVDS--DLTPVEEEAKLGLL-- 100
Query: 565 DHSLSDNPHLIDGIVLTKFDTIDDKVGAAISMT----YITGQPIVFV 607
P L +VL K D + + + + P++ V
Sbjct: 101 --RERGKPVL---LVLNKIDLVPESEEEELLRERKLELLPDLPVIAV 142
>gnl|CDD|222010 pfam13254, DUF4045, Domain of unknown function (DUF4045). This
presumed domain is functionally uncharacterized. This
domain family is found in bacteria and eukaryotes, and
is typically between 384 and 430 amino acids in length.
Length = 414
Score = 31.0 bits (70), Expect = 2.3
Identities = 21/90 (23%), Positives = 32/90 (35%), Gaps = 2/90 (2%)
Query: 134 MRTFEESSKSKKTIASMIID--KNKKEEKSVPSKKKGKAVETKVEPVTPPSPVQNGDAGI 191
MRT S SK S I D ++ EK+ P K + + E + P P + D
Sbjct: 207 MRTPPPGSHSKSPSKSGIPDLPSSRDSEKTKPEKPQQETSSMDTEKSSAPKPRETLDPKS 266
Query: 192 EEDIIMINRQKLAMKMGSPKNKTKPKTPKA 221
E I+ + +K K +
Sbjct: 267 PEKAPPIDTTEEELKSPEASPKESEEASAR 296
>gnl|CDD|237728 PRK14490, PRK14490, putative bifunctional molybdopterin-guanine
dinucleotide biosynthesis protein MobB/MobA;
Provisional.
Length = 369
Score = 30.8 bits (70), Expect = 2.4
Identities = 12/28 (42%), Positives = 17/28 (60%)
Query: 411 PFVMAFCGVNGVGKSTNLAKICFWLIEN 438
PF +AFCG +G GK+T + + L E
Sbjct: 5 PFEIAFCGYSGSGKTTLITALVRRLSER 32
>gnl|CDD|215641 PLN03237, PLN03237, DNA topoisomerase 2; Provisional.
Length = 1465
Score = 31.0 bits (70), Expect = 2.5
Identities = 43/242 (17%), Positives = 74/242 (30%), Gaps = 32/242 (13%)
Query: 74 LQLSYVDKLLDDVHLEFRDKYKNELGSDMH------LYDYDFESTYNVLLKEAEEWSKVQ 127
L L V +L D RDK N D+ L+ D ++ L K +E +K +
Sbjct: 1123 LTLEKVQELCAD-----RDK-LNIEVEDLKKTTPKSLWLKDLDALEKELDKLDKEDAKAE 1176
Query: 128 ACIPKQMRTFEESSKSKKTIASMIIDKNKKEEKSVPSKKKGKAVETKVEPVTPPSPVQNG 187
K R ++ ++ A+ + + + K P K KA E++ T S
Sbjct: 1177 EAREKLQR----AAARGESGAAKKVSRQAPK-KPAPKKTTKKASESETTEETYGSSAMET 1231
Query: 188 DAGIEEDIIMINRQKLAMKMGSPKNKTKPKTPKANAKEGKKPRIWELSGDQRDLSTLEYT 247
+ E + K + K P K +E + + + S +
Sbjct: 1232 ENVAEV---------VKPKGRAGAKKKAPAAAKEKEEEDEILDLKDRLAAYNLDSAPAQS 1282
Query: 248 KDKPSDSNALNITPDTHLVGKMVGGIKDLEVESSSEEESSDDEEDVRAETSHVSAKKANG 307
A+ V S+ + DD+ V + KK
Sbjct: 1283 AKMEETVKAVPARRAAA------RKKPLASVSVISDSDDDDDDFAVEVSLAERLKKKGGR 1336
Query: 308 KA 309
K
Sbjct: 1337 KP 1338
>gnl|CDD|224617 COG1703, ArgK, Putative periplasmic protein kinase ArgK and related
GTPases of G3E family [Amino acid transport and
metabolism].
Length = 323
Score = 30.4 bits (69), Expect = 2.7
Identities = 19/61 (31%), Positives = 26/61 (42%), Gaps = 5/61 (8%)
Query: 400 RDALEAKK--QGRPFVMAFCGVNGVGKSTNLAKICFWLIENNLNVLIAACD---TFRAGA 454
R+ L A G V+ GV G GKST + + L E V + A D F G+
Sbjct: 38 RELLRALYPRTGNAHVIGITGVPGAGKSTLIEALGRELRERGHRVAVLAVDPSSPFTGGS 97
Query: 455 V 455
+
Sbjct: 98 I 98
>gnl|CDD|226927 COG4555, NatA, ABC-type Na+ transport system, ATPase component
[Energy production and conversion / Inorganic ion
transport and metabolism].
Length = 245
Score = 30.1 bits (68), Expect = 2.9
Identities = 29/106 (27%), Positives = 41/106 (38%), Gaps = 11/106 (10%)
Query: 396 VDILRDALEAKKQGRPFVMAFCGVNGVGKSTNLAKICFWLIENNLNVLIAACDTFRAGAV 455
V +RD ++G + G NG GK+T L I LI ++ V I DT V
Sbjct: 15 VQAVRDVSFEAEEGE--ITGLLGENGAGKTTLLRMIATLLIPDSGKVTIDGVDT-----V 67
Query: 456 EQLRTHVRHLCSLHPA----AKHGGREMVQLFEKGYGKDPAEIAFR 497
R + L A+ RE ++ F + G EI R
Sbjct: 68 RDPSFVRRKIGVLFGERGLYARLTARENLKYFARLNGLSRKEIKAR 113
>gnl|CDD|183903 PRK13230, PRK13230, nitrogenase reductase-like protein; Reviewed.
Length = 279
Score = 30.1 bits (68), Expect = 3.0
Identities = 14/34 (41%), Positives = 18/34 (52%)
Query: 415 AFCGVNGVGKSTNLAKICFWLIENNLNVLIAACD 448
F G G+GKST + I L E+ VL+ CD
Sbjct: 5 CFYGKGGIGKSTTVCNIAAALAESGKKVLVVGCD 38
>gnl|CDD|201032 pfam00142, Fer4_NifH, 4Fe-4S iron sulfur cluster binding proteins,
NifH/frxC family.
Length = 272
Score = 30.0 bits (68), Expect = 3.5
Identities = 14/36 (38%), Positives = 16/36 (44%)
Query: 413 VMAFCGVNGVGKSTNLAKICFWLIENNLNVLIAACD 448
+A G G+GKST L E VLI CD
Sbjct: 2 KIAIYGKGGIGKSTTTQNTSAALAEMGKKVLIVGCD 37
>gnl|CDD|147379 pfam05165, GGDN, GGDN family. I have named this protein family of
unknown function GGDN after the most conserved motif.
The proteins are 200-270 amino acids in length.
Length = 246
Score = 29.9 bits (67), Expect = 3.9
Identities = 20/89 (22%), Positives = 38/89 (42%), Gaps = 12/89 (13%)
Query: 506 HIDVVLIDTAGRMQDNEPLMRALAKLVKVNQPDLLLFVGEALVGNEAVDQLVKFNNAMAD 565
HID+ + G + D +R +VN D++ + + L A+ Q + +N MA
Sbjct: 132 HIDIN--NITGTITDIVSPVRTY---YEVN--DVMAKLMKVLEKIGALTQFIGGDNFMAP 184
Query: 566 HSLSDNPHLIDGIVLTKFDTIDDKVGAAI 594
+ GIVL +++ + V +
Sbjct: 185 -----CNGIDAGIVLDINNSVKETVDVDL 208
>gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of
cellular Activities) superfamily represents an ancient
group of ATPases belonging to the ASCE (for additional
strand, catalytic E) division of the P-loop NTPase fold.
The ASCE division also includes ABC, RecA-like,
VirD4-like, PilT-like, and SF1/2 helicases. Members of
the AAA+ ATPases function as molecular chaperons, ATPase
subunits of proteases, helicases, or nucleic-acid
stimulated ATPases. The AAA+ proteins contain several
distinct features in addition to the conserved
alpha-beta-alpha core domain structure and the Walker A
and B motifs of the P-loop NTPases.
Length = 151
Score = 28.7 bits (64), Expect = 4.9
Identities = 13/62 (20%), Positives = 19/62 (30%)
Query: 395 RVDILRDALEAKKQGRPFVMAFCGVNGVGKSTNLAKICFWLIENNLNVLIAACDTFRAGA 454
+ + + EA + P + G G GK+T I L L G
Sbjct: 3 QEEAIEALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGL 62
Query: 455 VE 456
V
Sbjct: 63 VV 64
>gnl|CDD|234395 TIGR03918, GTP_HydF, [FeFe] hydrogenase H-cluster maturation GTPase
HydF. This model describes the family of the [Fe]
hydrogenase maturation protein HypF as characterized in
Chlamydomonas reinhardtii and found, in an operon with
radical SAM proteins HydE and HydG, in numerous
bacteria. It has GTPase activity, can bind an 4Fe-4S
cluster, and is essential for hydrogenase activity
[Protein fate, Protein modification and repair].
Length = 391
Score = 29.4 bits (67), Expect = 6.1
Identities = 31/121 (25%), Positives = 52/121 (42%), Gaps = 16/121 (13%)
Query: 509 VVLIDTAGRMQDNEPL--MRALAKLVKVNQPDLLLFVGEALVGNEAVD-QLVKFNNAMAD 565
VVLIDTAG + D L +R +++ DL L V +A VG + +L++
Sbjct: 57 VVLIDTAG-LDDEGELGELRVEKTREVLDKTDLALLVVDAGVGPGEYELELIEELKER-- 113
Query: 566 HSLSDNPHLIDGIVLTKFDTIDDKVGAAISMTYITGQPIVFVG--TGQTYTDLKSLNAKA 623
P++ +V+ K D ++ G P +FV TG+ +LK +
Sbjct: 114 ----KIPYI---VVINKIDLGEESAELEKLEKKF-GLPPIFVSALTGEGIDELKEAIIEL 165
Query: 624 V 624
+
Sbjct: 166 L 166
>gnl|CDD|234034 TIGR02858, spore_III_AA, stage III sporulation protein AA. Members
of this protein are the stage III sporulation protein
AA, encoded by one of several genes in the spoIIIA
locus. It seems that this protein is found in a species
if and only if that species is capable of endospore
formation [Cellular processes, Sporulation and
germination].
Length = 270
Score = 29.2 bits (66), Expect = 6.1
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 503 RDMHIDVVLIDTAGRMQDNEPLMRALAKLVKV 534
R M DV+++D GR +D E L+ AL V +
Sbjct: 191 RSMSPDVIVVDEIGREEDVEALLEALHAGVSI 222
>gnl|CDD|201133 pfam00289, CPSase_L_chain, Carbamoyl-phosphate synthase L chain,
N-terminal domain. Carbamoyl-phosphate synthase
catalyzes the ATP-dependent synthesis of
carbamyl-phosphate from glutamine or ammonia and
bicarbonate. This important enzyme initiates both the
urea cycle and the biosynthesis of arginine and/or
pyrimidines. The carbamoyl-phosphate synthase (CPS)
enzyme in prokaryotes is a heterodimer of a small and
large chain. The small chain promotes the hydrolysis of
glutamine to ammonia, which is used by the large chain
to synthesise carbamoyl phosphate. See pfam00988. The
small chain has a GATase domain in the carboxyl
terminus. See pfam00117.
Length = 108
Score = 27.8 bits (63), Expect = 6.1
Identities = 20/91 (21%), Positives = 32/91 (35%), Gaps = 20/91 (21%)
Query: 493 EIAFRAISHARDMHIDVVLIDTAGRMQDNEPLMRALAKLVKVNQPDLLLFVGEALVGN-- 550
EIA R I R++ I+ V +++ P + V D F+G
Sbjct: 11 EIAVRIIRALRELGIETVAVNS-------NPDTVSTH----VRLADEAYFLGPGPASESY 59
Query: 551 ---EAVDQLVKFNNAMADH----SLSDNPHL 574
E + + + A A H LS+N
Sbjct: 60 LNIERILDIAEKEGADAIHPGYGFLSENAEF 90
>gnl|CDD|206747 cd01854, YjeQ_EngC, Ribosomal interacting GTPase YjeQ/EngC, a
circularly permuted subfamily of the Ras GTPases. YjeQ
(YloQ in Bacillus subtilis) is a ribosomal small
subunit-dependent GTPase; hence also known as RsgA. YjeQ
is a late-stage ribosomal biogenesis factor involved in
the 30S subunit maturation, and it represents a protein
family whose members are broadly conserved in bacteria
and have been shown to be essential to the growth of E.
coli and B. subtilis. Proteins of the YjeQ family
contain all sequence motifs typical of the vast class of
P-loop-containing GTPases, but show a circular
permutation, with a G4-G1-G3 pattern of motifs as
opposed to the regular G1-G3-G4 pattern seen in most
GTPases. All YjeQ family proteins display a unique
domain architecture, which includes an N-terminal
OB-fold RNA-binding domain, the central permuted GTPase
domain, and a zinc knuckle-like C-terminal cysteine
domain.
Length = 211
Score = 28.9 bits (66), Expect = 6.9
Identities = 12/31 (38%), Positives = 16/31 (51%), Gaps = 6/31 (19%)
Query: 396 VDILRDALEAKKQGRPFVMAFCGVNGVGKST 426
+D LR+ L+ K G +GVGKST
Sbjct: 76 LDELRELLKGK------TSVLVGQSGVGKST 100
>gnl|CDD|206648 cd00882, Ras_like_GTPase, Rat sarcoma (Ras)-like superfamily of
small guanosine triphosphatases (GTPases). Ras-like
GTPase superfamily. The Ras-like superfamily of small
GTPases consists of several families with an extremely
high degree of structural and functional similarity. The
Ras superfamily is divided into at least four families
in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families.
This superfamily also includes proteins like the GTP
translation factors, Era-like GTPases, and G-alpha chain
of the heterotrimeric G proteins. Members of the Ras
superfamily regulate a wide variety of cellular
functions: the Ras family regulates gene expression, the
Rho family regulates cytoskeletal reorganization and
gene expression, the Rab and Sar1/Arf families regulate
vesicle trafficking, and the Ran family regulates
nucleocytoplasmic transport and microtubule
organization. The GTP translation factor family
regulates initiation, elongation, termination, and
release in translation, and the Era-like GTPase family
regulates cell division, sporulation, and DNA
replication. Members of the Ras superfamily are
identified by the GTP binding site, which is made up of
five characteristic sequence motifs, and the switch I
and switch II regions.
Length = 161
Score = 28.6 bits (64), Expect = 7.3
Identities = 16/88 (18%), Positives = 35/88 (39%), Gaps = 7/88 (7%)
Query: 507 IDVVLIDTAGRMQDNEPLMRALAKLVKVNQPDLLLFVGEALVGNEAVDQLVKFNNAMADH 566
+ +VL+DT G + + L R + + DL+L V ++ D + +
Sbjct: 47 VKLVLVDTPG-LDEFGGLGREELARLLLRGADLILLVVDSTDRESEEDAKLLILRRLRKE 105
Query: 567 SLSDNPHLIDGIVLTKFDTIDDKVGAAI 594
P + +V K D ++++ +
Sbjct: 106 ---GIPII---LVGNKIDLLEEREVEEL 127
>gnl|CDD|222795 PHA00441, PHA00441, hypothetical protein.
Length = 89
Score = 27.3 bits (60), Expect = 7.6
Identities = 19/99 (19%), Positives = 38/99 (38%), Gaps = 13/99 (13%)
Query: 213 KTKPKTPKANAKEGKKPRIWELSGDQRDLSTLEYTKDKPSDSNALNITPDTHLVGKMVGG 272
K KTPK + + + P L+ + ++++ D D+ G G
Sbjct: 4 SPKIKTPKVDTNQVRAPEPAPLT---EEPKSVDFGGDDDEDTT----------EGTSTSG 50
Query: 273 IKDLEVESSSEEESSDDEEDVRAETSHVSAKKANGKANK 311
K L+V+ S ++ +A+T S+ + + K
Sbjct: 51 RKSLKVKKDDSPAKSKASDNGKAKTGSKSSIRKSAFGGK 89
>gnl|CDD|238991 cd02034, CooC, The accessory protein CooC, which contains a
nucleotide-binding domain (P-loop) near the N-terminus,
participates in the maturation of the nickel center of
carbon monoxide dehydrogenase (CODH). CODH from
Rhodospirillum rubrum catalyzes the reversible oxidation
of CO to CO2. CODH contains a nickel-iron-sulfur cluster
(C-center) and an iron-sulfur cluster (B-center). CO
oxidation occurs at the C-center. Three accessory
proteins encoded by cooCTJ genes are involved in nickel
incorporation into a nickel site. CooC functions as a
nickel insertase that mobilizes nickel to apoCODH using
energy released from ATP hydrolysis. CooC is a homodimer
and has NTPase activities. Mutation at the P-loop
abolishs its function.
Length = 116
Score = 27.6 bits (62), Expect = 8.1
Identities = 13/36 (36%), Positives = 17/36 (47%)
Query: 413 VMAFCGVNGVGKSTNLAKICFWLIENNLNVLIAACD 448
+A G GVGK+T A + +L E VL D
Sbjct: 1 KIAITGKGGVGKTTIAALLARYLAEKGKPVLAIDAD 36
>gnl|CDD|224084 COG1162, COG1162, Predicted GTPases [General function prediction
only].
Length = 301
Score = 28.8 bits (65), Expect = 8.3
Identities = 10/40 (25%), Positives = 16/40 (40%), Gaps = 2/40 (5%)
Query: 387 VQILSPKRRVDILRDALEAKKQGRPFVMAFCGVNGVGKST 426
+L + + L G+ + G +GVGKST
Sbjct: 142 YPVLFVSAKNGDGLEELAELLAGK--ITVLLGQSGVGKST 179
>gnl|CDD|215332 PLN02616, PLN02616, tetrahydrofolate dehydrogenase/cyclohydrolase,
putative.
Length = 364
Score = 28.8 bits (64), Expect = 8.4
Identities = 30/111 (27%), Positives = 47/111 (42%), Gaps = 23/111 (20%)
Query: 179 TPPSPVQNGDAGIEEDIIMINRQKLAMKMGSPKNKTKPKTPKANAKEGKKPRIWE-LSGD 237
+ PSPV N D G E +I+ + +A K+ +++ + + G P + L GD
Sbjct: 57 SSPSPVINADTGSEGGAKVIDGKAVAKKI---RDEITIEVSRMKESIGVVPGLAVILVGD 113
Query: 238 QRDLSTLEYTKDKPSDSNALNITPDTHLVGKMVGGIKDLEV---ESSSEEE 285
++D +T K K DS GI EV E S+E+E
Sbjct: 114 RKDSATYVRNKKKACDSV----------------GINSFEVRLPEDSTEQE 148
>gnl|CDD|233608 TIGR01869, casC_Cse4, CRISPR-associated protein Cas7/Cse4/CasC,
subtype I-E/ECOLI. CRISPR is a term for Clustered,
Regularly Interspaced Short Palidromic Repeats. A number
of protein families appear only in association with
these repeats and are designated Cas (CRISPR-Associated)
proteins. This family is represented by CT1975 of
Chlorobium tepidum and is part of the Ecoli subtype of
CRISPR/Cas locis. It is designated Cse4, for CRISPR/Cas
Subtype Ecoli protein 4 [Mobile and extrachromosomal
element functions, Other].
Length = 325
Score = 29.0 bits (65), Expect = 8.6
Identities = 27/148 (18%), Positives = 48/148 (32%), Gaps = 23/148 (15%)
Query: 190 GIEEDIIMINRQKLAMKMGSPKNKTKPKTPKANAKE------GKKPRIWELSGDQRDLST 243
G +EDI + K+A + K K K +A E + EL+ +
Sbjct: 79 GYDEDIAEPDAAKIAYGLKLAKGKKSDKLLLLSAPETAWLARLAEELFDELAAAAEQDAV 138
Query: 244 LEYTKDKPS----DSNALNITPDTHLVGKMVGGIKDLEVE---------SSSEEESSDD- 289
+ K D+ L D L G+M+ + + V+ + E D
Sbjct: 139 ADKALKKNFKALLDAARLPGGVDIALFGRMLASLPEANVDAAVQVAHAFTVHAVEVEVDF 198
Query: 290 ---EEDVRAETSHVSAKKANGKANKGMF 314
+D++ S + + G F
Sbjct: 199 FTAVDDLKKAEDSGSGHLGETEFSSGTF 226
>gnl|CDD|200419 TIGR04168, TIGR04168, TIGR04168 family protein. Members of this
uncharacterized protein family are restricted, in 49 of
50 genomes, to organisms with a family TIGR04167 radical
SAM protein, which occasionally is a selenoprotein.
Length = 269
Score = 28.4 bits (64), Expect = 9.7
Identities = 12/23 (52%), Positives = 18/23 (78%), Gaps = 3/23 (13%)
Query: 536 QPDLLLFVGEALVGNEAVDQLVK 558
PDL+LFVG+ GNE++ +LV+
Sbjct: 5 GPDLVLFVGD--FGNESL-ELVR 24
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.316 0.133 0.373
Gapped
Lambda K H
0.267 0.0806 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 31,580,685
Number of extensions: 3140687
Number of successful extensions: 3923
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3831
Number of HSP's successfully gapped: 109
Length of query: 630
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 527
Effective length of database: 6,369,140
Effective search space: 3356536780
Effective search space used: 3356536780
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 62 (27.5 bits)