RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10020
(640 letters)
>gnl|CDD|233327 TIGR01241, FtsH_fam, ATP-dependent metalloprotease FtsH.
HflB(FtsH) is a pleiotropic protein required for correct
cell division in bacteria. It has ATP-dependent zinc
metalloprotease activity. It was formerly designated
cell division protein FtsH [Cellular processes, Cell
division, Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 495
Score = 131 bits (332), Expect = 1e-32
Identities = 47/70 (67%), Positives = 57/70 (81%)
Query: 1 MEFVDYLKRPEYYQNLGAKVPKGALLLGPPGCGKTLLAKAVATEANVPFLSMNGSEFIEM 60
ME VD+LK P + LGAK+PKG LL+GPPG GKTLLAKAVA EA VPF S++GS+F+EM
Sbjct: 68 MEIVDFLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEM 127
Query: 61 IGGLGAARVR 70
G+GA+RVR
Sbjct: 128 FVGVGASRVR 137
Score = 79.3 bits (196), Expect = 1e-15
Identities = 31/67 (46%), Positives = 41/67 (61%), Gaps = 2/67 (2%)
Query: 358 RQVAFHESGHALVGWLLPHTDALLKVTIVPRTSLALGFAQYTPSEQK-LYNKEEIFSPID 416
+ VA+HE+GHALVG LL D + KVTI+PR ALG+ Q+ P E K LY K ++ + I
Sbjct: 312 KLVAYHEAGHALVGLLLKDADPVHKVTIIPR-GQALGYTQFLPEEDKYLYTKSQLLAQIA 370
Query: 417 TSRSHRV 423
R
Sbjct: 371 VLLGGRA 377
Score = 78.5 bits (194), Expect = 2e-15
Identities = 31/58 (53%), Positives = 39/58 (67%), Gaps = 2/58 (3%)
Query: 494 KEEVAFHESGHALVGWLLPHTDALLKVTIVPRTSLALGFAQYTPSEQK-LYNKEETLD 550
K+ VA+HE+GHALVG LL D + KVTI+PR ALG+ Q+ P E K LY K + L
Sbjct: 311 KKLVAYHEAGHALVGLLLKDADPVHKVTIIPR-GQALGYTQFLPEEDKYLYTKSQLLA 367
Score = 74.6 bits (184), Expect = 5e-14
Identities = 29/54 (53%), Positives = 37/54 (68%), Gaps = 2/54 (3%)
Query: 444 RQVAFHESGHALVGWLLPHTDALLKVTIVPRTSLALGFAQYTPSEQK-LYNKEE 496
+ VA+HE+GHALVG LL D + KVTI+PR ALG+ Q+ P E K LY K +
Sbjct: 312 KLVAYHEAGHALVGLLLKDADPVHKVTIIPR-GQALGYTQFLPEEDKYLYTKSQ 364
>gnl|CDD|214386 CHL00176, ftsH, cell division protein; Validated.
Length = 638
Score = 113 bits (285), Expect = 3e-26
Identities = 46/69 (66%), Positives = 57/69 (82%)
Query: 2 EFVDYLKRPEYYQNLGAKVPKGALLLGPPGCGKTLLAKAVATEANVPFLSMNGSEFIEMI 61
E V +LK+PE + +GAK+PKG LL+GPPG GKTLLAKA+A EA VPF S++GSEF+EM
Sbjct: 197 EVVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGEAEVPFFSISGSEFVEMF 256
Query: 62 GGLGAARVR 70
G+GAARVR
Sbjct: 257 VGVGAARVR 265
Score = 53.5 bits (129), Expect = 2e-07
Identities = 27/59 (45%), Positives = 39/59 (66%), Gaps = 2/59 (3%)
Query: 358 RQVAFHESGHALVGWLLPHTDALLKVTIVPRTSLALGFAQYTPSE-QKLYNKEEIFSPI 415
R +A+HE GHA+VG LLP+ D + KVT++PR A G +TP E Q L ++ +I + I
Sbjct: 439 RLIAYHEVGHAIVGTLLPNHDPVQKVTLIPRGQ-AKGLTWFTPEEDQSLVSRSQILARI 496
Score = 53.1 bits (128), Expect = 4e-07
Identities = 24/50 (48%), Positives = 33/50 (66%), Gaps = 1/50 (2%)
Query: 493 NKEEVAFHESGHALVGWLLPHTDALLKVTIVPRTSLALGFAQYTPSEQKL 542
NK +A+HE GHA+VG LLP+ D + KVT++PR A G +TP E +
Sbjct: 437 NKRLIAYHEVGHAIVGTLLPNHDPVQKVTLIPRGQ-AKGLTWFTPEEDQS 485
Score = 51.6 bits (124), Expect = 9e-07
Identities = 23/48 (47%), Positives = 32/48 (66%), Gaps = 1/48 (2%)
Query: 444 RQVAFHESGHALVGWLLPHTDALLKVTIVPRTSLALGFAQYTPSEQKL 491
R +A+HE GHA+VG LLP+ D + KVT++PR A G +TP E +
Sbjct: 439 RLIAYHEVGHAIVGTLLPNHDPVQKVTLIPRGQ-AKGLTWFTPEEDQS 485
>gnl|CDD|223541 COG0465, HflB, ATP-dependent Zn proteases [Posttranslational
modification, protein turnover, chaperones].
Length = 596
Score = 109 bits (275), Expect = 4e-25
Identities = 48/70 (68%), Positives = 58/70 (82%)
Query: 1 MEFVDYLKRPEYYQNLGAKVPKGALLLGPPGCGKTLLAKAVATEANVPFLSMNGSEFIEM 60
E VD+LK P+ YQ LGAK+PKG LL+GPPG GKTLLAKAVA EA VPF S++GS+F+EM
Sbjct: 163 SELVDFLKNPKKYQALGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEM 222
Query: 61 IGGLGAARVR 70
G+GA+RVR
Sbjct: 223 FVGVGASRVR 232
Score = 73.5 bits (181), Expect = 1e-13
Identities = 32/67 (47%), Positives = 41/67 (61%), Gaps = 2/67 (2%)
Query: 358 RQVAFHESGHALVGWLLPHTDALLKVTIVPRTSLALGFAQYTPSEQK-LYNKEEIFSPID 416
+ A+HE+GHALVG LLP D + KVTI+PR ALG+ + P E K L +KEE+ ID
Sbjct: 407 KITAYHEAGHALVGLLLPDADPVHKVTIIPRGR-ALGYTLFLPEEDKYLMSKEELLDRID 465
Query: 417 TSRSHRV 423
R
Sbjct: 466 VLLGGRA 472
Score = 70.0 bits (172), Expect = 2e-12
Identities = 32/60 (53%), Positives = 40/60 (66%), Gaps = 2/60 (3%)
Query: 493 NKEEVAFHESGHALVGWLLPHTDALLKVTIVPRTSLALGFAQYTPSEQK-LYNKEETLDP 551
K+ A+HE+GHALVG LLP D + KVTI+PR ALG+ + P E K L +KEE LD
Sbjct: 405 EKKITAYHEAGHALVGLLLPDADPVHKVTIIPRGR-ALGYTLFLPEEDKYLMSKEELLDR 463
Score = 64.3 bits (157), Expect = 1e-10
Identities = 29/54 (53%), Positives = 37/54 (68%), Gaps = 2/54 (3%)
Query: 444 RQVAFHESGHALVGWLLPHTDALLKVTIVPRTSLALGFAQYTPSEQK-LYNKEE 496
+ A+HE+GHALVG LLP D + KVTI+PR ALG+ + P E K L +KEE
Sbjct: 407 KITAYHEAGHALVGLLLPDADPVHKVTIIPRGR-ALGYTLFLPEEDKYLMSKEE 459
>gnl|CDD|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed.
Length = 644
Score = 101 bits (253), Expect = 2e-22
Identities = 42/69 (60%), Positives = 56/69 (81%)
Query: 2 EFVDYLKRPEYYQNLGAKVPKGALLLGPPGCGKTLLAKAVATEANVPFLSMNGSEFIEMI 61
E V+YL+ P +Q LG K+PKG L++GPPG GKTLLAKA+A EA VPF +++GS+F+EM
Sbjct: 166 ELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDFVEMF 225
Query: 62 GGLGAARVR 70
G+GA+RVR
Sbjct: 226 VGVGASRVR 234
Score = 50.4 bits (120), Expect = 2e-06
Identities = 28/63 (44%), Positives = 38/63 (60%), Gaps = 8/63 (12%)
Query: 494 KEEVAFHESGHALVGWLLPHTDALLKVTIVPRTSLALGFAQYTP-------SEQKLYNKE 546
KE A+HE+GHA++G L+P D + KVTI+PR ALG + P S QKL ++
Sbjct: 408 KESTAYHEAGHAIIGRLVPEHDPVHKVTIIPRGR-ALGVTFFLPEGDAISASRQKLESQI 466
Query: 547 ETL 549
TL
Sbjct: 467 STL 469
Score = 44.6 bits (105), Expect = 1e-04
Identities = 24/52 (46%), Positives = 32/52 (61%), Gaps = 8/52 (15%)
Query: 361 AFHESGHALVGWLLPHTDALLKVTIVPRTSLALGFAQYTP-------SEQKL 405
A+HE+GHA++G L+P D + KVTI+PR ALG + P S QKL
Sbjct: 412 AYHEAGHAIIGRLVPEHDPVHKVTIIPRGR-ALGVTFFLPEGDAISASRQKL 462
Score = 44.6 bits (105), Expect = 1e-04
Identities = 24/52 (46%), Positives = 32/52 (61%), Gaps = 8/52 (15%)
Query: 447 AFHESGHALVGWLLPHTDALLKVTIVPRTSLALGFAQYTP-------SEQKL 491
A+HE+GHA++G L+P D + KVTI+PR ALG + P S QKL
Sbjct: 412 AYHEAGHAIIGRLVPEHDPVHKVTIIPRGR-ALGVTFFLPEGDAISASRQKL 462
>gnl|CDD|216502 pfam01434, Peptidase_M41, Peptidase family M41.
Length = 212
Score = 88.8 bits (221), Expect = 4e-20
Identities = 34/67 (50%), Positives = 44/67 (65%), Gaps = 2/67 (2%)
Query: 358 RQVAFHESGHALVGWLLPHTDALLKVTIVPRTSLALGFAQYTPSEQK-LYNKEEIFSPID 416
R VA+HE+GHALVG LLP D + KVTI+PR ALG+ Q+ P E K LY K ++ + ID
Sbjct: 29 RLVAYHEAGHALVGLLLPGADPVHKVTIIPRGQ-ALGYTQFLPEEDKLLYTKSQLLARID 87
Query: 417 TSRSHRV 423
+ R
Sbjct: 88 VALGGRA 94
Score = 87.3 bits (217), Expect = 1e-19
Identities = 32/59 (54%), Positives = 39/59 (66%), Gaps = 2/59 (3%)
Query: 493 NKEEVAFHESGHALVGWLLPHTDALLKVTIVPRTSLALGFAQYTPSEQK-LYNKEETLD 550
K VA+HE+GHALVG LLP D + KVTI+PR ALG+ Q+ P E K LY K + L
Sbjct: 27 EKRLVAYHEAGHALVGLLLPGADPVHKVTIIPRGQ-ALGYTQFLPEEDKLLYTKSQLLA 84
Score = 83.4 bits (207), Expect = 3e-18
Identities = 31/54 (57%), Positives = 38/54 (70%), Gaps = 2/54 (3%)
Query: 444 RQVAFHESGHALVGWLLPHTDALLKVTIVPRTSLALGFAQYTPSEQK-LYNKEE 496
R VA+HE+GHALVG LLP D + KVTI+PR ALG+ Q+ P E K LY K +
Sbjct: 29 RLVAYHEAGHALVGLLLPGADPVHKVTIIPRGQ-ALGYTQFLPEEDKLLYTKSQ 81
>gnl|CDD|224143 COG1222, RPT1, ATP-dependent 26S proteasome regulatory subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 406
Score = 85.8 bits (213), Expect = 8e-18
Identities = 34/64 (53%), Positives = 42/64 (65%)
Query: 7 LKRPEYYQNLGAKVPKGALLLGPPGCGKTLLAKAVATEANVPFLSMNGSEFIEMIGGLGA 66
LK PE ++ LG PKG LL GPPG GKTLLAKAVA + + F+ + GSE ++ G GA
Sbjct: 171 LKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAVANQTDATFIRVVGSELVQKYIGEGA 230
Query: 67 ARVR 70
VR
Sbjct: 231 RLVR 234
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 83.0 bits (206), Expect = 6e-17
Identities = 35/64 (54%), Positives = 44/64 (68%)
Query: 7 LKRPEYYQNLGAKVPKGALLLGPPGCGKTLLAKAVATEANVPFLSMNGSEFIEMIGGLGA 66
LK+PE ++ +G + PKG LL GPPG GKTLLAKAVA E N F+ + GSE ++ G GA
Sbjct: 151 LKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELVQKFIGEGA 210
Query: 67 ARVR 70
VR
Sbjct: 211 RLVR 214
>gnl|CDD|215649 pfam00004, AAA, ATPase family associated with various cellular
activities (AAA). AAA family proteins often perform
chaperone-like functions that assist in the assembly,
operation, or disassembly of protein complexes.
Length = 131
Score = 74.2 bits (183), Expect = 8e-16
Identities = 24/46 (52%), Positives = 29/46 (63%)
Query: 25 LLLGPPGCGKTLLAKAVATEANVPFLSMNGSEFIEMIGGLGAARVR 70
LL GPPG GKT LAKAVA E PF+ ++GSE + G R+R
Sbjct: 2 LLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYVGESEKRLR 47
>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many
proteins may score above the trusted cutoff because an
internal.
Length = 364
Score = 76.4 bits (188), Expect = 7e-15
Identities = 35/64 (54%), Positives = 42/64 (65%)
Query: 7 LKRPEYYQNLGAKVPKGALLLGPPGCGKTLLAKAVATEANVPFLSMNGSEFIEMIGGLGA 66
LK PE ++ +G + PKG LL GPPG GKTLLAKAVA E N F+ + GSE + G GA
Sbjct: 142 LKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELVRKYIGEGA 201
Query: 67 ARVR 70
VR
Sbjct: 202 RLVR 205
>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like
protein; Provisional.
Length = 438
Score = 73.3 bits (180), Expect = 9e-14
Identities = 35/64 (54%), Positives = 41/64 (64%)
Query: 7 LKRPEYYQNLGAKVPKGALLLGPPGCGKTLLAKAVATEANVPFLSMNGSEFIEMIGGLGA 66
L PE Y ++G K PKG +L GPPG GKTLLAKAVA E + FL + GSE I+ G G
Sbjct: 203 LTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANETSATFLRVVGSELIQKYLGDGP 262
Query: 67 ARVR 70
VR
Sbjct: 263 KLVR 266
>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational
modification, protein turnover, chaperones].
Length = 494
Score = 71.4 bits (175), Expect = 5e-13
Identities = 35/71 (49%), Positives = 45/71 (63%), Gaps = 1/71 (1%)
Query: 1 MEFVDY-LKRPEYYQNLGAKVPKGALLLGPPGCGKTLLAKAVATEANVPFLSMNGSEFIE 59
E ++ LKRPE ++ LG + PKG LL GPPG GKTLLAKAVA E+ F+S+ GSE +
Sbjct: 255 KEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVALESRSRFISVKGSELLS 314
Query: 60 MIGGLGAARVR 70
G +R
Sbjct: 315 KWVGESEKNIR 325
Score = 43.7 bits (103), Expect = 2e-04
Identities = 30/50 (60%), Positives = 36/50 (72%), Gaps = 1/50 (2%)
Query: 7 LKRPEYYQNLGAKVPKGALLLGPPGCGKTLLAKAVATEANVPFLSMNGSE 56
LK PE ++ LG + PKG LL GPPG GKTLLA+A+A E FLS+NG E
Sbjct: 4 LKEPELFKKLGIEPPKGVLLHGPPGTGKTLLARALANE-GAEFLSINGPE 52
>gnl|CDD|233328 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily. This
subfamily of the AAA family ATPases includes two members
each from three archaeal species. It also includes yeast
CDC48 (cell division control protein 48) and the human
ortholog, transitional endoplasmic reticulum ATPase
(valosin-containing protein). These proteins in
eukaryotes are involved in the budding and transfer of
membrane from the transitional endoplasmic reticulum to
the Golgi apparatus.
Length = 733
Score = 70.3 bits (172), Expect = 2e-12
Identities = 34/64 (53%), Positives = 43/64 (67%)
Query: 7 LKRPEYYQNLGAKVPKGALLLGPPGCGKTLLAKAVATEANVPFLSMNGSEFIEMIGGLGA 66
+K PE +++LG + PKG LL GPPG GKTLLAKAVA EA F+S+NG E + G
Sbjct: 198 MKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAGAYFISINGPEIMSKYYGESE 257
Query: 67 ARVR 70
R+R
Sbjct: 258 ERLR 261
Score = 66.1 bits (161), Expect = 3e-11
Identities = 36/83 (43%), Positives = 47/83 (56%), Gaps = 2/83 (2%)
Query: 7 LKRPEYYQNLGAKVPKGALLLGPPGCGKTLLAKAVATEANVPFLSMNGSEFIEMIGGLGA 66
LK PE ++ +G + PKG LL GPPG GKTLLAKAVATE+ F+++ G E + G
Sbjct: 473 LKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATESGANFIAVRGPEILSKWVGESE 532
Query: 67 ARVRTEVVFLHCRVFLHEITIFD 89
+R +F R I FD
Sbjct: 533 KAIRE--IFRKARQAAPAIIFFD 553
>gnl|CDD|240423 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like
protein; Provisional.
Length = 398
Score = 68.3 bits (167), Expect = 3e-12
Identities = 31/64 (48%), Positives = 39/64 (60%)
Query: 7 LKRPEYYQNLGAKVPKGALLLGPPGCGKTLLAKAVATEANVPFLSMNGSEFIEMIGGLGA 66
L PE Y+ +G P+G LL GPPG GKT+LAKAVA F+ + GSEF++ G G
Sbjct: 165 LTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHHTTATFIRVVGSEFVQKYLGEGP 224
Query: 67 ARVR 70
VR
Sbjct: 225 RMVR 228
>gnl|CDD|224144 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 368
Score = 63.7 bits (155), Expect = 9e-11
Identities = 30/67 (44%), Positives = 40/67 (59%), Gaps = 3/67 (4%)
Query: 4 VDYLKRPEYYQNLGAKVPKGALLLGPPGCGKTLLAKAVATEANVPFLSMNGSEFIEMIGG 63
++YL+ PE + G PK L GPPG GKT++AKA+A EA VP L + +E I G
Sbjct: 137 MEYLENPERF---GDWAPKNVLFYGPPGTGKTMMAKALANEAKVPLLLVKATELIGEHVG 193
Query: 64 LGAARVR 70
GA R+
Sbjct: 194 DGARRIH 200
>gnl|CDD|200312 TIGR03689, pup_AAA, proteasome ATPase. In the Actinobacteria, as
shown for Mycobacterium tuberculosis, some proteins are
modified by ligation between an epsilon-amino group of a
lysine side chain and the C-terminal carboxylate of the
ubiquitin-like protein Pup. This modification leads to
protein degradation by the archaeal-like proteasome
found in the Actinobacteria. Members of this protein
family belong to the AAA family of ATPases and tend to
be clustered with the genes for Pup, the Pup ligase
PafA, and structural components of the proteasome. This
protein forms hexameric rings with ATPase activity
[Protein fate, Degradation of proteins, peptides, and
glycopeptides].
Length = 512
Score = 57.8 bits (140), Expect = 9e-09
Identities = 24/34 (70%), Positives = 26/34 (76%)
Query: 10 PEYYQNLGAKVPKGALLLGPPGCGKTLLAKAVAT 43
PE Y+ G K PKG LL GPPGCGKTL+AKAVA
Sbjct: 205 PELYREYGLKPPKGVLLYGPPGCGKTLIAKAVAN 238
>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 = 52.1 bits (125), Expect = 5e-08
Identities = 22/53 (41%), Positives = 28/53 (52%), Gaps = 3/53 (5%)
Query: 21 PKGALLLGPPGCGKTLLAKAVATEA---NVPFLSMNGSEFIEMIGGLGAARVR 70
PK LL GPPG GKT LA+A+A E PFL +N S+ +E +
Sbjct: 19 PKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHF 71
>gnl|CDD|224145 COG1224, TIP49, DNA helicase TIP49, TBP-interacting protein
[Transcription].
Length = 450
Score = 46.2 bits (110), Expect = 4e-05
Identities = 19/38 (50%), Positives = 28/38 (73%), Gaps = 2/38 (5%)
Query: 22 KGALLLGPPGCGKTLLAKAVATE--ANVPFLSMNGSEF 57
+G L++GPPG GKT LA +A E +VPF++++GSE
Sbjct: 66 RGILIVGPPGTGKTALAMGIARELGEDVPFVAISGSEI 103
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 45.3 bits (108), Expect = 8e-05
Identities = 24/59 (40%), Positives = 31/59 (52%), Gaps = 7/59 (11%)
Query: 19 KVPKGALLL-GPPGCGKTLLAKAVATEANVPFLSMNGSEF-----IEMIGGLGAARVRT 71
PK ALLL GPPG GKT LA A+A + + +N S+ IE + G AA +
Sbjct: 36 GKPKKALLLYGPPGVGKTSLAHALANDYGWEVIELNASDQRTADVIERVAG-EAATSGS 93
>gnl|CDD|177094 CHL00195, ycf46, Ycf46; Provisional.
Length = 489
Score = 44.2 bits (105), Expect = 2e-04
Identities = 21/57 (36%), Positives = 32/57 (56%)
Query: 14 QNLGAKVPKGALLLGPPGCGKTLLAKAVATEANVPFLSMNGSEFIEMIGGLGAARVR 70
N G P+G LL+G G GK+L AKA+A + +P L ++ + I G +R+R
Sbjct: 252 SNYGLPTPRGLLLVGIQGTGKSLTAKAIANDWQLPLLRLDVGKLFGGIVGESESRMR 308
>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction
only].
Length = 329
Score = 44.0 bits (104), Expect = 2e-04
Identities = 16/35 (45%), Positives = 23/35 (65%)
Query: 25 LLLGPPGCGKTLLAKAVATEANVPFLSMNGSEFIE 59
LL GPPG GKTLLA+A+A +PF+ + + +
Sbjct: 47 LLEGPPGVGKTLLARALARALGLPFVRIQCTPDLL 81
>gnl|CDD|147949 pfam06068, TIP49, TIP49 C-terminus. This family consists of the
C-terminal region of several eukaryotic and archaeal
RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin
or TIP49b) proteins. The N-terminal domain contains the
pfam00004 domain. In zebrafish, the liebeskummer (lik)
mutation, causes development of hyperplastic embryonic
hearts. lik encodes Reptin, a component of a
DNA-stimulated ATPase complex. Beta-catenin and Pontin,
a DNA-stimulated ATPase that is often part of complexes
with Reptin, are in the same genetic pathways. The
Reptin/Pontin ratio serves to regulate heart growth
during development, at least in part via the
beta-catenin pathway. TBP-interacting protein 49
(TIP49) was originally identified as a TBP-binding
protein, and two related proteins are encoded by
individual genes, tip49a and b. Although the function
of this gene family has not been elucidated, they are
supposed to play a critical role in nuclear events
because they interact with various kinds of nuclear
factors and have DNA helicase activities.TIP49a has
been suggested to act as an autoantigen in some
patients with autoimmune diseases.
Length = 395
Score = 43.8 bits (104), Expect = 2e-04
Identities = 17/38 (44%), Positives = 24/38 (63%), Gaps = 2/38 (5%)
Query: 22 KGALLLGPPGCGKTLLAKAVATE--ANVPFLSMNGSEF 57
+ L+ GPPG GKT LA A++ E + PF ++GSE
Sbjct: 51 RAVLIAGPPGTGKTALAIAISKELGEDTPFCPISGSEV 88
>gnl|CDD|235422 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX;
Provisional.
Length = 412
Score = 43.6 bits (104), Expect = 3e-04
Identities = 15/25 (60%), Positives = 19/25 (76%)
Query: 25 LLLGPPGCGKTLLAKAVATEANVPF 49
LL+GP G GKTLLA+ +A +VPF
Sbjct: 112 LLIGPTGSGKTLLAQTLARILDVPF 136
>gnl|CDD|224140 COG1219, ClpX, ATP-dependent protease Clp, ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 408
Score = 43.4 bits (103), Expect = 3e-04
Identities = 16/25 (64%), Positives = 19/25 (76%)
Query: 25 LLLGPPGCGKTLLAKAVATEANVPF 49
LL+GP G GKTLLA+ +A NVPF
Sbjct: 101 LLIGPTGSGKTLLAQTLAKILNVPF 125
>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 41.6 bits (99), Expect = 0.001
Identities = 13/29 (44%), Positives = 20/29 (68%)
Query: 25 LLLGPPGCGKTLLAKAVATEANVPFLSMN 53
+L GPPG GKT LA+ +A + PF +++
Sbjct: 40 ILWGPPGTGKTTLARIIAGATDAPFEALS 68
>gnl|CDD|225165 COG2256, MGS1, ATPase related to the helicase subunit of the
Holliday junction resolvase [DNA replication,
recombination, and repair].
Length = 436
Score = 39.9 bits (94), Expect = 0.003
Identities = 13/30 (43%), Positives = 19/30 (63%)
Query: 24 ALLLGPPGCGKTLLAKAVATEANVPFLSMN 53
+L GPPG GKT LA+ +A N F +++
Sbjct: 51 MILWGPPGTGKTTLARLIAGTTNAAFEALS 80
>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 = 37.7 bits (87), Expect = 0.004
Identities = 16/42 (38%), Positives = 26/42 (61%), Gaps = 3/42 (7%)
Query: 21 PKGALLLGPPGCGKTLLAKAVATEANVP---FLSMNGSEFIE 59
+ L++GPPG GKT LA+A+A E P + ++G + +E
Sbjct: 2 GEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILE 43
>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common
bacterial type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. This family
represents the SMC protein of most bacteria. The smc
gene is often associated with scpB (TIGR00281) and scpA
genes, where scp stands for segregation and condensation
protein. SMC was shown (in Caulobacter crescentus) to be
induced early in S phase but present and bound to DNA
throughout the cell cycle [Cellular processes, Cell
division, DNA metabolism, Chromosome-associated
proteins].
Length = 1179
Score = 39.7 bits (93), Expect = 0.005
Identities = 29/117 (24%), Positives = 53/117 (45%), Gaps = 10/117 (8%)
Query: 118 NLEKEVMLRKKLEEEYSIELGRKLQDMEIKHAEELKKQEQCLRKEKVLKIDAELRHKKEL 177
LE+E+ +K EE S R++ + A + EQ E++ ++ EL EL
Sbjct: 709 ELEEELEQLRKELEELS----RQISALRKDLARLEAEVEQLE--ERIAQLSKEL---TEL 759
Query: 178 DLERQILLHEITKLKSELKNRELHIVKMETQLRAYESDKKLARKQLIDSVNREIAET 234
+ E + L + + + EL E I ++E Q+ + + K R+ L D + E+
Sbjct: 760 EAEIEELEERLEEAEEELAEAEAEIEELEAQIEQLKEELKALREAL-DELRAELTLL 815
>gnl|CDD|232949 TIGR00382, clpX, endopeptidase Clp ATP-binding regulatory subunit
(clpX). A member of the ATP-dependent proteases, ClpX
has ATP-dependent chaperone activity and is required for
specific ATP-dependent proteolytic activities expressed
by ClpPX. The gene is also found to be involved in
stress tolerance in Bacillus subtilis and is essential
for the efficient acquisition of genes specifying type
IA and IB restriction [Protein fate, Protein folding and
stabilization, Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 413
Score = 39.0 bits (91), Expect = 0.006
Identities = 16/25 (64%), Positives = 19/25 (76%)
Query: 25 LLLGPPGCGKTLLAKAVATEANVPF 49
LL+GP G GKTLLA+ +A NVPF
Sbjct: 120 LLIGPTGSGKTLLAQTLARILNVPF 144
>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y. Members of this family are
RNase Y, an endoribonuclease. The member from Bacillus
subtilis, YmdA, has been shown to be involved in
turnover of yitJ riboswitch [Transcription, Degradation
of RNA].
Length = 514
Score = 38.4 bits (90), Expect = 0.011
Identities = 32/125 (25%), Positives = 57/125 (45%), Gaps = 13/125 (10%)
Query: 118 NLEKEVMLRKKLE-EEYSIELGRKLQDMEIKHAEELKKQEQCLR-KEKVLKIDAELRHKK 175
L+KE +L K E + EL R+L++ EL++ E+ L +E+ L E KK
Sbjct: 47 TLKKEALLEAKEEVHKLRAELERELKERR----NELQRLERRLLQREETLDRKMESLDKK 102
Query: 176 ELDLERQILLHEITKLKSELKNRELHIVKMET-QLRAYESDKKL----ARKQLIDSVNRE 230
E +LE++ E++ + L +E + ++ Q E L A++ L++ V E
Sbjct: 103 EENLEKK--EKELSNKEKNLDEKEEELEELIAEQREELERISGLTQEEAKEILLEEVEEE 160
Query: 231 IAETI 235
Sbjct: 161 ARHEA 165
>gnl|CDD|233959 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit
clpA. [Protein fate, Degradation of proteins, peptides,
and glycopeptides].
Length = 730
Score = 38.5 bits (90), Expect = 0.013
Identities = 19/40 (47%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 21 PKGALLL-GPPGCGKTLLAKAVATEANVPFLSMNGSEFIE 59
P G+ L GP G GKT LAK +A E V L + SE++E
Sbjct: 482 PVGSFLFVGPTGVGKTELAKQLAEELGVHLLRFDMSEYME 521
>gnl|CDD|223616 COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ
chaperones [Posttranslational modification, protein
turnover, chaperones].
Length = 786
Score = 38.4 bits (90), Expect = 0.013
Identities = 18/43 (41%), Positives = 25/43 (58%), Gaps = 4/43 (9%)
Query: 21 PKGA-LLLGPPGCGKTLLAKAVA---TEANVPFLSMNGSEFIE 59
P G+ L LGP G GKT LAKA+A + ++ SE++E
Sbjct: 520 PIGSFLFLGPTGVGKTELAKALAEALFGDEQALIRIDMSEYME 562
>gnl|CDD|219536 pfam07724, AAA_2, AAA domain (Cdc48 subfamily). This Pfam entry
includes some of the AAA proteins not detected by the
pfam00004 model.
Length = 168
Score = 36.4 bits (85), Expect = 0.015
Identities = 16/38 (42%), Positives = 22/38 (57%), Gaps = 3/38 (7%)
Query: 25 LLLGPPGCGKTLLAKAVATEANV---PFLSMNGSEFIE 59
L LGP G GKT LAKA+A + ++ SE++E
Sbjct: 7 LFLGPTGVGKTELAKALAELLFGDERALIRIDMSEYME 44
>gnl|CDD|144608 pfam01078, Mg_chelatase, Magnesium chelatase, subunit ChlI.
Magnesium-chelatase is a three-component enzyme that
catalyzes the insertion of Mg2+ into protoporphyrin IX.
This is the first unique step in the synthesis of
(bacterio)chlorophyll. Due to this, it is thought that
Mg-chelatase has an important role in channelling
inter- mediates into the (bacterio)chlorophyll branch
in response to conditions suitable for photosynthetic
growth. ChlI and BchD have molecular weight between
38-42 kDa.
Length = 207
Score = 36.7 bits (86), Expect = 0.017
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 25 LLLGPPGCGKTLLAKAVAT 43
L++GPPG GKT+LAK +
Sbjct: 26 LMIGPPGSGKTMLAKRLPG 44
>gnl|CDD|213527 TIGR00390, hslU, ATP-dependent protease HslVU, ATPase subunit.
This model represents the ATPase subunit of HslVU,
while the proteasome-related peptidase subunit is HslV.
Residues 54-61 of the model contain a P-loop
ATP-binding motif. Cys-287 of E. coli (position 308 in
the seed alignment), studied in MEDLINE:98389714, is
Ser in other members of the seed alignment [Protein
fate, Protein folding and stabilization].
Length = 441
Score = 37.5 bits (87), Expect = 0.021
Identities = 17/41 (41%), Positives = 27/41 (65%)
Query: 20 VPKGALLLGPPGCGKTLLAKAVATEANVPFLSMNGSEFIEM 60
PK L++GP G GKT +A+ +A AN PF+ + ++F E+
Sbjct: 46 TPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEV 86
>gnl|CDD|224141 COG1220, HslU, ATP-dependent protease HslVU (ClpYQ), ATPase
subunit [Posttranslational modification, protein
turnover, chaperones].
Length = 444
Score = 36.9 bits (86), Expect = 0.035
Identities = 16/40 (40%), Positives = 25/40 (62%)
Query: 20 VPKGALLLGPPGCGKTLLAKAVATEANVPFLSMNGSEFIE 59
PK L++GP G GKT +A+ +A A PF+ + ++F E
Sbjct: 49 TPKNILMIGPTGVGKTEIARRLAKLAGAPFIKVEATKFTE 88
>gnl|CDD|204405 pfam10146, zf-C4H2, Zinc finger-containing protein. This is a
family of proteins which appears to have a highly
conserved zinc finger domain at the C terminal end,
described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is
predicted to contain a coiled coil. Members are
annotated as being tumour-associated antigen HCA127 in
humans but this could not confirmed.
Length = 215
Score = 36.0 bits (83), Expect = 0.038
Identities = 20/71 (28%), Positives = 38/71 (53%), Gaps = 1/71 (1%)
Query: 147 KHAEELKKQEQCLRKEKVLKIDAELRHKKELDLERQILLHEITKLKSELKNRELHIVKME 206
+EL+K + ++ E +++E +H KE D E + LL E + EL+ I ME
Sbjct: 8 NKTDELEKLKDEIKAE-EEALESEEKHLKEYDKEMEELLEEKMQHVEELRQIHADINDME 66
Query: 207 TQLRAYESDKK 217
T+++ +S+ +
Sbjct: 67 TEIKQSKSELE 77
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 36.7 bits (86), Expect = 0.039
Identities = 33/138 (23%), Positives = 68/138 (49%), Gaps = 29/138 (21%)
Query: 115 LKLNLEKEVMLRKK---------LEEEYSIELGRKLQDMEIKHAEELKKQEQCLRKEKVL 165
L+ EKE+ R+ L++E +++ RKL+ +E + E KK+++ +K++ L
Sbjct: 69 LRNEFEKELRERRNELQKLEKRLLQKEENLD--RKLELLEKREEELEKKEKELEQKQQEL 126
Query: 166 ---KIDAELRHKKELD-LE----------RQILLHEITKLKSELKNRELHIVKMETQLRA 211
+ + E +++L LE ++ILL K++ E ++ ++K E + A
Sbjct: 127 EKKEEELEELIEEQLQELERISGLTAEEAKEILL---EKVEEEARHEAAVLIK-EIEEEA 182
Query: 212 YESDKKLARKQLIDSVNR 229
E K A++ L ++ R
Sbjct: 183 KEEADKKAKEILAQAIQR 200
Score = 32.1 bits (74), Expect = 1.1
Identities = 26/105 (24%), Positives = 54/105 (51%), Gaps = 15/105 (14%)
Query: 137 LGRKLQDMEIKHAEELKKQ--EQCLRKEKVLKIDAELRHKKELDLERQILLHEITKLKSE 194
+ +K+ + +IK AEE K+ E+ ++ + +K +A L K+E+ R + + E
Sbjct: 24 VRKKIAEAKIKEAEEEAKRILEEAKKEAEAIKKEALLEAKEEIHKLRN-------EFEKE 76
Query: 195 LKNRELHIVKMETQLRAYES--DKKLA----RKQLIDSVNREIAE 233
L+ R + K+E +L E D+KL R++ ++ +E+ +
Sbjct: 77 LRERRNELQKLEKRLLQKEENLDRKLELLEKREEELEKKEKELEQ 121
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 36.3 bits (83), Expect = 0.055
Identities = 33/103 (32%), Positives = 50/103 (48%), Gaps = 7/103 (6%)
Query: 127 KKLEEEYSI---ELGRKLQDMEIKHAEELKKQEQCLRK-EKVLKIDAELRHKKELDLERQ 182
KK EEE I E +K ++ + K AEE KK E+ +K + LK +AE K+ + ++
Sbjct: 1653 KKAEEENKIKAAEEAKKAEE-DKKKAEEAKKAEEDEKKAAEALKKEAE--EAKKAEELKK 1709
Query: 183 ILLHEITKLKSELKNRELHIVKMETQLRAYESDKKLARKQLID 225
E K + K E + +K E + E DKK A + D
Sbjct: 1710 KEAEEKKKAEELKKAEEENKIKAEEAKKEAEEDKKKAEEAKKD 1752
Score = 35.5 bits (81), Expect = 0.11
Identities = 31/111 (27%), Positives = 48/111 (43%), Gaps = 12/111 (10%)
Query: 125 LRKKLEEEYSIELGRKLQDMEIKHAEELKKQE--------QCLRKEKVLKIDAELRHKKE 176
L+K EE+ +E +K + E K AEELKK E + +K + K AE K E
Sbjct: 1625 LKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAE 1684
Query: 177 LD---LERQILLHEITKLKSE-LKNRELHIVKMETQLRAYESDKKLARKQL 223
D + K+E LK +E K +L+ E + K+ ++
Sbjct: 1685 EDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEEA 1735
Score = 35.5 bits (81), Expect = 0.11
Identities = 30/112 (26%), Positives = 45/112 (40%), Gaps = 3/112 (2%)
Query: 125 LRKKLEEEYSIELGRKLQDMEIKHAEELKKQEQCLRKEKVLKIDAELRHKKE---LDLER 181
+KK EE+ + +K + + K A+ELKK +K K AE + K + E
Sbjct: 1383 AKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEE 1442
Query: 182 QILLHEITKLKSELKNRELHIVKMETQLRAYESDKKLARKQLIDSVNREIAE 233
E K E K E K E +A E+ KK + D ++ E
Sbjct: 1443 AKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEE 1494
Score = 34.7 bits (79), Expect = 0.18
Identities = 26/100 (26%), Positives = 46/100 (46%), Gaps = 4/100 (4%)
Query: 119 LEKEVMLRKKLEEEYSIELGRKLQDMEIKHAEELKKQEQCLRKEKVLKIDAELRHKKELD 178
++ +K E++ E +K ++ E K AE LKK+ + +K + LK KK +
Sbjct: 1661 IKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEE 1720
Query: 179 LERQILLHEITKLKSE-LKNRELHIVKMETQLRAYESDKK 217
L++ E K+K+E K K + + E +KK
Sbjct: 1721 LKKA---EEENKIKAEEAKKEAEEDKKKAEEAKKDEEEKK 1757
Score = 34.7 bits (79), Expect = 0.19
Identities = 33/113 (29%), Positives = 49/113 (43%), Gaps = 15/113 (13%)
Query: 120 EKEVMLRKKLEEEYSIELGRKLQDMEIKHAEELKKQEQCLRKEKV--LKIDAELRHKKEL 177
+ L+K+ EE E +K + E K AEELKK E+ K K K +AE KK
Sbjct: 1689 KAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEE-ENKIKAEEAKKEAEEDKKKAE 1747
Query: 178 DLER---------QILLHEITKLKSELKNRELHI---VKMETQLRAYESDKKL 218
+ ++ + E K + K +E I + E + R E DKK+
Sbjct: 1748 EAKKDEEEKKKIAHLKKEEEKKAEEIRKEKEAVIEEELDEEDEKRRMEVDKKI 1800
Score = 34.7 bits (79), Expect = 0.20
Identities = 27/95 (28%), Positives = 44/95 (46%), Gaps = 2/95 (2%)
Query: 127 KKLEEEYSIELGRKLQDMEIKHAEELKKQEQCLRKEKVLKIDAELRHKKELDLERQILLH 186
KK EE E+ + ++ + AEE KK E+ K + LK E + K E +++
Sbjct: 1587 KKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKE--AE 1644
Query: 187 EITKLKSELKNRELHIVKMETQLRAYESDKKLARK 221
E K + K E + +K + + E DKK A +
Sbjct: 1645 EKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEE 1679
Score = 34.3 bits (78), Expect = 0.23
Identities = 26/100 (26%), Positives = 47/100 (47%), Gaps = 3/100 (3%)
Query: 119 LEKEVMLRKKLEE-EYSIELGRKLQDMEIKHAEELKKQEQCLRKEKVLKIDAELRHKKEL 177
+K + K EE + + E +K++ ++ K AEE KK E+ + E+ KI A KK
Sbjct: 1612 AKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAE 1671
Query: 178 DLERQILLHEITKLKSELKNRELHIVKMETQLRAYESDKK 217
+ +++ E K + + K + K + + E KK
Sbjct: 1672 EDKKKA--EEAKKAEEDEKKAAEALKKEAEEAKKAEELKK 1709
Score = 32.0 bits (72), Expect = 1.1
Identities = 25/96 (26%), Positives = 40/96 (41%), Gaps = 7/96 (7%)
Query: 127 KKLEEEYSIELGRKLQDMEIKHAEELKKQEQCLRKEKVLKIDAELRHKKELDLERQILLH 186
KK EE+ + +K + E K A+E KK+ + +K K AE KK +++
Sbjct: 1284 KKAEEKKKADEAKKAE--EKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKA--- 1338
Query: 187 EITKLKSELKNRELHIVKMETQLRAYESDKKLARKQ 222
E K +E E + A E + A K+
Sbjct: 1339 EEAKKAAEAAKAEAE--AAADEAEAAEEKAEAAEKK 1372
Score = 32.0 bits (72), Expect = 1.4
Identities = 27/111 (24%), Positives = 46/111 (41%), Gaps = 7/111 (6%)
Query: 127 KKLEEEYSIELGRKLQDM----EIKHAEELKKQEQCLRKEKVLKIDAELRHKKELDLERQ 182
+K EEE E RK +D +K AEE KK + +K + + + E+R +E +
Sbjct: 1206 RKAEEERKAEEARKAEDAKKAEAVKKAEEAKKDAEEAKKAEEERNNEEIRKFEEARMAHF 1265
Query: 183 ILLHEITKLKSELKNRELHIVKMETQLRAYESDKKLARKQLIDSVNREIAE 233
K + K E +K + + + KK K+ D ++ E
Sbjct: 1266 ARRQAAIKAEEARKADE---LKKAEEKKKADEAKKAEEKKKADEAKKKAEE 1313
Score = 30.9 bits (69), Expect = 2.6
Identities = 24/97 (24%), Positives = 47/97 (48%), Gaps = 12/97 (12%)
Query: 127 KKLEEEYSIELGRKLQDMEIKHAEELKKQEQCLRKEKVLKIDAELRHKKELDLERQILLH 186
KK EE + +K + E K A+ELKK E+ + E+ K + K+ + ++ + L
Sbjct: 1528 KKAEEAKKADEAKKAE--EKKKADELKKAEELKKAEEKKKAE----EAKKAEEDKNMALR 1581
Query: 187 EITKLKSELKNRELHIVKMETQLRAYESDKKLARKQL 223
+ + K + R +E ++ YE +KK+ ++
Sbjct: 1582 KAEEAKKAEEAR------IEEVMKLYEEEKKMKAEEA 1612
Score = 30.9 bits (69), Expect = 2.8
Identities = 30/97 (30%), Positives = 48/97 (49%), Gaps = 9/97 (9%)
Query: 127 KKLEEEYSIELGRKLQDMEIKHAEELKKQEQCLRKEK----VLKIDAELRHKKELDLERQ 182
KK EE+ + +K + E+K AEE KK E+ + E+ L+ E + +E +E
Sbjct: 1540 KKAEEKKKADELKKAE--ELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEV 1597
Query: 183 ILLHEITKLK--SELKNRELHIVKMETQLRAYESDKK 217
+ L+E K E K E +K E +L+ E +KK
Sbjct: 1598 MKLYEEEKKMKAEEAKKAEEAKIKAE-ELKKAEEEKK 1633
Score = 30.5 bits (68), Expect = 3.7
Identities = 22/98 (22%), Positives = 37/98 (37%), Gaps = 2/98 (2%)
Query: 125 LRKKLEEEYSIELGRKLQDMEIKHAEELKKQEQCLRKEKVLKIDAELRHKKELDLERQIL 184
+KK EE + +K + K A+E KK + +K K E + E +
Sbjct: 1475 AKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAK 1534
Query: 185 LHEITKLKSELKNRELHIVKMETQLRAYESDKKLARKQ 222
+ K E K + +K +L+ E KK +
Sbjct: 1535 KADEAKKAEEKKKADE--LKKAEELKKAEEKKKAEEAK 1570
Score = 30.1 bits (67), Expect = 4.3
Identities = 27/93 (29%), Positives = 39/93 (41%), Gaps = 6/93 (6%)
Query: 125 LRKKLEEEYSIELGRKLQDMEIKHAEELKKQEQCLRKEKVLKIDAELRHKKELDLERQIL 184
+KK EE E +K + E K A+E KK+ + +K K AE KK + ++
Sbjct: 1449 AKKKAEEAKKAEEAKKKAE-EAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKA-- 1505
Query: 185 LHEITKLKSELKNRELHIVKMETQLRAYESDKK 217
E K E K E K + + E KK
Sbjct: 1506 -AEAKKKADEAKKAEE--AKKADEAKKAEEAKK 1535
Score = 30.1 bits (67), Expect = 5.0
Identities = 29/123 (23%), Positives = 48/123 (39%), Gaps = 12/123 (9%)
Query: 120 EKEVMLRKKLEEEYSIELGRKLQD----------MEIKHAEELKKQEQCLRKEKVLKIDA 169
K V + +K E+ E RK +D E++ AEEL+K E + E K +
Sbjct: 1151 AKRVEIARKAEDARKAEEARKAEDAKKAEAARKAEEVRKAEELRKAEDARKAEAARKAEE 1210
Query: 170 ELRHKKELDLERQILLHEITKLKSELKNRELHIVKMETQLRAYESDKKLARKQLIDSVNR 229
E + ++ E + K + E K K E + R E +K ++ R
Sbjct: 1211 ERKAEEARKAEDAKKAEAVKKAE-EAKKDAEEAKKAE-EERNNEEIRKFEEARMAHFARR 1268
Query: 230 EIA 232
+ A
Sbjct: 1269 QAA 1271
Score = 29.3 bits (65), Expect = 7.5
Identities = 25/114 (21%), Positives = 42/114 (36%), Gaps = 10/114 (8%)
Query: 121 KEVMLRKKLEE-EYSIELGRKLQDMEIKHAEELKKQEQCLRKEKVLKIDAELRHKKELDL 179
+ + E E E K ++ K A+ KK+ + +K K AE KK
Sbjct: 1351 EAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKA--- 1407
Query: 180 ERQILLHEITKLKSELKNRELHIVKMETQLRAYESDKKLARKQLIDSVNREIAE 233
E+ K + K + K E + +A E+ KK + D ++ E
Sbjct: 1408 ------DELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEE 1455
Score = 29.3 bits (65), Expect = 8.7
Identities = 23/101 (22%), Positives = 38/101 (37%), Gaps = 6/101 (5%)
Query: 125 LRKKLEEEYSIELGRKLQDMEIKHAEELKKQ-EQCLRKEKVLKIDAELRHKKELDLER-- 181
+KK EE + +K + K A+ KK+ E+ + + K +AE + E
Sbjct: 1307 AKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKA 1366
Query: 182 ---QILLHEITKLKSELKNRELHIVKMETQLRAYESDKKLA 219
+ E K K + K + + E DKK A
Sbjct: 1367 EAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKA 1407
>gnl|CDD|203260 pfam05496, RuvB_N, Holliday junction DNA helicase ruvB
N-terminus. The RuvB protein makes up part of the
RuvABC revolvasome which catalyzes the resolution of
Holliday junctions that arise during genetic
recombination and DNA repair. Branch migration is
catalyzed by the RuvB protein that is targeted to the
Holliday junction by the structure specific RuvA
protein. This family contains the N-terminal region of
the protein.
Length = 231
Score = 35.1 bits (82), Expect = 0.063
Identities = 14/25 (56%), Positives = 15/25 (60%)
Query: 25 LLLGPPGCGKTLLAKAVATEANVPF 49
LL GPPG GKT LA +A E V
Sbjct: 54 LLYGPPGLGKTTLANIIANEMGVNI 78
>gnl|CDD|220369 pfam09731, Mitofilin, Mitochondrial inner membrane protein.
Mitofilin controls mitochondrial cristae morphology.
Mitofilin is enriched in the narrow space between the
inner boundary and the outer membranes, where it forms a
homotypic interaction and assembles into a large
multimeric protein complex. The first 78 amino acids
contain a typical amino-terminal-cleavable mitochondrial
presequence rich in positive-charged and hydroxylated
residues and a membrane anchor domain. In addition, it
has three centrally located coiled coil domains.
Length = 493
Score = 35.8 bits (83), Expect = 0.072
Identities = 31/115 (26%), Positives = 53/115 (46%), Gaps = 9/115 (7%)
Query: 115 LKLNLEKEVM-LRKKLEEEYSIELGRKLQDMEIKHAEELKKQEQCLRKEKVLKIDAELRH 173
L+L E+E LRKK EE+ EL R+ + E K EL Q L++E +I
Sbjct: 224 LRLEFEREKEELRKKYEEKLRQELERQAEAHEQKLKNELALQAIELQREFNKEI------ 277
Query: 174 KKELDLERQILLHEITKLKSELKNRELHIVKMETQLRAYESDKKLARKQLIDSVN 228
K++++ ER L ++ +L S LK E + ++L ++++
Sbjct: 278 KEKVEEERNGRLAKLAELNSRLKGLEKALDSRSEAEDENHKVQQLW--LAVEALK 330
>gnl|CDD|234619 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed.
Length = 328
Score = 35.5 bits (83), Expect = 0.072
Identities = 14/25 (56%), Positives = 15/25 (60%)
Query: 25 LLLGPPGCGKTLLAKAVATEANVPF 49
LL GPPG GKT LA +A E V
Sbjct: 55 LLYGPPGLGKTTLANIIANEMGVNI 79
>gnl|CDD|222866 PHA02544, 44, clamp loader, small subunit; Provisional.
Length = 316
Score = 35.4 bits (82), Expect = 0.072
Identities = 15/37 (40%), Positives = 20/37 (54%)
Query: 19 KVPKGALLLGPPGCGKTLLAKAVATEANVPFLSMNGS 55
++P L PG GKT +AKA+ E L +NGS
Sbjct: 41 RIPNMLLHSPSPGTGKTTVAKALCNEVGAEVLFVNGS 77
>gnl|CDD|191114 pfam04859, DUF641, Plant protein of unknown function (DUF641).
Plant protein of unknown function.
Length = 132
Score = 33.9 bits (78), Expect = 0.078
Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 11/66 (16%)
Query: 169 AELRHKKEL-----------DLERQILLHEITKLKSELKNRELHIVKMETQLRAYESDKK 217
AEL+ EL + IL EI + +S LK E+ + K+E ++RA +S+
Sbjct: 53 AELKKLSELKRRYRRKRQKGAPQDAILAAEIQEQRSLLKTYEIMVKKLEAEVRAKDSEID 112
Query: 218 LARKQL 223
R++L
Sbjct: 113 SLREKL 118
>gnl|CDD|219538 pfam07728, AAA_5, AAA domain (dynein-related subfamily). This
Pfam entry includes some of the AAA proteins not
detected by the pfam00004 model.
Length = 135
Score = 33.8 bits (78), Expect = 0.085
Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 6/45 (13%)
Query: 25 LLLGPPGCGKTLLAKAVATEA--NVPFLSMNGSEFI---EMIGGL 64
LL+GPPG GK+ LA+ +A A N P + + ++ G
Sbjct: 3 LLVGPPGTGKSELAERLA-AALSNRPVFYVQLTRDTTEEDLKGRR 46
>gnl|CDD|131688 TIGR02640, gas_vesic_GvpN, gas vesicle protein GvpN. Members of
this family are the GvpN protein associated with the
production of gas vesicles produced in some prokaryotes
to give cells buoyancy. This family belongs to a larger
family of ATPases (pfam07728) [Cellular processes,
Other].
Length = 262
Score = 35.2 bits (81), Expect = 0.086
Identities = 14/29 (48%), Positives = 18/29 (62%)
Query: 26 LLGPPGCGKTLLAKAVATEANVPFLSMNG 54
L GP G GKT LA VA + + P + +NG
Sbjct: 26 LRGPAGTGKTTLAMHVARKRDRPVMLING 54
>gnl|CDD|223775 COG0703, AroK, Shikimate kinase [Amino acid transport and
metabolism].
Length = 172
Score = 34.1 bits (79), Expect = 0.10
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 26 LLGPPGCGKTLLAKAVATEANVPFL 50
L+G G GK+ + +A+A N+PF+
Sbjct: 7 LIGFMGAGKSTIGRALAKALNLPFI 31
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 33.0 bits (75), Expect = 0.12
Identities = 12/25 (48%), Positives = 18/25 (72%)
Query: 28 GPPGCGKTLLAKAVATEANVPFLSM 52
GPPG GK+ LAK +A + +P +S+
Sbjct: 6 GPPGSGKSTLAKKLAEKLGIPVISL 30
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 35.4 bits (82), Expect = 0.12
Identities = 20/107 (18%), Positives = 44/107 (41%), Gaps = 9/107 (8%)
Query: 125 LRKKLEEEYSIELGRKLQDMEIKHA---EELKKQEQCLRKEKVLKIDAELRHKKELDLER 181
L + E L +L+ ++ + + EL++ E E ++ R E++ E
Sbjct: 667 LFSRSEPAELQRLRERLEGLKRELSSLQSELRRIEN-RLDELSQELSDASRKIGEIEKEI 725
Query: 182 QILLHEITKLKSELKNRELHIVKMETQLRAYES-----DKKLARKQL 223
+ L E KLK L+ E + +E ++ +S + ++ +
Sbjct: 726 EQLEQEEEKLKERLEELEEDLSSLEQEIENVKSELKELEARIEELEE 772
Score = 32.3 bits (74), Expect = 1.0
Identities = 24/105 (22%), Positives = 45/105 (42%), Gaps = 7/105 (6%)
Query: 120 EKEVMLRKKLEEEYSIELGRKLQDMEIKHAEELKKQEQC-LRKEKVLKIDAELRHKKELD 178
+ L K+ E+ EL + D++ + K+ E +KE++ + EL D
Sbjct: 821 LNRLTLEKEYLEKEIQELQEQRIDLKEQIKSIEKEIENLNGKKEELEEELEELE-AALRD 879
Query: 179 LERQILLHEITKLKSELKNRELHIVKMETQLRAYESDKKLARKQL 223
LE + LK E E + ++E ++ E+ + RK+L
Sbjct: 880 LES-----RLGDLKKERDELEAQLRELERKIEELEAQIEKKRKRL 919
Score = 32.0 bits (73), Expect = 1.3
Identities = 27/124 (21%), Positives = 54/124 (43%), Gaps = 19/124 (15%)
Query: 127 KKLEEEYSIELGRKLQDME-----IKHAEELKKQEQCLRKEKVLKIDAELRHKKE--LDL 179
K L EE + + K+ ++E ++ + K++E +E++ K++AE+ +L
Sbjct: 282 KDLGEEEQLRVKEKIGELEAEIASLERSIAEKERELEDAEERLAKLEAEIDKLLAEIEEL 341
Query: 180 ERQI--LLHEITKLKSELKNRELHIVKMETQLRAYESDKKLA--------RKQLIDSVNR 229
ER+I KL E + + + E DK+ A ++ ++ + R
Sbjct: 342 EREIEEERKRRDKLTEEYAELK--EELEDLRAELEEVDKEFAETRDELKDYREKLEKLKR 399
Query: 230 EIAE 233
EI E
Sbjct: 400 EINE 403
Score = 30.4 bits (69), Expect = 3.6
Identities = 29/112 (25%), Positives = 46/112 (41%), Gaps = 23/112 (20%)
Query: 115 LKLNLEKEVMLRKKLEEEYSIELGRKLQDMEIKHAE----------ELKKQEQCLR--KE 162
LK L++ ++L EE + +L + +E K E E+KKQE L
Sbjct: 404 LKRELDRLQEELQRLSEELA-DLNAAIAGIEAKINELEEEKEDKALEIKKQEWKLEQLAA 462
Query: 163 KVLKIDAELRHKKELDLERQILLHEITKLKSELKNRELHIVKMETQLRAYES 214
+ K + EL KE E +++ EL + + + E Q RA E
Sbjct: 463 DLSKYEQELYDLKE----------EYDRVEKELSKLQRELAEAEAQARASEE 504
Score = 29.3 bits (66), Expect = 8.5
Identities = 30/100 (30%), Positives = 44/100 (44%), Gaps = 9/100 (9%)
Query: 136 ELGRKLQDMEIKHAEELKKQEQCLRKEKVLKIDAELRHKKELDLERQILLHEITKLKSEL 195
EL ++L D K E K+ EQ ++E+ LK +EL+ + L EI +KSEL
Sbjct: 706 ELSQELSDASRKIGEIEKEIEQLEQEEEKLK-----ERLEELEEDLSSLEQEIENVKSEL 760
Query: 196 KNRELHIVKMETQLRAYESDKKLARKQLIDSVNREIAETI 235
K E I ++E L E A L ++ I
Sbjct: 761 KELEARIEELEEDLHKLE----EALNDLEARLSHSRIPEI 796
>gnl|CDD|130902 TIGR01843, type_I_hlyD, type I secretion membrane fusion protein,
HlyD family. Type I secretion is an ABC transport
process that exports proteins, without cleavage of any
signal sequence, from the cytosol to extracellular
medium across both inner and outer membranes. The
secretion signal is found in the C-terminus of the
transported protein. This model represents the adaptor
protein between the ATP-binding cassette (ABC) protein
of the inner membrane and the outer membrane protein,
and is called the membrane fusion protein. This model
selects a subfamily closely related to HlyD; it is
defined narrowly and excludes, for example, colicin V
secretion protein CvaA and multidrug efflux proteins
[Protein fate, Protein and peptide secretion and
trafficking].
Length = 423
Score = 35.0 bits (81), Expect = 0.13
Identities = 28/120 (23%), Positives = 50/120 (41%), Gaps = 19/120 (15%)
Query: 125 LRKKLEEEYSIELGRKLQDMEIKHAEELKKQEQCLRKEKVLKIDAELRHKKELDLERQIL 184
LR + + + +IE L E EL K +Q L + + K L + +++
Sbjct: 100 LRAEADSQAAIEFPDDLLSAEDPAVPELIKGQQSLFESR----------KSTLRAQLELI 149
Query: 185 LHEITKLKSELKNRELHIVKMETQLRAYESD----KKLARKQLIDSVN-----REIAETI 235
L +I +L++EL + + + QL + +KL K L+ + RE AE
Sbjct: 150 LAQIKQLEAELAGLQAQLQALRQQLEVISEELEARRKLKEKGLVSRLELLELERERAEAQ 209
>gnl|CDD|237354 PRK13341, PRK13341, recombination factor protein RarA/unknown
domain fusion protein; Reviewed.
Length = 725
Score = 35.0 bits (81), Expect = 0.14
Identities = 14/30 (46%), Positives = 18/30 (60%)
Query: 24 ALLLGPPGCGKTLLAKAVATEANVPFLSMN 53
+L GPPG GKT LA+ +A F S+N
Sbjct: 55 LILYGPPGVGKTTLARIIANHTRAHFSSLN 84
>gnl|CDD|129721 TIGR00635, ruvB, Holliday junction DNA helicase, RuvB subunit.
All proteins in this family for which functions are
known are 5'-3' DNA helicases that, as part of a
complex with RuvA homologs serve as a 5'-3' Holliday
junction helicase. RuvA specifically binds Holliday
junctions as a sandwich of two tetramers and maintains
the configuration of the junction. It forms a complex
with two hexameric rings of RuvB, the subunit that
contains helicase activity. The complex drives
ATP-dependent branch migration of the Holliday junction
recombination intermediate. The endonuclease RuvC
resolves junctions [DNA metabolism, DNA replication,
recombination, and repair].
Length = 305
Score = 34.6 bits (80), Expect = 0.14
Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 9/54 (16%)
Query: 3 FVDYLKRPEYYQNL-----GAKVPKGA----LLLGPPGCGKTLLAKAVATEANV 47
+++ + + + L AK+ + A LL GPPG GKT LA +A E V
Sbjct: 3 LAEFIGQEKVKEQLQLFIEAAKMRQEALDHLLLYGPPGLGKTTLAHIIANEMGV 56
>gnl|CDD|238260 cd00464, SK, Shikimate kinase (SK) is the fifth enzyme in the
shikimate pathway, a seven-step biosynthetic pathway
which converts erythrose-4-phosphate to chorismic acid,
found in bacteria, fungi and plants. Chorismic acid is
a important intermediate in the synthesis of aromatic
compounds, such as aromatic amino acids, p-aminobenzoic
acid, folate and ubiquinone. Shikimate kinase catalyses
the phosphorylation of the 3-hydroxyl group of shikimic
acid using ATP.
Length = 154
Score = 33.3 bits (77), Expect = 0.14
Identities = 12/34 (35%), Positives = 20/34 (58%), Gaps = 2/34 (5%)
Query: 26 LLGPPGCGKTLLAKAVATEANVPFLSMNGSEFIE 59
L+G G GKT + + +A +PF+ ++ E IE
Sbjct: 4 LIGMMGAGKTTVGRLLAKALGLPFVDLD--ELIE 35
>gnl|CDD|216186 pfam00910, RNA_helicase, RNA helicase. This family includes RNA
helicases thought to be involved in duplex unwinding
during viral RNA replication. Members of this family
are found in a variety of single stranded RNA viruses.
Length = 105
Score = 32.6 bits (75), Expect = 0.14
Identities = 12/20 (60%), Positives = 14/20 (70%)
Query: 25 LLLGPPGCGKTLLAKAVATE 44
L GPPGCGK+ LAK +A
Sbjct: 2 WLYGPPGCGKSTLAKYLARA 21
>gnl|CDD|225164 COG2255, RuvB, Holliday junction resolvasome, helicase subunit
[DNA replication, recombination, and repair].
Length = 332
Score = 34.5 bits (80), Expect = 0.17
Identities = 14/23 (60%), Positives = 15/23 (65%)
Query: 25 LLLGPPGCGKTLLAKAVATEANV 47
LL GPPG GKT LA +A E V
Sbjct: 56 LLFGPPGLGKTTLAHIIANELGV 78
>gnl|CDD|238713 cd01428, ADK, Adenylate kinase (ADK) catalyzes the reversible
phosphoryl transfer from adenosine triphosphates (ATP)
to adenosine monophosphates (AMP) and to yield
adenosine diphosphates (ADP). This enzyme is required
for the biosynthesis of ADP and is essential for
homeostasis of adenosine phosphates.
Length = 194
Score = 33.7 bits (78), Expect = 0.18
Identities = 15/46 (32%), Positives = 23/46 (50%), Gaps = 9/46 (19%)
Query: 25 LLLGPPGCGKTLLAKAVATEANVPFLSM---------NGSEFIEMI 61
LLLGPPG GK A+ +A + +P +S +G+E +
Sbjct: 3 LLLGPPGSGKGTQAERLAKKYGLPHISTGDLLREEIASGTELGKKA 48
>gnl|CDD|183133 PRK11432, fbpC, ferric transporter ATP-binding subunit;
Provisional.
Length = 351
Score = 34.3 bits (79), Expect = 0.20
Identities = 14/30 (46%), Positives = 19/30 (63%), Gaps = 2/30 (6%)
Query: 15 NLGAKVPKGAL--LLGPPGCGKTLLAKAVA 42
NL + +G + LLGP GCGKT + + VA
Sbjct: 24 NLNLTIKQGTMVTLLGPSGCGKTTVLRLVA 53
>gnl|CDD|238978 cd02020, CMPK, Cytidine monophosphate kinase (CMPK) catalyzes the
reversible phosphorylation of cytidine monophosphate
(CMP) to produce cytidine diphosphate (CDP), using ATP
as the preferred phosphoryl donor.
Length = 147
Score = 32.8 bits (76), Expect = 0.22
Identities = 10/24 (41%), Positives = 16/24 (66%)
Query: 28 GPPGCGKTLLAKAVATEANVPFLS 51
GP G GK+ +AK +A + +P+L
Sbjct: 6 GPAGSGKSTVAKLLAKKLGLPYLD 29
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 34.3 bits (79), Expect = 0.24
Identities = 31/116 (26%), Positives = 66/116 (56%), Gaps = 11/116 (9%)
Query: 126 RKKLEEEYSIELGRKLQDMEIKHAEELKKQEQCLRKEKVLKIDAELRHKKELDLERQILL 185
RK+L EEY+ EL R +++ +E++++E+ LRKE +++ L+ + EL +++
Sbjct: 450 RKELLEEYTAELKRIEKEL-----KEIEEKERKLRKELR-ELEKVLKKESELIKLKEL-A 502
Query: 186 HEITKLKSELKNRELHIVKMETQLRAYESDKKLAR--KQLIDSVNREIAETILLKN 239
++ +L+ +LK + ++ ++E + YE K+ K I S+ +E+ + LK
Sbjct: 503 EQLKELEEKLK--KYNLEELEKKAEEYEKLKEKLIKLKGEIKSLKKELEKLEELKK 556
Score = 33.1 bits (76), Expect = 0.59
Identities = 25/90 (27%), Positives = 42/90 (46%), Gaps = 5/90 (5%)
Query: 120 EKEVMLRKKLE--EEYSIELGRKLQDMEIKHAEELKKQEQCLRKEKVLK-IDAELRHKKE 176
+K L K+LE EE E E LKK+ L EK+ K ++ + K+E
Sbjct: 345 KKLKELEKRLEELEERHELYEEAKAKKE--ELERLKKRLTGLTPEKLEKELEELEKAKEE 402
Query: 177 LDLERQILLHEITKLKSELKNRELHIVKME 206
++ E + I +LK E+K + I +++
Sbjct: 403 IEEEISKITARIGELKKEIKELKKAIEELK 432
>gnl|CDD|238979 cd02021, GntK, Gluconate kinase (GntK) catalyzes the phosphoryl
transfer from ATP to gluconate. The resulting product
gluconate-6-phoshate is an important precursor of
gluconate metabolism. GntK acts as a dimmer composed of
two identical subunits.
Length = 150
Score = 32.6 bits (75), Expect = 0.25
Identities = 9/26 (34%), Positives = 16/26 (61%)
Query: 25 LLLGPPGCGKTLLAKAVATEANVPFL 50
+++G G GK+ + KA+A PF+
Sbjct: 3 VVMGVSGSGKSTVGKALAERLGAPFI 28
>gnl|CDD|215651 pfam00006, ATP-synt_ab, ATP synthase alpha/beta family,
nucleotide-binding domain. This family includes the
ATP synthase alpha and beta subunits, the ATP synthase
associated with flagella and the termination factor
Rho.
Length = 213
Score = 33.2 bits (77), Expect = 0.25
Identities = 20/61 (32%), Positives = 31/61 (50%), Gaps = 10/61 (16%)
Query: 24 ALLLGPPGCGKTLLAKAVA--TEANVP--FLSM-----NGSEFIEMIGGLGAARVRTEVV 74
+ G G GKT+L +A +A+V ++ + +EFIE + G GA + RT VV
Sbjct: 18 IGIFGGSGTGKTVLLGMIARNAKADVVEVYVLIGERGREVAEFIEELLGEGALK-RTVVV 76
Query: 75 F 75
Sbjct: 77 A 77
>gnl|CDD|224045 COG1120, FepC, ABC-type cobalamin/Fe3+-siderophores transport
systems, ATPase components [Inorganic ion transport and
metabolism / Coenzyme metabolism].
Length = 258
Score = 33.3 bits (77), Expect = 0.30
Identities = 13/31 (41%), Positives = 19/31 (61%), Gaps = 2/31 (6%)
Query: 14 QNLGAKVPKGAL--LLGPPGCGKTLLAKAVA 42
+L +PKG + +LGP G GK+ L K +A
Sbjct: 19 DDLSFSIPKGEITGILGPNGSGKSTLLKCLA 49
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 33.9 bits (78), Expect = 0.34
Identities = 29/122 (23%), Positives = 62/122 (50%), Gaps = 12/122 (9%)
Query: 119 LEKEVMLRKKLEEEYSIE-LGRKLQDMEIKHAEELKKQEQCLRKEKVLKIDAELRHKKEL 177
LE ++L K E +E L +L +E + E ++ E+ ++++ ++ +EL +EL
Sbjct: 225 LELALLLAKLKELRKELEELEEELSRLEEELEELQEELEE--AEKEIEELKSEL---EEL 279
Query: 178 DLERQILLHEITKLKSELKNRELHIVKMETQLRAYESDKKLARKQL------IDSVNREI 231
E + L E+ +LK E++ E I + +L E++ + ++L I+++ E+
Sbjct: 280 REELEELQEELLELKEEIEELEGEISLLRERLEELENELEELEERLEELKEKIEALKEEL 339
Query: 232 AE 233
E
Sbjct: 340 EE 341
Score = 33.1 bits (76), Expect = 0.49
Identities = 42/230 (18%), Positives = 93/230 (40%), Gaps = 15/230 (6%)
Query: 96 ENIFDLETKIILSSFMMIVLKLNLEKEVMLRKKLEEEYSIELGRKLQDME--IKHAEELK 153
E + +L+ ++ + + LK LE+ ++L+EE EL +++++E I E +
Sbjct: 253 EELEELQEELEEAEKEIEELKSELEELREELEELQEELL-ELKEEIEELEGEISLLRE-R 310
Query: 154 KQEQCLRKEKVLKIDAELRHKKELDLERQILLHEITKLKSELKNRELHIVKMETQLRAYE 213
+E E++ + EL+ K E L+ ++ E L EL+ + + + +L
Sbjct: 311 LEELENELEELEERLEELKEKIE-ALKEELE--ERETLLEELEQLLAELEEAKEELEEKL 367
Query: 214 SDKKLARKQLIDSVNREIAETI-LLKNFAHQLIVKCPLMMTYSSEEGRNLNIPASFKMMK 272
S ++L +++ E+AE L ++L E
Sbjct: 368 SALLEELEELFEALREELAELEAELAEIRNELEEL-------KREIESLEERLERLSERL 420
Query: 273 KQNFLPQTSTASNVNQSHNIPQEIYDDILNLKLNLEKEVMLRKKLEEEYS 322
+ + + + +E+ +++ L+ LE+ K+LE E +
Sbjct: 421 EDLKEELKELEAELEELQTELEELNEELEELEEQLEELRDRLKELERELA 470
Score = 32.8 bits (75), Expect = 0.69
Identities = 28/132 (21%), Positives = 64/132 (48%), Gaps = 3/132 (2%)
Query: 87 IFDLETKIIENIFDLETKIILSSFMMIVLKLNLEKEVMLRKKLEEEYSIELGRKLQDMEI 146
+ +L + E + +LE ++ + LK +E ++L E +L +L+++E
Sbjct: 374 LEELFEALREELAELEAELAEIRNELEELKREIESLEERLERLSERLE-DLKEELKELEA 432
Query: 147 KHAEELKKQEQCLRKEKVLKIDAELRHKKELDLERQI--LLHEITKLKSELKNRELHIVK 204
+ E + E+ + + L+ E + +LER++ L E+ +L+ EL + E + +
Sbjct: 433 ELEELQTELEELNEELEELEEQLEELRDRLKELERELAELQEELQRLEKELSSLEARLDR 492
Query: 205 METQLRAYESDK 216
+E + RA + +
Sbjct: 493 LEAEQRASQGVR 504
Score = 32.4 bits (74), Expect = 0.93
Identities = 32/114 (28%), Positives = 59/114 (51%), Gaps = 10/114 (8%)
Query: 127 KKLEEEYSIELGRKLQDMEIKHAEELKKQEQCLRKE-KVLKIDAE-----LRHKKEL-DL 179
K +E E RKL+ E ++ E L+ + L K+ + L+ AE K EL +L
Sbjct: 168 SKYKERK-EEAERKLERTE-ENLERLEDLLEELEKQLEKLERQAEKAERYQELKAELREL 225
Query: 180 ERQILLHEITKLKSELKNRELHIVKMETQLRAYESDKKLARKQLIDSVNREIAE 233
E +LL ++ +L+ EL+ E + ++E +L + + + A K+ I+ + E+ E
Sbjct: 226 ELALLLAKLKELRKELEELEEELSRLEEELEELQEELEEAEKE-IEELKSELEE 278
Score = 31.2 bits (71), Expect = 2.4
Identities = 27/110 (24%), Positives = 55/110 (50%), Gaps = 5/110 (4%)
Query: 118 NLEKEVMLRKKLEEEYSIELGRKLQDME--IKHAEELKKQEQCLRKEKV-LKIDAELRHK 174
LE+E+ ++ + EL Q E + EEL+++ + L ++ L+ + E K
Sbjct: 797 ELEEELEEAERRLDALERELESLEQRRERLEQEIEELEEEIEELEEKLDELEEELEELEK 856
Query: 175 KELDLERQI--LLHEITKLKSELKNRELHIVKMETQLRAYESDKKLARKQ 222
+ +L+ ++ L E +L+ ELK E ++E +LR ES+ +++
Sbjct: 857 ELEELKEELEELEAEKEELEDELKELEEEKEELEEELRELESELAELKEE 906
>gnl|CDD|213213 cd03246, ABCC_Protease_Secretion, ATP-binding cassette domain of
PrtD, subfamily C. This family represents the ABC
component of the protease secretion system PrtD, a
60-kDa integral membrane protein sharing 37% identity
with HlyB, the ABC component of the alpha-hemolysin
secretion pathway, in the C-terminal domain. They
export degradative enzymes by using a type I protein
secretion system and lack an N-terminal signal peptide,
but contain a C-terminal secretion signal. The Type I
secretion apparatus is made up of three components, an
ABC transporter, a membrane fusion protein (MFP), and
an outer membrane protein (OMP). For the HlyA
transporter complex, HlyB (ABC transporter) and HlyD
(MFP) reside in the inner membrane of E. coli. The OMP
component is TolC, which is thought to interact with
the MFP to form a continuous channel across the
periplasm from the cytoplasm to the exterior. HlyB
belongs to the family of ABC transporters, which are
ubiquitous, ATP-dependent transmembrane pumps or
channels. The spectrum of transport substrates ranges
from inorganic ions, nutrients such as amino acids,
sugars, or peptides, hydrophobic drugs, to large
polypeptides, such as HlyA.
Length = 173
Score = 32.6 bits (75), Expect = 0.38
Identities = 10/31 (32%), Positives = 17/31 (54%), Gaps = 2/31 (6%)
Query: 14 QNLGAKVPKGALL--LGPPGCGKTLLAKAVA 42
+N+ + G L +GP G GK+ LA+ +
Sbjct: 19 RNVSFSIEPGESLAIIGPSGSGKSTLARLIL 49
>gnl|CDD|235244 PRK04182, PRK04182, cytidylate kinase; Provisional.
Length = 180
Score = 32.1 bits (74), Expect = 0.54
Identities = 13/33 (39%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 28 GPPGCGKTLLAKAVATEANVPFLSMNGSEFIEM 60
GPPG GKT +A+ +A + + +S G F E+
Sbjct: 7 GPPGSGKTTVARLLAEKLGLKHVS-AGEIFREL 38
>gnl|CDD|218896 pfam06098, Radial_spoke_3, Radial spoke protein 3. This family
consists of several radial spoke protein 3 (RSP3)
sequences. Eukaryotic cilia and flagella present in
diverse types of cells perform motile, sensory, and
developmental functions in organisms from protists to
humans. They are centred by precisely organised,
microtubule-based structures, the axonemes. The axoneme
consists of two central singlet microtubules, called the
central pair, and nine outer doublet microtubules. These
structures are well-conserved during evolution. The
outer doublet microtubules, each composed of A and B
sub-fibres, are connected to each other by nexin links,
while the central pair is held at the centre of the
axoneme by radial spokes. The radial spokes are T-shaped
structures extending from the A-tubule of each outer
doublet microtubule to the centre of the axoneme. Radial
spoke protein 3 (RSP3), is present at the proximal end
of the spoke stalk and helps in anchoring the radial
spoke to the outer doublet. It is thought that radial
spokes regulate the activity of inner arm dynein through
protein phosphorylation and dephosphorylation.
Length = 288
Score = 32.3 bits (74), Expect = 0.60
Identities = 27/105 (25%), Positives = 43/105 (40%), Gaps = 31/105 (29%)
Query: 89 DLETKIIEN---IFDLETKIILSSFMMIVLKLNLEKEVMLRKKLE-------EEYSIELG 138
D+ET+I E FDLE + IL EV++ K LE EE +
Sbjct: 112 DVETQIEEGELFDFDLEVEPIL--------------EVLVGKTLEQALLEVLEEEELAEL 157
Query: 139 RKLQD-------MEIKHAEELKKQEQCLRKEKVLKIDAELRHKKE 176
R+ Q E+ + L++ E+ R+EK + + K+
Sbjct: 158 RQQQRQFEQRRNAELAETQRLEEAERRRREEKERRKKQDKERKQR 202
>gnl|CDD|214396 CHL00206, ycf2, Ycf2; Provisional.
Length = 2281
Score = 33.0 bits (75), Expect = 0.61
Identities = 14/44 (31%), Positives = 28/44 (63%)
Query: 16 LGAKVPKGALLLGPPGCGKTLLAKAVATEANVPFLSMNGSEFIE 59
L +G L++G G G++ L K +AT + VPF+++ ++F++
Sbjct: 1625 LALSPSRGILVIGSIGTGRSYLVKYLATNSYVPFITVFLNKFLD 1668
>gnl|CDD|110677 pfam01695, IstB_IS21, IstB-like ATP binding protein. This
protein contains an ATP/GTP binding P-loop motif. It is
found associated with IS21 family insertion sequences.
The function of this protein is unknown, but it may
perform a transposase function.
Length = 178
Score = 31.8 bits (73), Expect = 0.62
Identities = 14/21 (66%), Positives = 16/21 (76%)
Query: 25 LLLGPPGCGKTLLAKAVATEA 45
LLLGPPG GKT LA A+ +A
Sbjct: 51 LLLGPPGVGKTHLACALGHQA 71
>gnl|CDD|233355 TIGR01313, therm_gnt_kin, carbohydrate kinase, thermoresistant
glucokinase family. This model represents a subfamily
of proteins that includes thermoresistant and
thermosensitve isozymes of gluconate kinase
(gluconokinase) in E. coli and other related proteins;
members of this family are often named by similarity to
the thermostable isozyme. These proteins show homology
to shikimate kinases and adenylate kinases but not to
gluconate kinases from the FGGY family of carbohydrate
kinases.
Length = 163
Score = 31.6 bits (72), Expect = 0.70
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 26 LLGPPGCGKTLLAKAVATEANVPFL 50
L+G G GK+ +A A+A F+
Sbjct: 3 LMGVAGSGKSTIASALAHRLGAKFI 27
>gnl|CDD|226889 COG4487, COG4487, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 438
Score = 32.5 bits (74), Expect = 0.73
Identities = 19/110 (17%), Positives = 36/110 (32%), Gaps = 6/110 (5%)
Query: 98 IFDLETKIILSSFMMIVLKLNLEKEVMLRKKLEEEYSIELGRKLQDMEIKHAEELKKQEQ 157
I E I K +++ EE+ E K +EL + E+
Sbjct: 15 IPKCEDSIKGEQAR---YKQIEQEDQSRILNTLEEFEKEANEKRAQYRSAKKKELSQLEE 71
Query: 158 CLRKEKVLKIDAELRHKKELDLERQILLHEITKLKSELKNRELHIVKMET 207
L +K + + +++ L EI KL++ ++E
Sbjct: 72 QLINQKK---EQKNLFNEQIKQFELALQDEIAKLEALELLNLEKDKELEL 118
Score = 29.4 bits (66), Expect = 6.5
Identities = 34/121 (28%), Positives = 57/121 (47%), Gaps = 15/121 (12%)
Query: 82 LHEITIFDLETKIIENIFDLETKIILSSFMMIVLKLNLEKEVMLRKKLEEEYSIELGRKL 141
L I E + + I LE +L+ L +KE+ L +K +E S EL ++L
Sbjct: 83 LFNEQIKQFELALQDEIAKLEALELLN--------LEKDKELELLEKELDELSKELQKQL 134
Query: 142 QDMEIKHAEELKKQEQCLRKEKVLKIDAELRHKKELDLERQ---ILLHEITKLKSELKNR 198
Q AE ++K+ + + E+ LK + E + ++ L+LER+ LHE +N
Sbjct: 135 Q----NTAEIIEKKRENNKNEERLKFENEKKLEESLELEREKFEEQLHEANLDLEFKENE 190
Query: 199 E 199
E
Sbjct: 191 E 191
>gnl|CDD|234173 TIGR03346, chaperone_ClpB, ATP-dependent chaperone ClpB. Members
of this protein family are the bacterial ATP-dependent
chaperone ClpB. This protein belongs to the AAA family,
ATPases associated with various cellular activities
(pfam00004). This molecular chaperone does not act as a
protease, but rather serves to disaggregate misfolded
and aggregated proteins [Protein fate, Protein folding
and stabilization].
Length = 852
Score = 32.6 bits (75), Expect = 0.75
Identities = 18/40 (45%), Positives = 23/40 (57%), Gaps = 7/40 (17%)
Query: 25 LLLGPPGCGKTLLAKAVA-----TEANVPFLSMNGSEFIE 59
L LGP G GKT LAKA+A E + + M SE++E
Sbjct: 599 LFLGPTGVGKTELAKALAEFLFDDEDAMVRIDM--SEYME 636
>gnl|CDD|175978 cd04011, C2B_Ferlin, C2 domain second repeat in Ferlin. Ferlins
are involved in vesicle fusion events. Ferlins and
other proteins, such as Synaptotagmins, are implicated
in facilitating the fusion process when cell membranes
fuse together. There are six known human Ferlins:
Dysferlin (Fer1L1), Otoferlin (Fer1L2), Myoferlin
(Fer1L3), Fer1L4, Fer1L5, and Fer1L6. Defects in these
genes can lead to a wide range of diseases including
muscular dystrophy (dysferlin), deafness (otoferlin),
and infertility (fer-1, fertilization factor-1).
Structurally they have 6 tandem C2 domains, designated
as (C2A-C2F) and a single C-terminal transmembrane
domain, though there is a new study that disputes this
and claims that there are actually 7 tandem C2 domains
with another C2 domain inserted between C2D and C2E.
In a subset of them (Dysferlin, Myoferlin, and Fer1)
there is an additional conserved domain called DysF. C2
domains fold into an 8-standed beta-sandwich that can
adopt 2 structural arrangements: Type I and Type II,
distinguished by a circular permutation involving their
N- and C-terminal beta strands. Many C2 domains are
Ca2+-dependent membrane-targeting modules that bind a
wide variety of substances including bind phospholipids,
inositol polyphosphates, and intracellular proteins.
Most C2 domain proteins are either signal transduction
enzymes that contain a single C2 domain, such as protein
kinase C, or membrane trafficking proteins which contain
at least two C2 domains, such as synaptotagmin 1.
However, there are a few exceptions to this including
RIM isoforms and some splice variants of piccolo/aczonin
and intersectin which only have a single C2 domain. C2
domains with a calcium binding region have negatively
charged residues, primarily aspartates, that serve as
ligands for calcium ions. This cd contains the second C2
repeat, C2B, and has a type-II topology.
Length = 111
Score = 30.6 bits (70), Expect = 0.79
Identities = 13/54 (24%), Positives = 27/54 (50%), Gaps = 2/54 (3%)
Query: 290 HNIPQEIYDDILNLKLNLEKEVMLRKKLEEEYSIELGSPIDTSRSHRVLRKWVL 343
H P E++D I+ + + + + L + +++G+ + H LRKW+L
Sbjct: 56 HESPDELFDKIIKISV-YDSRSLRSDTLIGSFKLDVGT-VYDQPDHAFLRKWLL 107
>gnl|CDD|163064 TIGR02894, DNA_bind_RsfA, transcription factor, RsfA family. In a
subset of endospore-forming members of the Firmcutes,
members of this protein family are found, several to a
genome. Two very strongly conserved sequences regions
are separated by a highly variable linker region. Much
of the linker region was excised from the seed alignment
for this model. A characterized member is the
prespore-specific transcription RsfA from Bacillus
subtilis, previously called YwfN, which is controlled by
sigma factor F and seems to fine-tune expression of some
genes in the sigma-F regulon. A paralog in Bacillus
subtilis is designated YlbO [Regulatory functions, DNA
interactions, Cellular processes, Sporulation and
germination].
Length = 161
Score = 31.3 bits (71), Expect = 0.85
Identities = 27/108 (25%), Positives = 48/108 (44%), Gaps = 17/108 (15%)
Query: 126 RKKLEEEYSIELGRKLQDMEIKHAEELKKQEQCLRKEKVLKIDAELRHK----KELDLER 181
RK+ EE +IEL +K +ELK++ L + V+ L+ + L E
Sbjct: 56 RKQYEE--AIELAKK-------QRKELKREAGSLTLQDVISFLQNLKTTNPSDQALQKEN 106
Query: 182 QILLHEITKLKSELKNRELHIVKMETQLRAYESDKKLARKQLIDSVNR 229
+ L ++ L+ + E + K+ +L E D + LID ++R
Sbjct: 107 ERLKNQNESLQKRNEELEKELEKLRQRLSTIEED----YQTLIDIMDR 150
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 32.4 bits (74), Expect = 0.86
Identities = 28/122 (22%), Positives = 59/122 (48%), Gaps = 12/122 (9%)
Query: 116 KLNLEKEVMLRKKLEEEYSIELGRKLQDMEIKHAEELKKQEQCLRKEKVL---------- 165
++ +E + + E+E EL +L ++E E LK +E+ LR+ + L
Sbjct: 233 EIEALEERLAELEEEKERLEELKARLLEIESLELEALKIREEELRELERLLEELEEKIER 292
Query: 166 --KIDAELRHKKELDLERQILLHEITKLKSELKNRELHIVKMETQLRAYESDKKLARKQL 223
+++ E+ +E + LL E+ +L +LK+ E + K+E +L ES+ + ++
Sbjct: 293 LEELEREIEELEEELEGLRALLEELEELLEKLKSLEERLEKLEEKLEKLESELEELAEEK 352
Query: 224 ID 225
+
Sbjct: 353 NE 354
Score = 32.0 bits (73), Expect = 1.2
Identities = 26/129 (20%), Positives = 49/129 (37%), Gaps = 19/129 (14%)
Query: 115 LKLNLEKEVMLRKKLEEEYSIELGRKLQDMEIKHAEELKKQEQCLRKEKVLKID------ 168
L LE+E+ KKLEE + +L+ E L + E+ + + LK
Sbjct: 204 LLEALEEELKELKKLEEIQEEQEEEELEQEIEALEERLAELEEEKERLEELKARLLEIES 263
Query: 169 -----AELRHKKELDLERQIL--------LHEITKLKSELKNRELHIVKMETQLRAYESD 215
++R ++ +LER + L E+ + EL+ + + +L
Sbjct: 264 LELEALKIREEELRELERLLEELEEKIERLEELEREIEELEEELEGLRALLEELEELLEK 323
Query: 216 KKLARKQLI 224
K ++L
Sbjct: 324 LKSLEERLE 332
Score = 29.7 bits (67), Expect = 5.5
Identities = 27/132 (20%), Positives = 56/132 (42%)
Query: 114 VLKLNLEKEVMLRKKLEEEYSIELGRKLQDMEIKHAEELKKQEQCLRKEKVLKIDAELRH 173
L+ L+ + ++ EE E+ R+LQ +E + E K +E +E++ ++ EL
Sbjct: 647 ELEELLQAALEELEEKVEELEAEIRRELQRIENEEQLEEKLEELEQLEEELEQLREELEE 706
Query: 174 KKELDLERQILLHEITKLKSELKNRELHIVKMETQLRAYESDKKLARKQLIDSVNREIAE 233
+ E + L+ E+ K+EL+ + + K+E L E ++ K + +
Sbjct: 707 LLKKLGEIEQLIEELESRKAELEELKKELEKLEKALELLEELREKLGKAGLRADILRNLL 766
Query: 234 TILLKNFAHQLI 245
+ L
Sbjct: 767 AQIEAEANEILS 778
Score = 29.7 bits (67), Expect = 5.9
Identities = 22/113 (19%), Positives = 47/113 (41%), Gaps = 2/113 (1%)
Query: 89 DLETKIIENIFDLETKIILSSFMMIVLKLNLEKEVMLRKKLEEEYSIELGRKLQDMEIKH 148
+ K + +++LE + + + L +E+ +K E EL L+ E
Sbjct: 469 EEHEKELLELYELELEELEEELSREKEEAELREEIEELEKELRELEEELIELLELEEALK 528
Query: 149 AEELKKQEQCLRKEKVLKIDAELR-HKKELDLERQILLHEITKLKSELKNREL 200
EEL+++ + L + + + ++L E + L + +LK L+ L
Sbjct: 529 -EELEEKLEKLENLLEELEELKEKLQLQQLKEELRQLEDRLQELKELLEELRL 580
>gnl|CDD|188437 TIGR03922, T7SS_EccA, type VII secretion AAA-ATPase EccA. This
model represents the AAA family ATPase, EccA, of the
actinobacterial flavor of type VII secretion systems.
Species such as Mycobacterium tuberculosis have several
instances of this system per genome, designated EccA1,
EccA2, etc [Protein fate, Protein and peptide secretion
and trafficking].
Length = 557
Score = 32.1 bits (73), Expect = 0.93
Identities = 13/29 (44%), Positives = 17/29 (58%), Gaps = 3/29 (10%)
Query: 17 GAKVPKGA---LLLGPPGCGKTLLAKAVA 42
G V + + L GPPG GKT +A+ VA
Sbjct: 305 GLPVAQTSNHMLFAGPPGTGKTTIARVVA 333
>gnl|CDD|219444 pfam07516, SecA_SW, SecA Wing and Scaffold domain. SecA protein
binds to the plasma membrane where it interacts with
proOmpA to support translocation of proOmpA through the
membrane. SecA protein achieves this translocation, in
association with SecY protein, in an ATP dependent
manner. This family is composed of two C-terminal alpha
helical subdomains: the wing and scaffold subdomains.
Length = 213
Score = 31.4 bits (72), Expect = 0.93
Identities = 35/136 (25%), Positives = 60/136 (44%), Gaps = 24/136 (17%)
Query: 89 DLETKIIENIFDLETKII--LSSFMMIVLKLNLEKEVMLRKKLEEEYSIELGRKLQDMEI 146
DL+ I+E I D+ I+ + + +LE L ++L E ++L +++E
Sbjct: 55 DLKEIILEMIEDVIDDIVEEYAPEKSYPEEWDLEG---LEEELRELLGLDLDIDEEELEG 111
Query: 147 KHAEELKKQ--EQCLR--KEKVLKIDAELRHKKELDLERQILLHEITKLKSELKNRELHI 202
EELK++ E +EK ++ EL ++ER I+L I +L E H+
Sbjct: 112 LTEEELKERLIEAAKEAYEEKEAELGEELMR----EIERSIMLQVIDELWKE------HL 161
Query: 203 VKMET-----QLRAYE 213
M+ LR Y
Sbjct: 162 DAMDHLREGIGLRGYG 177
>gnl|CDD|233119 TIGR00763, lon, ATP-dependent protease La. This protein is induced
by heat shock and other stresses in E. coli, B.
subtilis, and other species. The yeast member,
designated PIM1, is located in the mitochondrial matrix,
required for mitochondrial function, and also induced by
heat shock [Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 775
Score = 32.3 bits (74), Expect = 1.0
Identities = 13/24 (54%), Positives = 16/24 (66%)
Query: 26 LLGPPGCGKTLLAKAVATEANVPF 49
L+GPPG GKT L K++A N F
Sbjct: 352 LVGPPGVGKTSLGKSIAKALNRKF 375
>gnl|CDD|116340 pfam07726, AAA_3, ATPase family associated with various cellular
activities (AAA). This Pfam entry includes some of the
AAA proteins not detected by the pfam00004 model.
Length = 131
Score = 30.6 bits (70), Expect = 1.1
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 25 LLLGPPGCGKTLLAKAVA 42
LL G PG KTLLA+ +A
Sbjct: 3 LLEGVPGLAKTLLARTLA 20
>gnl|CDD|223543 COG0467, RAD55, RecA-superfamily ATPases implicated in signal
transduction [Signal transduction mechanisms].
Length = 260
Score = 31.7 bits (72), Expect = 1.2
Identities = 14/31 (45%), Positives = 20/31 (64%), Gaps = 2/31 (6%)
Query: 16 LGAKVPKGALLL--GPPGCGKTLLAKAVATE 44
LG +P+G+++L GPPG GKT+ A E
Sbjct: 16 LGGGLPRGSVVLITGPPGTGKTIFALQFLYE 46
>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
protein; Reviewed.
Length = 782
Score = 32.1 bits (74), Expect = 1.2
Identities = 21/83 (25%), Positives = 35/83 (42%), Gaps = 8/83 (9%)
Query: 125 LRKKLEEEYSIELGRKLQDMEIKHAEELKKQEQCLRKEKVLKIDAELRH-------KKEL 177
L ++LE++ E L++ E E +K+E+ +E L +AE KKE
Sbjct: 528 LERELEQKA-EEAEALLKEAEKLKEELEEKKEKLQEEEDKLLEEAEKEAQQAIKEAKKEA 586
Query: 178 DLERQILLHEITKLKSELKNREL 200
D + L + +K EL
Sbjct: 587 DEIIKELRQLQKGGYASVKAHEL 609
>gnl|CDD|233761 TIGR02173, cyt_kin_arch, cytidylate kinase, putative. Proteins
in this family are believed to be cytidylate kinase.
Members of this family are found in the archaea and in
spirochaetes, and differ considerably from the common
bacterial form of cytidylate kinase described by
TIGR00017.
Length = 171
Score = 30.9 bits (70), Expect = 1.2
Identities = 14/33 (42%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 28 GPPGCGKTLLAKAVATEANVPFLSMNGSEFIEM 60
GPPG GKT +AK +A + ++ +S G F E+
Sbjct: 7 GPPGSGKTTVAKILAEKLSLKLIS-AGDIFREL 38
>gnl|CDD|182778 PRK10851, PRK10851, sulfate/thiosulfate transporter subunit;
Provisional.
Length = 353
Score = 31.6 bits (72), Expect = 1.2
Identities = 24/88 (27%), Positives = 40/88 (45%), Gaps = 9/88 (10%)
Query: 6 YLKRPEYYQNLGAKVPKGAL--LLGPPGCGKTLLAKAVA--TEANVPFLSMNGSEFIEMI 61
R + ++ +P G + LLGP G GKT L + +A + +G++ +
Sbjct: 11 SFGRTQVLNDISLDIPSGQMVALLGPSGSGKTTLLRIIAGLEHQTSGHIRFHGTD----V 66
Query: 62 GGLGAARVRTEVVFLHCRVFLHEITIFD 89
L A + VF H +F H +T+FD
Sbjct: 67 SRLHARDRKVGFVFQHYALFRH-MTVFD 93
>gnl|CDD|204553 pfam10779, XhlA, Haemolysin XhlA. XhlA is a cell-surface
associated haemolysin that lyses the two most prevalent
types of insect immune cells (granulocytes and
plasmatocytes) as well as rabbit and horse erythrocytes.
This family has had DUF1267, pfam06895, merged into it.
Length = 71
Score = 29.2 bits (66), Expect = 1.3
Identities = 12/42 (28%), Positives = 22/42 (52%)
Query: 182 QILLHEITKLKSELKNRELHIVKMETQLRAYESDKKLARKQL 223
Q + + +++++LK E I +E + A E D K K+L
Sbjct: 2 QDIEERLNRIETKLKEIEEDIRNLEKRDAANEKDIKNLNKRL 43
>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function
unknown].
Length = 652
Score = 31.6 bits (72), Expect = 1.3
Identities = 27/92 (29%), Positives = 48/92 (52%), Gaps = 10/92 (10%)
Query: 127 KKLEEEYSIELGRKLQDMEIKHAEELKKQEQCLRKEKVLKIDAELRHKKELDLERQILLH 186
++LEEE S EL R+L EELK++ + L ++ + E+R K D E +
Sbjct: 432 ERLEEENS-ELKREL--------EELKREIEKLES-ELERFRREVRDKVRKDREIRARDR 481
Query: 187 EITKLKSELKNRELHIVKMETQLRAYESDKKL 218
I +L+ EL+ ++ + ++E +L +KL
Sbjct: 482 RIERLEKELEEKKKRVEELERKLAELRKMRKL 513
>gnl|CDD|183044 PRK11231, fecE, iron-dicitrate transporter ATP-binding subunit;
Provisional.
Length = 255
Score = 31.1 bits (71), Expect = 1.4
Identities = 13/31 (41%), Positives = 18/31 (58%), Gaps = 2/31 (6%)
Query: 14 QNLGAKVPKGAL--LLGPPGCGKTLLAKAVA 42
+L +P G + L+GP GCGK+ L K A
Sbjct: 19 NDLSLSLPTGKITALIGPNGCGKSTLLKCFA 49
>gnl|CDD|192445 pfam10018, Med4, Vitamin-D-receptor interacting Mediator subunit 4.
Members of this family function as part of the Mediator
(Med) complex, which links DNA-bound transcriptional
regulators and the general transcription machinery,
particularly the RNA polymerase II enzyme. They play a
role in basal transcription by mediating activation or
repression according to the specific complement of
transcriptional regulators bound to the promoter.
Length = 176
Score = 30.8 bits (70), Expect = 1.4
Identities = 18/85 (21%), Positives = 40/85 (47%), Gaps = 3/85 (3%)
Query: 162 EKVLKIDAELRHKKELDLERQILLHEITKLKSELKNRELHIVKMETQLRAYES--DKKLA 219
E ++ D EL+ + E Q I +L++E+++ + I + +L+ E
Sbjct: 5 EDLISADDELKSALKELEEHQENQQRILELRAEVESLDEKIKDILKELKEAEKELRTLPD 64
Query: 220 RKQLIDSVNREIAETILLKNFAHQL 244
+ + R+++ LLK +AH++
Sbjct: 65 LSSINKANKRKVSSEELLK-YAHRI 88
>gnl|CDD|236153 PRK08116, PRK08116, hypothetical protein; Validated.
Length = 268
Score = 31.1 bits (71), Expect = 1.5
Identities = 16/45 (35%), Positives = 21/45 (46%), Gaps = 3/45 (6%)
Query: 23 GALLLGPPGCGKTLLAKAVAT---EANVPFLSMNGSEFIEMIGGL 64
G LL G G GKT LA +A E VP + +N + + I
Sbjct: 116 GLLLWGSVGTGKTYLAACIANELIEKGVPVIFVNFPQLLNRIKST 160
>gnl|CDD|233369 TIGR01351, adk, adenylate kinase. Adenylate kinase (EC 2.7.4.3)
converts ATP + AMP to ADP + ADP, that is, uses ATP as a
phosphate donor for AMP. Most members of this family
are known or believed to be adenylate kinase. However,
some members accept other nucleotide triphosphates as
donors, may be unable to use ATP, and may fail to
complement adenylate kinase mutants. An example of a
nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10)
is a GTP:AMP phosphotransferase. This family is
designated subfamily rather than equivalog for this
reason [Purines, pyrimidines, nucleosides, and
nucleotides, Nucleotide and nucleoside
interconversions].
Length = 210
Score = 31.0 bits (71), Expect = 1.5
Identities = 13/27 (48%), Positives = 18/27 (66%)
Query: 25 LLLGPPGCGKTLLAKAVATEANVPFLS 51
+LLGPPG GK AK +A + +P +S
Sbjct: 3 VLLGPPGSGKGTQAKRIAEKYGLPHIS 29
>gnl|CDD|222102 pfam13398, Peptidase_M50B, Peptidase M50B-like. This is a family
of bacterial and plant peptidases in the same family as
MEROPS:M50B.
Length = 201
Score = 30.6 bits (70), Expect = 1.6
Identities = 8/15 (53%), Positives = 8/15 (53%)
Query: 496 EVAFHESGHALVGWL 510
FHE GHAL L
Sbjct: 24 VTFFHELGHALAALL 38
Score = 30.6 bits (70), Expect = 2.1
Identities = 8/14 (57%), Positives = 8/14 (57%)
Query: 360 VAFHESGHALVGWL 373
FHE GHAL L
Sbjct: 25 TFFHELGHALAALL 38
Score = 30.6 bits (70), Expect = 2.1
Identities = 8/14 (57%), Positives = 8/14 (57%)
Query: 446 VAFHESGHALVGWL 459
FHE GHAL L
Sbjct: 25 TFFHELGHALAALL 38
>gnl|CDD|237495 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional.
Length = 637
Score = 31.5 bits (72), Expect = 1.6
Identities = 10/18 (55%), Positives = 16/18 (88%)
Query: 25 LLLGPPGCGKTLLAKAVA 42
+++G PG GK++LAKA+A
Sbjct: 54 MMIGSPGTGKSMLAKAMA 71
>gnl|CDD|234152 TIGR03265, PhnT2, putative 2-aminoethylphosphonate ABC
transporter, ATP-binding protein. This ABC transporter
ATP-binding protein is found in a number of genomes in
operon-like contexts strongly suggesting a substrate
specificity for 2-aminoethylphosphonate (2-AEP). The
characterized PhnSTUV system is absent in the genomes
in which this system is found. These genomes encode
systems for the catabolism of 2-AEP, making the need
for a 2-AEP-specific transporter likely [Transport and
binding proteins, Amino acids, peptides and amines].
Length = 353
Score = 31.2 bits (71), Expect = 1.7
Identities = 14/25 (56%), Positives = 16/25 (64%), Gaps = 2/25 (8%)
Query: 20 VPKGAL--LLGPPGCGKTLLAKAVA 42
V KG LLGP GCGKT L + +A
Sbjct: 27 VKKGEFVCLLGPSGCGKTTLLRIIA 51
>gnl|CDD|213179 cd00267, ABC_ATPase, ATP-binding cassette transporter
nucleotide-binding domain. ABC transporters are a
large family of proteins involved in the transport of a
wide variety of different compounds, like sugars, ions,
peptides, and more complex organic molecules. The
nucleotide-binding domain shows the highest similarity
between all members of the family. ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and
GTP-binding and hydrolyzing proteins.
Length = 157
Score = 30.3 bits (69), Expect = 1.7
Identities = 10/26 (38%), Positives = 16/26 (61%), Gaps = 2/26 (7%)
Query: 19 KVPKGAL--LLGPPGCGKTLLAKAVA 42
+ G + L+GP G GK+ L +A+A
Sbjct: 21 TLKAGEIVALVGPNGSGKSTLLRAIA 46
>gnl|CDD|223542 COG0466, Lon, ATP-dependent Lon protease, bacterial type
[Posttranslational modification, protein turnover,
chaperones].
Length = 782
Score = 31.4 bits (72), Expect = 1.8
Identities = 12/28 (42%), Positives = 17/28 (60%)
Query: 25 LLLGPPGCGKTLLAKAVATEANVPFLSM 52
L+GPPG GKT L K++A F+ +
Sbjct: 354 CLVGPPGVGKTSLGKSIAKALGRKFVRI 381
>gnl|CDD|226646 COG4178, COG4178, ABC-type uncharacterized transport system,
permease and ATPase components [General function
prediction only].
Length = 604
Score = 31.1 bits (71), Expect = 1.8
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 25 LLLGPPGCGKTLLAKAVA 42
L+ G G GKT L +A+A
Sbjct: 423 LITGESGAGKTSLLRALA 440
>gnl|CDD|223679 COG0606, COG0606, Predicted ATPase with chaperone activity
[Posttranslational modification, protein turnover,
chaperones].
Length = 490
Score = 31.1 bits (71), Expect = 1.8
Identities = 11/15 (73%), Positives = 13/15 (86%)
Query: 25 LLLGPPGCGKTLLAK 39
LL+GPPG GKT+LA
Sbjct: 202 LLVGPPGTGKTMLAS 216
>gnl|CDD|213263 cd03296, ABC_CysA_sulfate_importer, ATP-binding cassette domain
of the sulfate transporter. Part of the ABC
transporter complex cysAWTP involved in sulfate import.
Responsible for energy coupling to the transport
system. The complex is composed of two ATP-binding
proteins (cysA), two transmembrane proteins (cysT and
cysW), and a solute-binding protein (cysP). ABC
transporters are a large family of proteins involved in
the transport of a wide variety of different compounds,
like sugars, ions, peptides, and more complex organic
molecules. The nucleotide binding domain shows the
highest similarity between all members of the family.
ABC transporters are a subset of nucleotide hydrolases
that contain a signature motif, Q-loop, and
H-loop/switch region, in addition to, the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 239
Score = 30.8 bits (70), Expect = 1.8
Identities = 23/77 (29%), Positives = 32/77 (41%), Gaps = 15/77 (19%)
Query: 20 VPKGAL--LLGPPGCGKTLLAKAVA-----TEANVPFLSMNGSEFIEMIGGLGAARVRTE 72
+P G L LLGP G GKT L + +A + F G + +
Sbjct: 25 IPSGELVALLGPSGSGKTTLLRLIAGLERPDSGTILF---GGED----ATDVPVQERNVG 77
Query: 73 VVFLHCRVFLHEITIFD 89
VF H +F H +T+FD
Sbjct: 78 FVFQHYALFRH-MTVFD 93
>gnl|CDD|215758 pfam00158, Sigma54_activat, Sigma-54 interaction domain.
Length = 168
Score = 30.0 bits (69), Expect = 1.9
Identities = 12/32 (37%), Positives = 20/32 (62%), Gaps = 3/32 (9%)
Query: 25 LLLGPPGCGKTLLAKAV---ATEANVPFLSMN 53
L+ G G GK L A+A+ + A+ PF+++N
Sbjct: 26 LITGESGTGKELFARAIHQLSPRADGPFVAVN 57
>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 = 30.2 bits (68), Expect = 2.0
Identities = 10/35 (28%), Positives = 15/35 (42%)
Query: 11 EYYQNLGAKVPKGALLLGPPGCGKTLLAKAVATEA 45
+ + + P LL GP G GKT L + +
Sbjct: 14 DALRRARSGGPPSVLLTGPSGTGKTSLLRELLEGL 48
>gnl|CDD|235364 PRK05201, hslU, ATP-dependent protease ATP-binding subunit HslU;
Provisional.
Length = 443
Score = 31.2 bits (72), Expect = 2.0
Identities = 15/31 (48%), Positives = 21/31 (67%)
Query: 20 VPKGALLLGPPGCGKTLLAKAVATEANVPFL 50
PK L++GP G GKT +A+ +A AN PF+
Sbjct: 49 TPKNILMIGPTGVGKTEIARRLAKLANAPFI 79
>gnl|CDD|190347 pfam02562, PhoH, PhoH-like protein. PhoH is a cytoplasmic
protein and predicted ATPase that is induced by
phosphate starvation.
Length = 205
Score = 30.5 bits (70), Expect = 2.1
Identities = 11/19 (57%), Positives = 13/19 (68%)
Query: 27 LGPPGCGKTLLAKAVATEA 45
+GP G GKT LA A A +A
Sbjct: 25 IGPAGTGKTYLAVAAAVDA 43
>gnl|CDD|213200 cd03233, ABCG_PDR_domain1, First domain of the pleiotropic drug
resistance-like subfamily G of ATP-binding cassette
transporters. The pleiotropic drug resistance (PDR) is
a well-described phenomenon occurring in fungi and
shares several similarities with processes in bacteria
and higher eukaryotes. This PDR subfamily represents
domain I of its (ABC-IM)2 organization. ABC
transporters are a large family of proteins involved in
the transport of a wide variety of different compounds
including sugars, ions, peptides, and more complex
organic molecules. The nucleotide-binding domain shows
the highest similarity between all members of the
family. ABC transporters are a subset of nucleotide
hydrolases that contain a signature motif, Q-loop, and
H-loop/switch region, in addition to, the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 202
Score = 30.3 bits (69), Expect = 2.3
Identities = 12/31 (38%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 25 LLLGPPGCGKTLLAKAVATEANVPFLSMNGS 55
L+LG PG G + L KA+A +S+ G
Sbjct: 37 LVLGRPGSGCSTLLKALAN-RTEGNVSVEGD 66
>gnl|CDD|115336 pfam06673, L_lactis_ph-MCP, Lactococcus lactis bacteriophage major
capsid protein. This family consists of several
Lactococcus lactis bacteriophage major capsid proteins.
Length = 347
Score = 30.9 bits (69), Expect = 2.3
Identities = 18/51 (35%), Positives = 32/51 (62%), Gaps = 5/51 (9%)
Query: 134 SIELGRKLQDMEIKHAEELKKQEQCLRKEKVLKIDAELRHKKELDLERQIL 184
+IE G K++++E K EEL K+ + L+KE+ +A + +K D ER+ +
Sbjct: 13 AIEAGVKVRELEAK-VEELNKEREELKKER----EANIPSEKPEDAERKFM 58
>gnl|CDD|233120 TIGR00764, lon_rel, lon-related putative ATP-dependent protease.
This model represents a set of proteins with extensive
C-terminal homology to the ATP-dependent protease La,
product of the lon gene of E. coli. The model is based
on a seed alignment containing only archaeal members,
but several bacterial proteins match the model well.
Because several species, including Thermotoga maritima
and Treponema pallidum, contain both a close homolog of
the lon protease and nearly full-length homolog of the
members of this family, we suggest there may also be a
functional division between the two families. Members
of this family from Pyrococcus horikoshii and
Pyrococcus abyssi each contain a predicted intein
[Protein fate, Degradation of proteins, peptides, and
glycopeptides].
Length = 608
Score = 31.0 bits (70), Expect = 2.4
Identities = 14/25 (56%), Positives = 19/25 (76%)
Query: 18 AKVPKGALLLGPPGCGKTLLAKAVA 42
AK + LL+G PG GK++LAKA+A
Sbjct: 34 AKQKRNVLLIGEPGVGKSMLAKAMA 58
>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 = 30.4 bits (69), Expect = 2.5
Identities = 13/41 (31%), Positives = 19/41 (46%), Gaps = 8/41 (19%)
Query: 2 EFVDYLKRPEYYQNLGAKVPKGALLLGPPGCGKTLLAKAVA 42
+ + YL R N L++ PP CGKT L + +A
Sbjct: 100 KLLPYLVRNNRVLN--------TLIISPPQCGKTTLLRDLA 132
>gnl|CDD|206034 pfam13863, DUF4200, Domain of unknown function (DUF4200). This
family is found in eukaryotes. It is a coiled-coil
domain of unknwon function.
Length = 126
Score = 29.5 bits (67), Expect = 2.5
Identities = 26/104 (25%), Positives = 50/104 (48%), Gaps = 18/104 (17%)
Query: 127 KKLEEEYSIELGRKLQDME------IKHAEELKKQEQCLRKEKVL-----------KIDA 169
++ EE + L K ++ E + EEL+K+E+ L++ + + A
Sbjct: 6 RREMEEVQLALDAKREEFERREELLKQREEELEKKEEELQESLIKFDKFLKENEAKRRRA 65
Query: 170 ELRHKKELDLERQILLHEITKLKSELKNRELHIVKMETQLRAYE 213
E + ++E R+ EI +LK+EL+ + I K+E +L Y+
Sbjct: 66 EKKAEEEK-KLRKEKEEEIKELKAELEELKAEIEKLEEKLEEYQ 108
>gnl|CDD|213181 cd03214, ABC_Iron-Siderophores_B12_Hemin, ATP-binding component
of iron-siderophores, vitamin B12 and hemin
transporters and related proteins. ABC transporters,
involved in the uptake of siderophores, heme, and
vitamin B12, are widely conserved in bacteria and
archaea. Only very few species lack representatives of
the siderophore family transporters. The E. coli BtuCD
protein is an ABC transporter mediating vitamin B12
uptake. The two ATP-binding cassettes (BtuD) are in
close contact with each other, as are the two
membrane-spanning subunits (BtuC); this arrangement is
distinct from that observed for the E. coli lipid
flippase MsbA. The BtuC subunits provide 20
transmembrane helices grouped around a translocation
pathway that is closed to the cytoplasm by a gate
region, whereas the dimer arrangement of the BtuD
subunits resembles the ATP-bound form of the Rad50 DNA
repair enzyme. A prominent cytoplasmic loop of BtuC
forms the contact region with the ATP-binding cassette
and represent a conserved motif among the ABC
transporters.
Length = 180
Score = 30.1 bits (69), Expect = 2.6
Identities = 11/31 (35%), Positives = 17/31 (54%), Gaps = 2/31 (6%)
Query: 14 QNLGAKVPKGAL--LLGPPGCGKTLLAKAVA 42
+L + G + +LGP G GK+ L K +A
Sbjct: 16 DDLSLSIEAGEIVGILGPNGAGKSTLLKTLA 46
>gnl|CDD|218636 pfam05557, MAD, Mitotic checkpoint protein. This family consists
of several eukaryotic mitotic checkpoint (Mitotic arrest
deficient or MAD) proteins. The mitotic spindle
checkpoint monitors proper attachment of the bipolar
spindle to the kinetochores of aligned sister chromatids
and causes a cell cycle arrest in prometaphase when
failures occur. Multiple components of the mitotic
spindle checkpoint have been identified in yeast and
higher eukaryotes. In S.cerevisiae, the existence of a
Mad1-dependent complex containing Mad2, Mad3, Bub3 and
Cdc20 has been demonstrated.
Length = 722
Score = 31.1 bits (70), Expect = 2.6
Identities = 26/98 (26%), Positives = 42/98 (42%), Gaps = 3/98 (3%)
Query: 117 LNLEKEVMLRKKLEEEYSIELGRKLQDMEIKHAEELKKQEQCLRKEKVLKIDAELRHKKE 176
+ LE E+M ++ + IEL RK + + EL + L E LK EL K E
Sbjct: 71 IQLENELMQKELEHKRAQIELERKASTLAENYERELDR---NLELEVRLKALEELEKKAE 127
Query: 177 LDLERQILLHEITKLKSELKNRELHIVKMETQLRAYES 214
+ ++ K K + ++ +L K + A ES
Sbjct: 128 NEAAEAEEEAKLLKDKLDAESLKLQNEKEDQLKEAKES 165
Score = 29.9 bits (67), Expect = 5.2
Identities = 50/241 (20%), Positives = 90/241 (37%), Gaps = 26/241 (10%)
Query: 115 LKLNLEKEVMLRKKLEEEYSIELGRKLQDMEIKHAEELKKQEQCLRKEKV-LKIDAELRH 173
LKL EKE + K +E + L +M+ + A+ + + L E L+ E
Sbjct: 149 LKLQNEKE--DQLKEAKESISRIKNDLSEMQCR-AQNADTELKLLESELEELREQLEECQ 205
Query: 174 KKELDLERQILLHEITKLKSELKNRELHIVKMETQLRAYESDKKLARKQLIDSVNREIAE 233
K+ + E++ L +T ++ + + I +E +L+ YE D ++ + + +
Sbjct: 206 KELAEAEKK--LQSLTSEQASSADNSVKIKHLEEELKRYEQDAEVVKS----MKEQLLQI 259
Query: 234 TILLKNFAHQLIVKCPLMMTYSSEEGRNLNIPASFKMMKKQNFLPQTSTASNVNQSHNIP 293
L + A EE R L + K+ S +
Sbjct: 260 PELERELAAL------------REENRKLRSMKEDNELLKEELEDLQSRLERFEKM---- 303
Query: 294 QEIYDDILNLKLNLEKEVMLRKKLEEEYSIELGSPIDTSRSHRVLRKWVLSSLLTVNKFA 353
+E D+ K LE E+ K L ++ + L +P D SR VL+ L +
Sbjct: 304 REKLADLELEKEKLENELKSWKSLLQDIGLNLRTPDDLSRRIVVLQNEELQLKEKNGSIS 363
Query: 354 S 354
S
Sbjct: 364 S 364
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 30.6 bits (70), Expect = 2.7
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 23 GALLLGPPGCGKTLLAKAVAT 43
G L+ G PG GK+ A+A+A
Sbjct: 259 GILIAGAPGAGKSTFAQALAE 279
>gnl|CDD|224616 COG1702, PhoH, Phosphate starvation-inducible protein PhoH,
predicted ATPase [Signal transduction mechanisms].
Length = 348
Score = 30.3 bits (69), Expect = 2.8
Identities = 11/19 (57%), Positives = 13/19 (68%)
Query: 27 LGPPGCGKTLLAKAVATEA 45
+GP G GKT LA A A +A
Sbjct: 149 IGPAGTGKTYLAVAKAVDA 167
>gnl|CDD|213190 cd03223, ABCD_peroxisomal_ALDP, ATP-binding cassette domain of
peroxisomal transporter, subfamily D. Peroxisomal
ATP-binding cassette transporter (Pat) is involved in
the import of very long-chain fatty acids (VLCFA) into
the peroxisome. The peroxisomal membrane forms a
permeability barrier for a wide variety of metabolites
required for and formed during fatty acid
beta-oxidation. To communicate with the cytoplasm and
mitochondria, peroxisomes need dedicated proteins to
transport such hydrophilic molecules across their
membranes. X-linked adrenoleukodystrophy (X-ALD) is
caused by mutations in the ALD gene, which encodes ALDP
(adrenoleukodystrophy protein ), a peroxisomal integral
membrane protein that is a member of the ATP-binding
cassette (ABC) transporter protein family. The disease
is characterized by a striking and unpredictable
variation in phenotypic expression. Phenotypes include
the rapidly progressive childhood cerebral form
(CCALD), the milder adult form, adrenomyeloneuropathy
(AMN), and variants without neurologic involvement
(i.e. asymptomatic).
Length = 166
Score = 29.8 bits (68), Expect = 2.8
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 25 LLLGPPGCGKTLLAKAVA 42
L+ GP G GK+ L +A+A
Sbjct: 31 LITGPSGTGKSSLFRALA 48
>gnl|CDD|223683 COG0610, COG0610, Type I site-specific restriction-modification
system, R (restriction) subunit and related helicases
[Defense mechanisms].
Length = 962
Score = 30.8 bits (70), Expect = 2.9
Identities = 27/155 (17%), Positives = 52/155 (33%), Gaps = 31/155 (20%)
Query: 87 IFDLETKIIENIFD--LETKIILSSFMMIVLKLNLE---KEVMLRKKLEEEYSIELGRKL 141
+ KI+ +F L+ L L E E +L+ +LE++Y + +
Sbjct: 720 KVERGNKILAKLFGRFLKAFNALKKLYEFAYTLEEEIQYLEDLLKARLEKDYQSKYLDLI 779
Query: 142 QDMEIKHAEELKKQEQCLRKEKVLKIDAELRHKKELDLERQILLHEITKLKSELKNRELH 201
++ + KE ++ + EL +++I + I +L
Sbjct: 780 DNLNDAREIK--------DKESKAIDLDDIDFELELIGKQEINIDYILELLQTFN----- 826
Query: 202 IVKMETQLRAYESDKKLARKQLIDSVNREIAETIL 236
DK A + L + + R I E I
Sbjct: 827 -------------DKNGAYESLKELIERIIKEWIE 848
>gnl|CDD|226412 COG3896, COG3896, Chloramphenicol 3-O-phosphotransferase [Defense
mechanisms].
Length = 205
Score = 29.9 bits (67), Expect = 3.0
Identities = 15/56 (26%), Positives = 26/56 (46%), Gaps = 2/56 (3%)
Query: 8 KRPEYYQNLGAKVPKGALLL--GPPGCGKTLLAKAVATEANVPFLSMNGSEFIEMI 61
+R Y A +P+G ++L G GK+ +A A A P++ + F E +
Sbjct: 8 RRMRYRLAAMAGMPEGRIVLLNGGSSAGKSSIALAFQDLAAEPWMHIGIDLFWEAL 63
>gnl|CDD|226809 COG4372, COG4372, Uncharacterized protein conserved in bacteria
with the myosin-like domain [Function unknown].
Length = 499
Score = 30.4 bits (68), Expect = 3.0
Identities = 18/121 (14%), Positives = 46/121 (38%), Gaps = 8/121 (6%)
Query: 116 KLNLEKEVMLRKKLEEEYSIELGRKLQDMEIK-HAEELKKQEQCL--RKEKVLKIDAELR 172
+L + + + + + + S K Q +++K + +++++ Q L R EL
Sbjct: 162 QLEAQAQSLQASQKQLQASAT-QLKSQVLDLKLRSAQIEQEAQNLATRANAAQARTEELA 220
Query: 173 HKKELDLERQILLHEITKLKSELKNRELHIVKMETQLRAYESDKKLARKQLIDSVNREIA 232
+ Q I + +++ + I Q+R E + + +E+A
Sbjct: 221 RRAA---AAQQTAQAIQQRDAQISQKAQQIAARAEQIRERERQLQRLETAQ-ARLEQEVA 276
Query: 233 E 233
+
Sbjct: 277 Q 277
>gnl|CDD|226361 COG3842, PotA, ABC-type spermidine/putrescine transport systems,
ATPase components [Amino acid transport and
metabolism].
Length = 352
Score = 30.3 bits (69), Expect = 3.1
Identities = 11/17 (64%), Positives = 13/17 (76%)
Query: 26 LLGPPGCGKTLLAKAVA 42
LLGP GCGKT L + +A
Sbjct: 36 LLGPSGCGKTTLLRMIA 52
>gnl|CDD|234053 TIGR02903, spore_lon_C, ATP-dependent protease, Lon family.
Members of this protein family resemble the widely
distributed ATP-dependent protease La, also called Lon
and LonA. It resembles even more closely LonB, which is
a LonA paralog found in genomes if and only if the
species is capable of endospore formation (as in
Bacillus subtilis, Clostridium tetani, and select other
members of the Firmicutes) and expressed specifically in
the forespore compartment. Members of this family are
restricted to a subset of spore-forming species, and are
very likely to participate in the program of endospore
formation. We propose the designation LonC [Protein
fate, Degradation of proteins, peptides, and
glycopeptides, Cellular processes, Sporulation and
germination].
Length = 615
Score = 30.5 bits (69), Expect = 3.1
Identities = 18/50 (36%), Positives = 24/50 (48%), Gaps = 8/50 (16%)
Query: 14 QNLGAKV----PKGALLLGPPGCGKTLLAKAVATEANVPFLSMNGSEFIE 59
+ L AKV P+ +L GPPG GKT A+ EA + + F E
Sbjct: 164 KALLAKVASPFPQHIILYGPPGVGKTTAARLALEEAK----KLKHTPFAE 209
>gnl|CDD|213193 cd03226, ABC_cobalt_CbiO_domain2, Second domain of the
ATP-binding cassette component of cobalt transport
system. Domain II of the ABC component of a cobalt
transport family found in bacteria, archaea, and
eukaryota. The transition metal cobalt is an essential
component of many enzymes and must be transported into
cells in appropriate amounts when needed. The CbiMNQO
family ABC transport system is involved in cobalt
transport in association with the cobalamin (vitamin
B12) biosynthetic pathways. Most cobalt (Cbi) transport
systems possess a separate CbiN component, the
cobalt-binding periplasmic protein, and they are
encoded by the conserved gene cluster cbiMNQO. Both the
CbiM and CbiQ proteins are integral cytoplasmic
membrane proteins, and the CbiO protein has the linker
peptide and the Walker A and B motifs commonly found in
the ATPase components of the ABC-type transport
systems.
Length = 205
Score = 29.9 bits (68), Expect = 3.1
Identities = 15/41 (36%), Positives = 19/41 (46%), Gaps = 2/41 (4%)
Query: 4 VDYLKRPEYYQNLGAKVPKGAL--LLGPPGCGKTLLAKAVA 42
Y K E +L + G + L G G GKT LAK +A
Sbjct: 7 FSYKKGTEILDDLSLDLYAGEIIALTGKNGAGKTTLAKILA 47
>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin. Trichoplein
or mitostatin, was first defined as a meiosis-specific
nuclear structural protein. It has since been linked
with mitochondrial movement. It is associated with the
mitochondrial outer membrane, and over-expression leads
to reduction in mitochondrial motility whereas lack of
it enhances mitochondrial movement. The activity appears
to be mediated through binding the mitochondria to the
actin intermediate filaments (IFs).
Length = 349
Score = 30.3 bits (69), Expect = 3.3
Identities = 25/124 (20%), Positives = 46/124 (37%), Gaps = 15/124 (12%)
Query: 121 KEVMLRKKLEEEYSIELGRKLQDMEIKHAEELKKQEQCLRKEKVLKIDAELRHKKELDLE 180
+E K E+E + ME + + L ++E+ RK K + + L+
Sbjct: 27 EEKKRIKAEEKEEERRIDEM---MEEERLKALAEEEERERKRKEERR----EGRAV--LQ 77
Query: 181 RQILLHEITKLKSELKNRELHIVKMETQLRAYESD------KKLARKQLIDSVNREIAET 234
QI E + + + + E R E D K+ +K+L + ++ E
Sbjct: 78 EQIEEREKRRQEEYEERLQEREQMDEIIERIQEEDEAEAQEKREKQKKLREEIDEFNEER 137
Query: 235 ILLK 238
I K
Sbjct: 138 IERK 141
>gnl|CDD|129465 TIGR00368, TIGR00368, Mg chelatase-related protein. The N-terminal
end matches very strongly a pfam Mg_chelatase domain
[Unknown function, General].
Length = 499
Score = 30.2 bits (68), Expect = 3.4
Identities = 11/15 (73%), Positives = 12/15 (80%)
Query: 25 LLLGPPGCGKTLLAK 39
LL GPPG GKT+LA
Sbjct: 215 LLFGPPGSGKTMLAS 229
>gnl|CDD|179433 PRK02496, adk, adenylate kinase; Provisional.
Length = 184
Score = 29.7 bits (67), Expect = 3.4
Identities = 11/30 (36%), Positives = 16/30 (53%)
Query: 22 KGALLLGPPGCGKTLLAKAVATEANVPFLS 51
+ LGPPG GK A +A ++P +S
Sbjct: 2 TRLIFLGPPGAGKGTQAVVLAEHLHIPHIS 31
>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain. This domain is
found at the N terminus of SMC proteins. The SMC
(structural maintenance of chromosomes) superfamily
proteins have ATP-binding domains at the N- and
C-termini, and two extended coiled-coil domains
separated by a hinge in the middle. The eukaryotic SMC
proteins form two kind of heterodimers: the SMC1/SMC3
and the SMC2/SMC4 types. These heterodimers constitute
an essential part of higher order complexes, which are
involved in chromatin and DNA dynamics. This family also
includes the RecF and RecN proteins that are involved in
DNA metabolism and recombination.
Length = 1162
Score = 30.3 bits (68), Expect = 3.6
Identities = 30/150 (20%), Positives = 51/150 (34%), Gaps = 4/150 (2%)
Query: 91 ETKIIENIFDLETKIILSSFMMIVLKLNLEKEVMLRKKLEE-EYSIELGRKLQDMEIKHA 149
+ +II + I + +K+ L+K +EE E EL L++
Sbjct: 144 KVEIIAMMKPERRLEIE--EEAAGSREKRKKKERLKKLIEETENLAELIIDLEE-LKLQE 200
Query: 150 EELKKQEQCLRKEKVLKIDAELRHKKELDLERQILLHEITKLKSELKNRELHIVKMETQL 209
+LK+Q + + LK EL + L L+ L E L EL E ++ Q
Sbjct: 201 LKLKEQAKKALEYYQLKEKLELEEENLLYLDYLKLNEERIDLLQELLRDEQEEIESSKQE 260
Query: 210 RAYESDKKLARKQLIDSVNREIAETILLKN 239
E + + +E
Sbjct: 261 LEKEEEILAQVLKENKEEEKEKKLQEEELK 290
>gnl|CDD|225822 COG3284, AcoR, Transcriptional activator of acetoin/glycerol
metabolism [Secondary metabolites biosynthesis,
transport, and catabolism / Transcription].
Length = 606
Score = 30.4 bits (69), Expect = 3.7
Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 8/51 (15%)
Query: 25 LLLGPPGCGKTLLAKAV--ATEANVPFLSMN----GSEFI--EMIGGLGAA 67
LL G G GK +LA+A+ +EA PF+++N I E+ G + A
Sbjct: 340 LLQGETGTGKEVLARAIHQNSEAAGPFVAVNCAAIPEALIESELFGYVAGA 390
>gnl|CDD|216270 pfam01057, Parvo_NS1, Parvovirus non-structural protein NS1. This
family also contains the NS2 protein. Parvoviruses
encode two non-structural proteins, NS1 and NS2. The
mRNA for NS2 contains the coding sequence for the first
87 amino acids of NS1, then by an alternative splicing
mechanism mRNA from a different reading frame, encoding
the last 78 amino acids, makes up the full length of the
NS2 mRNA. NS1, is the major non-structural protein. It
is essential for DNA replication. It is an 83-kDa
nuclear phosphoprotein. It has DNA helicase and ATPase
activity.
Length = 271
Score = 30.0 bits (68), Expect = 3.8
Identities = 11/32 (34%), Positives = 15/32 (46%), Gaps = 3/32 (9%)
Query: 19 KVPKGALLL-GPPGCGKTLLAKAVATEANVPF 49
+ + GP GKT LA+A+A VP
Sbjct: 110 GGKRNTVWFYGPASTGKTNLAQAIAH--AVPL 139
>gnl|CDD|100085 cd06164, S2P-M50_SpoIVFB_CBS, SpoIVFB Site-2 protease (S2P), a zinc
metalloprotease (MEROPS family M50B), regulates
intramembrane proteolysis (RIP), and is involved in the
pro-sigmaK pathway of bacterial spore formation. In this
subgroup, SpoIVFB (sporulation protein, stage IV cell
wall formation, F locus, promoter-distal B) contains two
tandem repeats of the cystathionine beta-synthase (CBS
pair) domain. SpoIVFB is one of 4 proteins involved in
endospore formation; the others are SpoIVFA (sporulation
protein, stage IV cell wall formation, F locus,
promoter-proximal A), BofA (bypass-of-forespore A), and
SpoIVB (sporulation protein, stage IV cell wall
formation, B locus). SpoIVFB is negatively regulated by
SpoIVFA and BofA and activated by SpoIVB. It is thought
that SpoIVFB, SpoIVFA, and BofA are located in the
mother-cell membrane that surrounds the forespore and
that SpoIVB is secreted from the forespore into the
space between the two where it activates SpoIVFB. It has
been proposed that the CBS domain may play a regulatory
role, although its exact function is unknown.
Length = 227
Score = 29.8 bits (68), Expect = 3.9
Identities = 19/79 (24%), Positives = 26/79 (32%), Gaps = 28/79 (35%)
Query: 341 WVLSSLLTVNKFASLVCRQVAFHESGHALVG------------WLL---------PHT-D 378
W+L + FAS++ HE GH+LV +L P T
Sbjct: 42 WLLGLAAALLLFASVL-----LHELGHSLVARRYGIPVRSITLFLFGGVARLEREPETPG 96
Query: 379 ALLKVTIV-PRTSLALGFA 396
+ I P SL L
Sbjct: 97 QEFVIAIAGPLVSLVLALL 115
Score = 29.8 bits (68), Expect = 3.9
Identities = 19/79 (24%), Positives = 26/79 (32%), Gaps = 28/79 (35%)
Query: 427 WVLSSLLTVNKFASLVCRQVAFHESGHALVG------------WLL---------PHT-D 464
W+L + FAS++ HE GH+LV +L P T
Sbjct: 42 WLLGLAAALLLFASVL-----LHELGHSLVARRYGIPVRSITLFLFGGVARLEREPETPG 96
Query: 465 ALLKVTIV-PRTSLALGFA 482
+ I P SL L
Sbjct: 97 QEFVIAIAGPLVSLVLALL 115
>gnl|CDD|223544 COG0468, RecA, RecA/RadA recombinase [DNA replication,
recombination, and repair].
Length = 279
Score = 29.9 bits (68), Expect = 4.2
Identities = 22/108 (20%), Positives = 40/108 (37%), Gaps = 15/108 (13%)
Query: 16 LGAKVPKGAL--LLGPPGCGKTLLAKAVATEANVPFLSMNGSEFIEMIGGLGAARVR--- 70
LG +P+G + + GP GKT LA + A P + FI+ L R +
Sbjct: 53 LGGGLPRGRITEIYGPESSGKTTLALQLVANAQKPGGK---AAFIDTEHALDPERAKQLG 109
Query: 71 ----TEVVFLHCRVFLHEITIFDLETKIIENIFDLETKIILSSFMMIV 114
++ ++ I + + DL +++ S +V
Sbjct: 110 VDLLDNLLVSQPDTGEQQLEIAEKLARSGAEKIDL---LVVDSVAALV 154
>gnl|CDD|224027 COG1102, Cmk, Cytidylate kinase [Nucleotide transport and
metabolism].
Length = 179
Score = 29.2 bits (66), Expect = 4.3
Identities = 13/33 (39%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 28 GPPGCGKTLLAKAVATEANVPFLSMNGSEFIEM 60
G PG GKT +A+ +A + +S G+ F EM
Sbjct: 7 GLPGSGKTTVARELAEHLGLKLVS-AGTIFREM 38
>gnl|CDD|218215 pfam04696, Pinin_SDK_memA, pinin/SDK/memA/ protein conserved
region. Members of this family have very varied
localisations within the eukaryotic cell. pinin is known
to localise at the desmosomes and is implicated in
anchoring intermediate filaments to the desmosomal
plaque. SDK2/3 is a dynamically localised nuclear
protein thought to be involved in modulation of
alternative pre-mRNA splicing. memA is a tumour marker
preferentially expressed in human melanoma cell lines. A
common feature of the members of this family is that
they may all participate in regulating protein-protein
interactions.
Length = 131
Score = 28.6 bits (64), Expect = 4.3
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 2/72 (2%)
Query: 126 RKKLEEEYSIELGRKLQDMEIKHAEELKKQEQCLRKEKVLKIDAELRHKKELDLERQILL 185
R +E+ E+ +KL++ E + EEL+K+++ L +E+ + ELR K E +E + L
Sbjct: 29 RLTSKEKRRAEIEQKLEEQEKQEREELRKEKRELFEER-RRKQLELR-KLEQKMEDEKLQ 86
Query: 186 HEITKLKSELKN 197
+ L N
Sbjct: 87 ETWHEHNLALAN 98
>gnl|CDD|222194 pfam13521, AAA_28, AAA domain.
Length = 162
Score = 29.1 bits (66), Expect = 4.4
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 26 LLGPPGCGKTLLAKAVA 42
+ G P GKT L +A+A
Sbjct: 4 ITGGPSTGKTTLLEALA 20
>gnl|CDD|223637 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide
transport and metabolism].
Length = 178
Score = 29.2 bits (66), Expect = 4.5
Identities = 14/27 (51%), Positives = 19/27 (70%)
Query: 25 LLLGPPGCGKTLLAKAVATEANVPFLS 51
L+LGPPG GK+ LAK +A + +P L
Sbjct: 4 LILGPPGAGKSTLAKKLAKKLGLPHLD 30
>gnl|CDD|225804 COG3265, GntK, Gluconate kinase [Carbohydrate transport and
metabolism].
Length = 161
Score = 29.2 bits (66), Expect = 4.5
Identities = 9/32 (28%), Positives = 15/32 (46%), Gaps = 8/32 (25%)
Query: 28 GPPGCGKTLLAKAVATEANVPFLSMNGSEFIE 59
G G GK+ + A+A G++FI+
Sbjct: 2 GVSGSGKSTVGSALAERL--------GAKFID 25
>gnl|CDD|216158 pfam00860, Xan_ur_permease, Permease family. This family includes
permeases for diverse substrates such as xanthine,
uracil, and vitamin C. However many members of this
family are functionally uncharacterized and may
transport other substrates. Members of this family have
ten predicted transmembrane helices.
Length = 389
Score = 30.0 bits (68), Expect = 4.6
Identities = 16/60 (26%), Positives = 26/60 (43%)
Query: 23 GALLLGPPGCGKTLLAKAVATEANVPFLSMNGSEFIEMIGGLGAARVRTEVVFLHCRVFL 82
G L P + LLA +AT + F + + + E IG + +V + V + V L
Sbjct: 260 GRDLKPKPDLRRGLLADGLATLLSGLFGAFPTTTYAENIGVVALTKVYSRRVGVTAGVIL 319
>gnl|CDD|224401 COG1484, DnaC, DNA replication protein [DNA replication,
recombination, and repair].
Length = 254
Score = 29.7 bits (67), Expect = 4.8
Identities = 13/26 (50%), Positives = 16/26 (61%)
Query: 21 PKGALLLGPPGCGKTLLAKAVATEAN 46
+ +LLGPPG GKT LA A+ E
Sbjct: 105 GENLVLLGPPGVGKTHLAIAIGNELL 130
>gnl|CDD|227053 COG4709, COG4709, Predicted membrane protein [Function unknown].
Length = 195
Score = 29.3 bits (66), Expect = 4.8
Identities = 18/74 (24%), Positives = 30/74 (40%), Gaps = 8/74 (10%)
Query: 271 MKKQNFLPQTSTASNVNQSHNIPQEIYDDILNLKLNLEKEVMLRKKLEEEYSIELGSPID 330
M K FL + +P+E +I+ +E K EEE + +LG P +
Sbjct: 1 MTKTEFLNELEQYLE-----GLPREERREIMYDYEEHFREAQEAGKSEEEIAKDLGDPKE 55
Query: 331 TS---RSHRVLRKW 341
+ S R ++K
Sbjct: 56 IAAEILSERGIKKE 69
>gnl|CDD|214361 CHL00095, clpC, Clp protease ATP binding subunit.
Length = 821
Score = 30.0 bits (68), Expect = 4.9
Identities = 17/40 (42%), Positives = 22/40 (55%), Gaps = 7/40 (17%)
Query: 25 LLLGPPGCGKTLLAKAVA-----TEANVPFLSMNGSEFIE 59
L GP G GKT L KA+A +E + L M SE++E
Sbjct: 543 LFSGPTGVGKTELTKALASYFFGSEDAMIRLDM--SEYME 580
>gnl|CDD|219014 pfam06414, Zeta_toxin, Zeta toxin. This family consists of
several bacterial zeta toxin proteins. Zeta toxin is
thought to be part of a postregulational killing system
in bacteria. It relies on antitoxin/toxin systems that
secure stable inheritance of low and medium copy number
plasmids during cell division and kill cells that have
lost the plasmid.
Length = 191
Score = 29.2 bits (66), Expect = 5.0
Identities = 14/38 (36%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 21 PKGALLLGPPGCGKTLLAKAVATE-ANVPFLSMNGSEF 57
P LL G PG GKT LA+A+ E + ++ E
Sbjct: 12 PVAVLLGGQPGAGKTELARALLEELGGGNVVRIDPDEL 49
>gnl|CDD|129694 TIGR00606, rad50, rad50. All proteins in this family for which
functions are known are involvedin recombination,
recombinational repair, and/or non-homologous end
joining.They are components of an exonuclease complex
with MRE11 homologs. This family is distantly related to
the SbcC family of bacterial proteins.This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University).
Length = 1311
Score = 30.0 bits (67), Expect = 5.1
Identities = 25/115 (21%), Positives = 56/115 (48%), Gaps = 11/115 (9%)
Query: 115 LKLNLEKEVMLRKKLEEEYSIELGRKLQDMEIKHAEELKKQEQC---LRKEKVLKIDAEL 171
+ LE+ ++K+ E+ + QD++ + +E Q+ R+ ++ +++ EL
Sbjct: 982 VNAQLEECEKHQEKINED----MRLMRQDIDTQKIQERWLQDNLTLRKRENELKEVEEEL 1037
Query: 172 R-HKKELDLERQILL--HEITKLKSELKNRELHIVKMETQLRAYESDKKLARKQL 223
+ H KE+ + Q+L E KL+ + + + V + + YE + K +K+L
Sbjct: 1038 KQHLKEMG-QMQVLQMKQEHQKLEENIDLIKRNHVLALGRQKGYEKEIKHFKKEL 1091
>gnl|CDD|205790 pfam13612, DDE_Tnp_1_3, Transposase DDE domain. Transposase
proteins are necessary for efficient DNA transposition.
This domain is a member of the DDE superfamily, which
contains three carboxylate residues that are believed to
be responsible for coordinating metal ions needed for
catalysis. The catalytic activity of this enzyme
involves DNA cleavage at a specific site followed by a
strand transfer reaction.
Length = 155
Score = 28.7 bits (65), Expect = 5.5
Identities = 19/60 (31%), Positives = 26/60 (43%), Gaps = 20/60 (33%)
Query: 185 LHEITKLKSELKNRELHIVKMETQLRAYESDKKLARKQLIDSVNREIAETI--LLKNFAH 242
+ ITKL+ +KN+ + + DK L RK R I ETI LKN +
Sbjct: 105 IQLITKLRKNMKNKLMSL-----------WDKILLRK-------RSIIETINDQLKNISQ 146
>gnl|CDD|234654 PRK00131, aroK, shikimate kinase; Reviewed.
Length = 175
Score = 29.0 bits (66), Expect = 5.5
Identities = 7/25 (28%), Positives = 13/25 (52%)
Query: 26 LLGPPGCGKTLLAKAVATEANVPFL 50
L+G G GK+ + + +A F+
Sbjct: 9 LIGFMGAGKSTIGRLLAKRLGYDFI 33
>gnl|CDD|216360 pfam01202, SKI, Shikimate kinase.
Length = 158
Score = 28.7 bits (65), Expect = 5.6
Identities = 8/30 (26%), Positives = 16/30 (53%), Gaps = 2/30 (6%)
Query: 30 PGCGKTLLAKAVATEANVPFLSMNGSEFIE 59
G GK+ + + +A +PF+ + + IE
Sbjct: 1 MGAGKSTIGRLLAKALGLPFIDTD--QEIE 28
>gnl|CDD|204935 pfam12474, PKK, Polo kinase kinase. This domain family is found in
eukaryotes, and is approximately 140 amino acids in
length. The family is found in association with
pfam00069. Polo-like kinase 1 (Plx1) is essential during
mitosis for the activation of Cdc25C, for spindle
assembly, and for cyclin B degradation. This family is
Polo kinase kinase (PKK) which phosphorylates Polo
kinase and Polo-like kinase to activate them. PKK is a
serine/threonine kinase.
Length = 142
Score = 28.4 bits (64), Expect = 5.6
Identities = 26/105 (24%), Positives = 49/105 (46%), Gaps = 9/105 (8%)
Query: 139 RKLQDMEIKHAEELKKQEQCLRKE---KVLKIDAELRH-KKELDLERQILLHEITKLKSE 194
R ++ +E + +EL++ + +R E ++ L+ KKEL E + L + K
Sbjct: 37 RTIEKLEQRQTQELRRLPKRIRAEQKTRLKMFKESLKIEKKELKQEVEKLPRFQEQEKKR 96
Query: 195 LKNRELHI-VKMETQLRAY----ESDKKLARKQLIDSVNREIAET 234
+K + K + Q R + E + + A +QL + E+AET
Sbjct: 97 MKAEKEEQEQKHQKQEREFLAKQEENLEEALQQLQNEKRHELAET 141
>gnl|CDD|184458 PRK14021, PRK14021, bifunctional shikimate
kinase/3-dehydroquinate synthase; Provisional.
Length = 542
Score = 29.8 bits (67), Expect = 5.6
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 24 ALLLGPPGCGKTLLAKAVATEANVPFL 50
A+++G G GKT + K VA +PF
Sbjct: 9 AVIIGMMGAGKTRVGKEVAQMMRLPFA 35
>gnl|CDD|202833 pfam03962, Mnd1, Mnd1 family. This family of proteins includes
MND1 from S. cerevisiae. The mnd1 protein forms a
complex with hop2 to promote homologous chromosome
pairing and meiotic double-strand break repair.
Length = 188
Score = 29.1 bits (66), Expect = 5.6
Identities = 26/101 (25%), Positives = 45/101 (44%), Gaps = 16/101 (15%)
Query: 136 ELGRKLQDMEIKHAEELKKQEQCLRKEKVLKIDAELRHKKELDLERQILLHEITKLKSEL 195
+ KL+ K +EL++ +Q R ++ +L+ +E ER LL E+ +L+ EL
Sbjct: 62 QALNKLKTRLEKLKKELEELKQ--RIAELQAQIEKLKKGREETEERTELLEELKQLEKEL 119
Query: 196 KNRELHIVKMETQLRAYES-------DKKLARKQLIDSVNR 229
K K++ +L YE K K ++ NR
Sbjct: 120 K-------KLKAELEKYEKNDPERIEKLKEETKVAKEAANR 153
>gnl|CDD|140006 PRK13949, PRK13949, shikimate kinase; Provisional.
Length = 169
Score = 28.9 bits (65), Expect = 5.7
Identities = 26/70 (37%), Positives = 36/70 (51%), Gaps = 10/70 (14%)
Query: 26 LLGPPGCGKTLLAKAVATEANVPFLSMNGSEFIE-----MIGGLGAARVRTEVVFLHC-R 79
L+G G GKT L KA+A E + F+ ++ FIE +G + A R E VF R
Sbjct: 6 LVGYMGAGKTTLGKALARELGLSFIDLD--FFIENRFHKTVGDIFAE--RGEAVFRELER 61
Query: 80 VFLHEITIFD 89
LHE+ F+
Sbjct: 62 NMLHEVAEFE 71
>gnl|CDD|213217 cd03250, ABCC_MRP_domain1, ATP-binding cassette domain 1 of
multidrug resistance-associated protein, subfamily C.
This subfamily is also known as MRP (multidrug
resistance-associated protein). Some of the MRP members
have five additional transmembrane segments in their
N-terminus, but the function of these additional
membrane-spanning domains is not clear. The MRP was
found in the multidrug-resisting lung cancer cell in
which p-glycoprotein was not overexpressed. MRP exports
glutathione by drug stimulation, as well as, certain
substrates in conjugated forms with anions, such as
glutathione, glucuronate, and sulfate.
Length = 204
Score = 29.0 bits (66), Expect = 5.8
Identities = 16/46 (34%), Positives = 26/46 (56%), Gaps = 4/46 (8%)
Query: 14 QNLGAKVPKGALL--LGPPGCGKTLLAKAVA--TEANVPFLSMNGS 55
+++ +VPKG L+ +GP G GK+ L A+ E +S+ GS
Sbjct: 22 KDINLEVPKGELVAIVGPVGSGKSSLLSALLGELEKLSGSVSVPGS 67
>gnl|CDD|213267 cd03300, ABC_PotA_N, ATP-binding cassette domain of the polyamine
transporter. PotA is an ABC-type transporter and the
ATPase component of the
spermidine/putrescine-preferential uptake system
consisting of PotA, -B, -C, and -D. PotA has two
domains with the N-terminal domain containing the
ATPase activity and the residues required for
homodimerization with PotA and heterdimerization with
PotB. ABC transporters are a large family of proteins
involved in the transport of a wide variety of
different compounds, like sugars, ions, peptides, and
more complex organic molecules. The nucleotide binding
domain shows the highest similarity between all members
of the family. ABC transporters are a subset of
nucleotide hydrolases that contain a signature motif,
Q-loop, and H-loop/switch region, in addition to, the
Walker A motif/P-loop and Walker B motif commonly found
in a number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 232
Score = 29.1 bits (66), Expect = 5.9
Identities = 11/17 (64%), Positives = 13/17 (76%)
Query: 26 LLGPPGCGKTLLAKAVA 42
LLGP GCGKT L + +A
Sbjct: 31 LLGPSGCGKTTLLRLIA 47
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 28.4 bits (64), Expect = 6.0
Identities = 13/71 (18%), Positives = 22/71 (30%), Gaps = 10/71 (14%)
Query: 24 ALLLGPPGCGKTLLAKAVATEANVPFL-------SMNGSEFIEMIG---GLGAARVRTEV 73
+L G G GKT L + +A + + + + I GL + T
Sbjct: 7 GVLTGESGSGKTTLLRRLARQLPNRRVVYVEAPSLGTPKDLLRKILRALGLPLSGGTTAE 66
Query: 74 VFLHCRVFLHE 84
+ L
Sbjct: 67 LLEAILDALKR 77
>gnl|CDD|237745 PRK14527, PRK14527, adenylate kinase; Provisional.
Length = 191
Score = 29.0 bits (65), Expect = 6.0
Identities = 13/32 (40%), Positives = 17/32 (53%)
Query: 20 VPKGALLLGPPGCGKTLLAKAVATEANVPFLS 51
K + LGPPG GK A+ +A E + LS
Sbjct: 5 KNKVVIFLGPPGAGKGTQAERLAQELGLKKLS 36
>gnl|CDD|213226 cd03259, ABC_Carb_Solutes_like, ATP-binding cassette domain of
the carbohydrate and solute transporters-like. This
family is comprised of proteins involved in the
transport of apparently unrelated solutes and proteins
specific for di- and oligosaccharides and polyols. ABC
transporters are a large family of proteins involved in
the transport of a wide variety of different compounds,
like sugars, ions, peptides and more complex organic
molecules. The nucleotide-binding domain shows the
highest similarity between all members of the family.
ABC transporters are a subset of nucleotide hydrolases
that contain a signature motif, Q-loop, and
H-loop/switch region, in addition to, the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 213
Score = 29.0 bits (66), Expect = 6.0
Identities = 13/25 (52%), Positives = 15/25 (60%), Gaps = 2/25 (8%)
Query: 20 VPKGAL--LLGPPGCGKTLLAKAVA 42
V G LLGP GCGKT L + +A
Sbjct: 23 VEPGEFLALLGPSGCGKTTLLRLIA 47
>gnl|CDD|188098 TIGR00957, MRP_assoc_pro, multi drug resistance-associated protein
(MRP). This model describes multi drug
resistance-associated protein (MRP) in eukaryotes. The
multidrug resistance-associated protein is an integral
membrane protein that causes multidrug resistance when
overexpressed in mammalian cells. It belongs to ABC
transporter superfamily. The protein topology and
function was experimentally demonstrated by epitope
tagging and immunofluorescence. Insertion of tags in the
critical regions associated with drug efflux, abrogated
its function. The C-terminal domain seem to highly
conserved [Transport and binding proteins, Other].
Length = 1522
Score = 29.9 bits (67), Expect = 6.1
Identities = 13/37 (35%), Positives = 20/37 (54%), Gaps = 2/37 (5%)
Query: 10 PEYYQNLGAKVPKGALL--LGPPGCGKTLLAKAVATE 44
P + +P+GAL+ +G GCGK+ L A+ E
Sbjct: 651 PPTLNGITFSIPEGALVAVVGQVGCGKSSLLSALLAE 687
>gnl|CDD|220366 pfam09728, Taxilin, Myosin-like coiled-coil protein. Taxilin
contains an extraordinarily long coiled-coil domain in
its C-terminal half and is ubiquitously expressed. It is
a novel binding partner of several syntaxin family
members and is possibly involved in Ca2+-dependent
exocytosis in neuroendocrine cells. Gamma-taxilin,
described as leucine zipper protein Factor Inhibiting
ATF4-mediated Transcription (FIAT), localises to the
nucleus in osteoblasts and dimerises with ATF4 to form
inactive dimers, thus inhibiting ATF4-mediated
transcription.
Length = 309
Score = 29.3 bits (66), Expect = 6.2
Identities = 32/122 (26%), Positives = 50/122 (40%), Gaps = 23/122 (18%)
Query: 114 VLKLNLEKEVMLRKKLEEEYSIELGRKLQDMEIKHAEELKKQEQCLRKEKVLKIDAELRH 173
L+ K ++ R KLE L R+LQ KH + LK E+ + D E
Sbjct: 61 KLQSEHSKAILARSKLES-----LCRELQ----KHNKTLK--EENKAR-----SDEEEEK 104
Query: 174 KKELDLERQILLHEITKLKSELKNRELHIVKMETQLRAYESDKKLA-----RKQLIDSVN 228
+KEL + Q L +I E N + + +LR E K+L R+Q + +
Sbjct: 105 RKELTEKFQSTLKDIQDQMEEHSNPNHKLCEENEELR--EKLKELIEQYELREQHFEKLL 162
Query: 229 RE 230
+
Sbjct: 163 KT 164
>gnl|CDD|238687 cd01393, recA_like, RecA is a bacterial enzyme which has roles
in homologous recombination, DNA repair, and the
induction of the SOS response. RecA couples ATP
hydrolysis to DNA strand exchange. While prokaryotes
have a single RecA protein, eukaryotes have multiple
RecA homologs such as Rad51, DMC1 and Rad55/57.
Archaea have the RecA-like homologs radA and radB.
Length = 226
Score = 29.1 bits (66), Expect = 6.4
Identities = 17/54 (31%), Positives = 23/54 (42%), Gaps = 11/54 (20%)
Query: 16 LGAKVPKGAL--LLGPPGCGKTLLAKAVATEANVPFLSMNGSEFIEMIGGLGAA 67
LG +P G + + G G GKT L +A EA +P E+ G G
Sbjct: 12 LGGGIPTGRITEIFGEFGSGKTQLCLQLAVEAQLP---------GELGGLEGKV 56
>gnl|CDD|182791 PRK10865, PRK10865, protein disaggregation chaperone; Provisional.
Length = 857
Score = 29.4 bits (66), Expect = 6.4
Identities = 16/38 (42%), Positives = 24/38 (63%), Gaps = 3/38 (7%)
Query: 25 LLLGPPGCGKTLLAKAVAT---EANVPFLSMNGSEFIE 59
L LGP G GKT L KA+A +++ + ++ SEF+E
Sbjct: 602 LFLGPTGVGKTELCKALANFMFDSDDAMVRIDMSEFME 639
>gnl|CDD|233448 TIGR01526, nadR_NMN_Atrans, nicotinamide-nucleotide
adenylyltransferase, NadR type. The NadR protein of E.
coli and closely related bacteria is both enzyme and
regulatory protein. The first 60 or so amino acids,
N-terminal to the region covered by this model, is a
DNA-binding helix-turn-helix domain (pfam01381)
responsible for repressing the nadAB genes of NAD de
novo biosynthesis. The NadR homologs in Mycobacterium
tuberculosis, Haemophilus influenzae, and others appear
to lack the repressor domain. NadR has recently been
shown to act as an enzyme of the salvage pathway of NAD
biosynthesis, nicotinamide-nucleotide
adenylyltransferase; members of this family are presumed
to share this activity. E. coli NadR has also been found
to regulate the import of its substrate, nicotinamide
ribonucleotide, but it is not known if the other members
of this model share that activity.
Length = 325
Score = 29.4 bits (66), Expect = 6.6
Identities = 10/38 (26%), Positives = 15/38 (39%)
Query: 26 LLGPPGCGKTLLAKAVATEANVPFLSMNGSEFIEMIGG 63
+LG GK+ L +A N E++E G
Sbjct: 167 ILGGESTGKSTLVNKLAAVFNTTSAWEYAREYVEEKLG 204
>gnl|CDD|224768 COG1855, COG1855, ATPase (PilT family) [General function prediction
only].
Length = 604
Score = 29.6 bits (67), Expect = 6.7
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 22 KGALLLGPPGCGKTLLAKAVAT 43
+G L+ G PG GK+ A+A+A
Sbjct: 264 EGILIAGAPGAGKSTFAQALAE 285
>gnl|CDD|222307 pfam13671, AAA_33, AAA domain. This family of domains contain
only a P-loop motif, that is characteristic of the AAA
superfamily. Many of the proteins in this family are
just short fragments so there is no Walker B motif.
Length = 143
Score = 28.4 bits (64), Expect = 7.0
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 25 LLLGPPGCGKTLLAKAVATEANVPFLS 51
L++G PG GK+ A+ + E LS
Sbjct: 3 LMVGLPGSGKSTFARRLLRELGAVVLS 29
>gnl|CDD|217429 pfam03215, Rad17, Rad17 cell cycle checkpoint protein.
Length = 490
Score = 29.2 bits (65), Expect = 7.1
Identities = 21/105 (20%), Positives = 35/105 (33%), Gaps = 22/105 (20%)
Query: 25 LLLGPPGCGKTLLAKAVATEANVPFLSMNGSEFIEMIGGLGAARVRTEVVFLHCRVFLHE 84
LL GP GCGK+ K ++ E + E IE +LH +
Sbjct: 49 LLTGPSGCGKSTTVKVLSKELGI--------EIIEWSNP----------EYLHNPDNECQ 90
Query: 85 ITIFDLETKIIENIFDLETKIILSSFMMIVLKLNLEKEVMLRKKL 129
+ + + L F++ + + L+KKL
Sbjct: 91 KP----DFRGDCIVNSLSQMEQFREFLLRGARYGSLQGGGLKKKL 131
>gnl|CDD|213196 cd03229, ABC_Class3, ATP-binding cassette domain of the binding
protein-dependent transport systems. This class is
comprised of all BPD (Binding Protein Dependent)
systems that are largely represented in archaea and
eubacteria and are primarily involved in scavenging
solutes from the environment. ABC transporters are a
large family of proteins involved in the transport of a
wide variety of different compounds, like sugars, ions,
peptides, and more complex organic molecules. The
nucleotide binding domain shows the highest similarity
between all members of the family. ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and
GTP-binding and hydrolyzing proteins.
Length = 178
Score = 28.7 bits (65), Expect = 7.2
Identities = 18/69 (26%), Positives = 32/69 (46%), Gaps = 9/69 (13%)
Query: 26 LLGPPGCGKTLLAKAVA-----TEANVPFLSMNGSEFIEMIGGLGAARVRTEVVFLHCRV 80
LLGP G GK+ L + +A ++ +G + ++ L R R +VF +
Sbjct: 31 LLGPSGSGKSTLLRCIAGLEEPDSGSILI---DGEDLTDLEDELPPLRRRIGMVFQDFAL 87
Query: 81 FLHEITIFD 89
F H +T+ +
Sbjct: 88 FPH-LTVLE 95
>gnl|CDD|223401 COG0324, MiaA, tRNA delta(2)-isopentenylpyrophosphate transferase
[Translation, ribosomal structure and biogenesis].
Length = 308
Score = 29.1 bits (66), Expect = 7.4
Identities = 13/34 (38%), Positives = 18/34 (52%)
Query: 19 KVPKGALLLGPPGCGKTLLAKAVATEANVPFLSM 52
K PK ++ GP GKT LA A+A +S+
Sbjct: 1 KKPKLIVIAGPTASGKTALAIALAKRLGGEIISL 34
>gnl|CDD|213262 cd03295, ABC_OpuCA_Osmoprotection, ATP-binding cassette domain of
the osmoprotectant transporter. OpuCA is a the ATP
binding component of a bacterial solute transporter
that serves a protective role to cells growing in a
hyperosmolar environment. ABC (ATP-binding cassette)
transporter nucleotide-binding domain; ABC transporters
are a large family of proteins involved in the
transport of a wide variety of different compounds,
like sugars, ions, peptides, and more complex organic
molecules. The nucleotide binding domain shows the
highest similarity between all members of the family.
ABC transporters are a subset of nucleotide hydrolases
that contain a signature motif, Q-loop, and
H-loop/switch region, in addition, to the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 242
Score = 28.8 bits (65), Expect = 7.6
Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 2/30 (6%)
Query: 14 QNLGAKVPKGAL--LLGPPGCGKTLLAKAV 41
NL ++ KG L+GP G GKT K +
Sbjct: 18 NNLNLEIAKGEFLVLIGPSGSGKTTTMKMI 47
>gnl|CDD|226359 COG3839, MalK, ABC-type sugar transport systems, ATPase
components [Carbohydrate transport and metabolism].
Length = 338
Score = 29.2 bits (66), Expect = 7.6
Identities = 11/26 (42%), Positives = 15/26 (57%), Gaps = 2/26 (7%)
Query: 19 KVPKGAL--LLGPPGCGKTLLAKAVA 42
+ G LLGP GCGK+ L + +A
Sbjct: 25 DIEDGEFVVLLGPSGCGKSTLLRMIA 50
>gnl|CDD|236461 PRK09302, PRK09302, circadian clock protein KaiC; Reviewed.
Length = 509
Score = 29.1 bits (66), Expect = 7.7
Identities = 11/20 (55%), Positives = 12/20 (60%), Gaps = 2/20 (10%)
Query: 21 PKG--ALLLGPPGCGKTLLA 38
PKG L+ G G GKTL A
Sbjct: 29 PKGRPTLVSGTAGTGKTLFA 48
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 28.9 bits (65), Expect = 8.0
Identities = 8/22 (36%), Positives = 10/22 (45%)
Query: 29 PPGCGKTLLAKAVATEANVPFL 50
P G GKT++A E L
Sbjct: 63 PTGAGKTVVAAEAIAELKRSTL 84
>gnl|CDD|227569 COG5244, NIP100, Dynactin complex subunit involved in mitotic
spindle partitioning in anaphase B [Cell division and
chromosome partitioning].
Length = 669
Score = 29.3 bits (65), Expect = 8.3
Identities = 26/102 (25%), Positives = 44/102 (43%), Gaps = 8/102 (7%)
Query: 125 LRKKLEEEYSIELGRKLQDMEIKHAEELKKQEQCLRKEKVLKIDAELRHKKELDLERQIL 184
+ ++E L +L + I+ E L ++E L +E +KI DLER+ L
Sbjct: 510 DSENIKENSL--LSDRLNEENIRLKEVLVQKENMLTEETKIKI------IIGRDLERKTL 561
Query: 185 LHEITKLKSELKNRELHIVKMETQLRAYESDKKLARKQLIDS 226
I LK EL N+ + + L + +L Q+ D+
Sbjct: 562 EENIKTLKVELNNKNNKLKEENFNLVNRLKNMELKLYQIKDN 603
>gnl|CDD|221389 pfam12037, DUF3523, Domain of unknown function (DUF3523). This
presumed domain is functionally uncharacterized. This
domain is found in eukaryotes. This domain is typically
between 257 to 277 amino acids in length. This domain is
found associated with pfam00004. This domain has a
conserved LER sequence motif.
Length = 276
Score = 29.0 bits (65), Expect = 8.4
Identities = 29/107 (27%), Positives = 42/107 (39%), Gaps = 16/107 (14%)
Query: 132 EYSIELGRK-----LQDMEIKHAEELKKQE-QCLRKEKVLKIDAE--LRHKKELDLERQI 183
+Y EL RK L+ ++ E LK QE LR+E + + E L ++E E
Sbjct: 110 QYQDELARKRYQKELEQQRRQNEELLKMQEESVLRQEAMRRATEEEILEMRRETIEEEAE 169
Query: 184 LLHEITKLKSELKNRELHIVKMETQLRAYESDKKLARKQLIDSVNRE 230
L E + K E + R K E + R+ L N E
Sbjct: 170 LERENIRAKIEAEARGR--AKEERENEDIN------REMLKLKANEE 208
>gnl|CDD|153308 cd07624, BAR_SNX7_30, The Bin/Amphiphysin/Rvs (BAR) domain of
Sorting Nexins 7 and 30. BAR domains are dimerization,
lipid binding and curvature sensing modules found in
many different proteins with diverse functions. Sorting
nexins (SNXs) are Phox homology (PX) domain containing
proteins that are involved in regulating membrane
traffic and protein sorting in the endosomal system.
SNXs differ from each other in their lipid-binding
specificity, subcellular localization and specific
function in the endocytic pathway. A subset of SNXs also
contain BAR domains. The PX-BAR structural unit
determines the specific membrane targeting of SNXs. This
subfamily consists of SNX7, SNX30, and similar proteins.
The specific functions of SNX7 and SNX30 have not been
elucidated. BAR domains form dimers that bind to
membranes, induce membrane bending and curvature, and
may also be involved in protein-protein interactions.
Length = 200
Score = 28.5 bits (64), Expect = 8.6
Identities = 24/96 (25%), Positives = 49/96 (51%), Gaps = 13/96 (13%)
Query: 121 KEVMLRKKLEEEYSIELGRKLQDMEIKHAEELKKQEQCLRKEKVLKIDAELRHKKELDLE 180
K+V+ R+ +++ IE ++++ K E LK+ E+ ++K+ +A+L+ DLE
Sbjct: 112 KDVLKRR---DQFQIEYELSVEELNKKRLELLKEVEKL--QDKLECANADLKA----DLE 162
Query: 181 R--QILLHEITKLKSELKNRELHIVKMETQLRAYES 214
R Q ++ K+ ++ + I E L A+E
Sbjct: 163 RWKQNKRQDLKKILLDMAEK--QIQYYEQCLAAWEE 196
>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 = 28.9 bits (65), Expect = 8.7
Identities = 22/118 (18%), Positives = 43/118 (36%), Gaps = 9/118 (7%)
Query: 24 ALLLGPPGCGKTLLAKAVAT---EANVPFLSMN-GSEFIEMIGGLGAARVR----TEVVF 75
L++GP G GK+ L K +A + ++ E+ + LG + + +
Sbjct: 4 MLIVGPSGSGKSTLLKLLALRLLARGGRVIVIDPKGEYSGLARALGGEVIDLGPGSGISL 63
Query: 76 LHCRVFLHEITIFDLETKIIENIFDLETKIILSSFMMIVLKLNLEKEVMLRKKLEEEY 133
+F +LE DL ++ + ++ L +E L + L Y
Sbjct: 64 NPLDIFPTGEDAEELEADAHARKLDLLLALLELAALLGR-DLTPREETALDRALRALY 120
>gnl|CDD|222165 pfam13481, AAA_25, AAA domain. This AAA domain is found in a
wide variety of presumed DNA repair proteins.
Length = 154
Score = 28.0 bits (63), Expect = 8.7
Identities = 18/37 (48%), Positives = 21/37 (56%), Gaps = 8/37 (21%)
Query: 20 VPKG--ALLLGPPGCGKTLL----AKAVATEANVPFL 50
+P+G LL G PG GK+ L A AVAT PFL
Sbjct: 30 LPRGGLTLLAGAPGTGKSTLALDLAAAVATG--RPFL 64
>gnl|CDD|218719 pfam05729, NACHT, NACHT domain. This NTPase domain is found in
apoptosis proteins as well as those involved in MHC
transcription activation. This family is closely
related to pfam00931.
Length = 165
Score = 28.0 bits (63), Expect = 8.8
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 25 LLLGPPGCGKTLLAKAVATEA 45
+L G G GKT L + +A
Sbjct: 4 ILQGEAGSGKTTLLQKIALLW 24
>gnl|CDD|237259 PRK12904, PRK12904, preprotein translocase subunit SecA; Reviewed.
Length = 830
Score = 29.3 bits (67), Expect = 8.9
Identities = 20/90 (22%), Positives = 37/90 (41%), Gaps = 15/90 (16%)
Query: 125 LRKKLEEEYSIELGRKLQDMEIKHAEELKK--QEQCLR--KEKVLKIDAELRHKKELDLE 180
L + L+ ++ +EL + E EEL++ E +EK ++ E + E
Sbjct: 688 LEEALKTDFGLELPIEEWLEEGLDEEELRERILEAAEEAYEEKEEELGEEQMR----EFE 743
Query: 181 RQILLHEITKLKSELKNRELHIVKMETQLR 210
R ++L + E H+ M+ LR
Sbjct: 744 RVVMLQVLDTKWRE------HLAAMD-HLR 766
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 29.2 bits (65), Expect = 8.9
Identities = 17/47 (36%), Positives = 24/47 (51%)
Query: 20 VPKGALLLGPPGCGKTLLAKAVATEANVPFLSMNGSEFIEMIGGLGA 66
V K LL G PG GKT L A+A + + +N SE ++ G+
Sbjct: 1542 VGKPILLEGSPGVGKTSLITALARKTGKKLIRINLSEQTDLCDLFGS 1588
>gnl|CDD|237178 PRK12705, PRK12705, hypothetical protein; Provisional.
Length = 508
Score = 28.9 bits (65), Expect = 9.0
Identities = 26/124 (20%), Positives = 47/124 (37%)
Query: 139 RKLQDMEIKHAEELKKQEQCLRKEKVLKIDAELRHKKELDLERQILLHEITKLKSELKNR 198
L+ + E + ++ ++ + A L K+ L ER E + + EL+
Sbjct: 23 VLLKKRQRLAKEAERILQEAQKEAEEKLEAALLEAKELLLRERNQQRQEARREREELQRE 82
Query: 199 ELHIVKMETQLRAYESDKKLARKQLIDSVNREIAETILLKNFAHQLIVKCPLMMTYSSEE 258
E +V+ E QL A QL + A + L+ QL + + + E+
Sbjct: 83 EERLVQKEEQLDARAEKLDNLENQLEEREKALSARELELEELEKQLDNELYRVAGLTPEQ 142
Query: 259 GRNL 262
R L
Sbjct: 143 ARKL 146
>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division
and chromosome partitioning].
Length = 420
Score = 28.9 bits (65), Expect = 9.2
Identities = 20/69 (28%), Positives = 32/69 (46%), Gaps = 5/69 (7%)
Query: 166 KIDAEL-RHKKELDLERQILLHEITKLKSELKNRELHIVKMETQLRAYESDKKLARKQLI 224
+I E+ +K++ ++ KL+ +LK+ E I +E QL D K RKQ+
Sbjct: 42 QIQKEIAALEKKIREQQDQR----AKLEKQLKSLETEIASLEAQLIETADDLKKLRKQIA 97
Query: 225 DSVNREIAE 233
D R A
Sbjct: 98 DLNARLNAL 106
>gnl|CDD|131948 TIGR02902, spore_lonB, ATP-dependent protease LonB. Members of
this protein are LonB, a paralog of the ATP-dependent
protease La (LonA, TIGR00763). LonB proteins are found
strictly, and almost universally, in endospore-forming
bacteria. This protease was shown, in Bacillus subtilis,
to be expressed specifically in the forespore, during
sporulation, under control of sigma(F). The lonB gene,
despite location immediately upstream of lonA, was shown
to be monocistronic. LonB appears able to act on
sigma(H) for post-translation control, but lonB mutation
did not produce an obvious sporulation defect under the
conditions tested. Note that additional paralogs of LonA
and LonB occur in the Clostridium lineage and this model
selects only one per species as the protein that
corresponds to LonB in B. subtilis [Protein fate,
Degradation of proteins, peptides, and glycopeptides,
Cellular processes, Sporulation and germination].
Length = 531
Score = 29.0 bits (65), Expect = 9.5
Identities = 17/44 (38%), Positives = 24/44 (54%), Gaps = 6/44 (13%)
Query: 21 PKGALLLGPPGCGKTLLAKAVATEAN----VPFLSMNGSEFIEM 60
P+ ++ GPPG GKT A+ V EA PF G+ F+E+
Sbjct: 86 PQHVIIYGPPGVGKTAAARLVLEEAKKNPASPF--KEGAAFVEI 127
>gnl|CDD|224160 COG1239, ChlI, Mg-chelatase subunit ChlI [Coenzyme metabolism].
Length = 423
Score = 28.9 bits (65), Expect = 9.5
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 22 KGALLLGPPGCGKTLLAKAVAT 43
GAL+ G G K+ LA+A+A
Sbjct: 39 GGALIAGEKGTAKSTLARALAD 60
>gnl|CDD|226372 COG3854, SpoIIIAA, ncharacterized protein conserved in bacteria
[Function unknown].
Length = 308
Score = 28.6 bits (64), Expect = 9.5
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 25 LLLGPPGCGKTLLAKAVA 42
L++GPP GKT L + +A
Sbjct: 141 LIIGPPQVGKTTLLRDIA 158
>gnl|CDD|182120 PRK09862, PRK09862, putative ATP-dependent protease; Provisional.
Length = 506
Score = 28.8 bits (64), Expect = 9.7
Identities = 11/14 (78%), Positives = 13/14 (92%)
Query: 25 LLLGPPGCGKTLLA 38
LL+GPPG GKT+LA
Sbjct: 214 LLIGPPGTGKTMLA 227
>gnl|CDD|233596 TIGR01846, type_I_sec_HlyB, type I secretion system ABC
transporter, HlyB family. Type I protein secretion is a
system in some Gram-negative bacteria to export proteins
(often proteases) across both inner and outer membranes
to the extracellular medium. This is one of three
proteins of the type I secretion apparatus. Targeted
proteins are not cleaved at the N-terminus, but rather
carry signals located toward the extreme C-terminus to
direct type I secretion [Protein fate, Protein and
peptide secretion and trafficking].
Length = 694
Score = 28.9 bits (65), Expect = 10.0
Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 2/34 (5%)
Query: 10 PEYYQNLGAKVPKGALL--LGPPGCGKTLLAKAV 41
PE NL + G + +GP G GK+ L K +
Sbjct: 470 PEVLSNLNLDIKPGEFIGIVGPSGSGKSTLTKLL 503
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
0.318 0.133 0.375
Gapped
Lambda K H
0.267 0.0788 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 32,373,420
Number of extensions: 3251859
Number of successful extensions: 4185
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4004
Number of HSP's successfully gapped: 451
Length of query: 640
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 537
Effective length of database: 6,369,140
Effective search space: 3420228180
Effective search space used: 3420228180
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 (21.7 bits)
S2: 62 (27.5 bits)