RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5910
(225 letters)
>gnl|CDD|235422 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX;
Provisional.
Length = 412
Score = 323 bits (830), Expect = e-110
Identities = 117/231 (50%), Positives = 159/231 (68%), Gaps = 12/231 (5%)
Query: 3 LDRHIIGQHETKKIVSVGVYNHYKRLFLLKSKN--IYLEKSNILLVGPTGCGKTLMVKTL 60
LD+++IGQ KK++SV VYNHYKRL K+ + L+KSNILL+GPTG GKTL+ +TL
Sbjct: 69 LDQYVIGQERAKKVLSVAVYNHYKRLRHGDKKDDDVELQKSNILLIGPTGSGKTLLAQTL 128
Query: 61 AKIINVPIIVVDATSFTEAGYVGDDVESIIQKLLHECDYDVELAEQSIIYIDEIDKISKK 120
A+I++VP + DAT+ TEAGYVG+DVE+I+ KLL DYDVE A++ I+YIDEIDKI++K
Sbjct: 129 ARILDVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVEKAQRGIVYIDEIDKIARK 188
Query: 121 TDVVSG-KDVSGEGVQQSLLKLIEGVNLSITSLAEKKNPSQNPQVFNIDTTNILFIAGGA 179
++ S +DVSGEGVQQ+LLK++EG S+ +K+P Q + +DTTNILFI GGA
Sbjct: 189 SENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRKHPQQ--EFIQVDTTNILFICGGA 246
Query: 180 FSGIENFIINRIN-------QETNFLEKLNNNYNLICETNTEDLINFGIIP 223
F G+E I R+ E ++ L+ + EDLI FG+IP
Sbjct: 247 FDGLEKIIKQRLGKKGIGFGAEVKSKKEKRTEGELLKQVEPEDLIKFGLIP 297
>gnl|CDD|224140 COG1219, ClpX, ATP-dependent protease Clp, ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 408
Score = 300 bits (770), Expect = e-101
Identities = 120/230 (52%), Positives = 157/230 (68%), Gaps = 11/230 (4%)
Query: 3 LDRHIIGQHETKKIVSVGVYNHYKRLFLLKSKN-IYLEKSNILLVGPTGCGKTLMVKTLA 61
LD ++IGQ + KK++SV VYNHYKRL + + + L KSNILL+GPTG GKTL+ +TLA
Sbjct: 59 LDEYVIGQEQAKKVLSVAVYNHYKRLNNKEDNDDVELSKSNILLIGPTGSGKTLLAQTLA 118
Query: 62 KIINVPIIVVDATSFTEAGYVGDDVESIIQKLLHECDYDVELAEQSIIYIDEIDKISKKT 121
KI+NVP + DAT+ TEAGYVG+DVE+I+ KLL DYDVE AE+ IIYIDEIDKI++K+
Sbjct: 119 KILNVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVERAERGIIYIDEIDKIARKS 178
Query: 122 DVVSG-KDVSGEGVQQSLLKLIEGVNLSITSLAEKKNPSQNPQVFNIDTTNILFIAGGAF 180
+ S +DVSGEGVQQ+LLK+IEG S+ +K+P Q +DT+NILFI GGAF
Sbjct: 179 ENPSITRDVSGEGVQQALLKIIEGTVASVPPQGGRKHPQQE--FIQVDTSNILFICGGAF 236
Query: 181 SGIENFIINRIN-------QETNFLEKLNNNYNLICETNTEDLINFGIIP 223
+G+E I R+ E K L+ + EDL+ FG+IP
Sbjct: 237 AGLEKIIKKRLGKKGIGFGAEVKSKSKKKEEGELLKQVEPEDLVKFGLIP 286
>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 = 262 bits (671), Expect = 9e-87
Identities = 120/231 (51%), Positives = 160/231 (69%), Gaps = 12/231 (5%)
Query: 3 LDRHIIGQHETKKIVSVGVYNHYKRLFLLKSK----NIYLEKSNILLVGPTGCGKTLMVK 58
LD ++IGQ + KK++SV VYNHYKRL K+K + L KSNILL+GPTG GKTL+ +
Sbjct: 75 LDEYVIGQEQAKKVLSVAVYNHYKRLNFEKNKKSDNGVELSKSNILLIGPTGSGKTLLAQ 134
Query: 59 TLAKIINVPIIVVDATSFTEAGYVGDDVESIIQKLLHECDYDVELAEQSIIYIDEIDKIS 118
TLA+I+NVP + DAT+ TEAGYVG+DVE+I+ KLL DYDVE A++ IIYIDEIDKIS
Sbjct: 135 TLARILNVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVEKAQKGIIYIDEIDKIS 194
Query: 119 KKTDVVS-GKDVSGEGVQQSLLKLIEGVNLSITSLAEKKNPSQNPQVFNIDTTNILFIAG 177
+K++ S +DVSGEGVQQ+LLK+IEG ++ +K+P Q IDT+NILFI G
Sbjct: 195 RKSENPSITRDVSGEGVQQALLKIIEGTVANVPPQGGRKHPYQE--FIQIDTSNILFICG 252
Query: 178 GAFSGIENFIINRINQET-NFLEKLNNN----YNLICETNTEDLINFGIIP 223
GAF G+E I R + + F ++ +L+ + EDL+ FG+IP
Sbjct: 253 GAFVGLEKIIKKRTGKSSIGFGAEVKKKSKEKADLLRQVEPEDLVKFGLIP 303
>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 = 100 bits (252), Expect = 8e-27
Identities = 48/200 (24%), Positives = 75/200 (37%), Gaps = 57/200 (28%)
Query: 39 EKSNILLVGPTGCGKTLMVKTLAKIINV---PIIVVDATSFTEAGYVGDDVESIIQKLLH 95
+ L +GPTG GKT + K LA+++ +I +D + + E E + +L+
Sbjct: 2 PIGSFLFLGPTGVGKTELAKALAELLFGDERALIRIDMSEYME--------EHSVSRLIG 53
Query: 96 ECDYDVELAE------------QSIIYIDEIDKISKKTDVVSGKDVSGEGVQQSLLKLIE 143
V E SI+ IDEI+K GVQ LL+++E
Sbjct: 54 APPGYVGYEEGGQLTEAVRRKPYSIVLIDEIEKAHP-------------GVQNDLLQILE 100
Query: 144 GVNLSITSLAEKKNPSQNPQVFNIDTTNILFIAGGAFSGIENFIINRINQETNFLEKLNN 203
G L+ Q +V D N LFI G F + +R+ ++
Sbjct: 101 GGTLT---------DKQGRKV---DFRNTLFIMTGNFGSEKISDASRLGDSPDYELL--- 145
Query: 204 NYNLICETNTEDLINFGIIP 223
+ DL+ G IP
Sbjct: 146 ------KELVMDLLKKGFIP 159
>gnl|CDD|224141 COG1220, HslU, ATP-dependent protease HslVU (ClpYQ), ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 444
Score = 105 bits (263), Expect = 2e-26
Identities = 47/92 (51%), Positives = 63/92 (68%)
Query: 2 ELDRHIIGQHETKKIVSVGVYNHYKRLFLLKSKNIYLEKSNILLVGPTGCGKTLMVKTLA 61
ELDR+IIGQ E KK V++ + N ++R+ L + + NIL++GPTG GKT + + LA
Sbjct: 12 ELDRYIIGQDEAKKAVAIALRNRWRRMQLEEELRDEVTPKNILMIGPTGVGKTEIARRLA 71
Query: 62 KIINVPIIVVDATSFTEAGYVGDDVESIIQKL 93
K+ P I V+AT FTE GYVG DVESII+ L
Sbjct: 72 KLAGAPFIKVEATKFTEVGYVGRDVESIIRDL 103
Score = 71.9 bits (177), Expect = 1e-14
Identities = 40/97 (41%), Positives = 56/97 (57%), Gaps = 22/97 (22%)
Query: 85 DVESIIQKLLHECDYDVELAEQS-IIYIDEIDKISKKTDVVSGKDVSGEGVQQSLLKLIE 143
D E I Q+ + + AEQ+ I++IDEIDKI+K+ G DVS EGVQ+ LL L+E
Sbjct: 236 DQEEIKQEAI-------DAAEQNGIVFIDEIDKIAKRGGS-GGPDVSREGVQRDLLPLVE 287
Query: 144 GVNLSITSLAEKKNPSQNPQVFNIDTTNILFIAGGAF 180
G ++++ K P + T +ILFIA GAF
Sbjct: 288 G-----STVSTKYGP--------VKTDHILFIASGAF 311
>gnl|CDD|235364 PRK05201, hslU, ATP-dependent protease ATP-binding subunit HslU;
Provisional.
Length = 443
Score = 104 bits (261), Expect = 5e-26
Identities = 47/95 (49%), Positives = 66/95 (69%), Gaps = 6/95 (6%)
Query: 2 ELDRHIIGQHETKKIVSVGVYNHYKRLFLLKSKNIYLE---KSNILLVGPTGCGKTLMVK 58
ELD++IIGQ + K+ V++ + N ++R+ L + + E K NIL++GPTG GKT + +
Sbjct: 12 ELDKYIIGQDDAKRAVAIALRNRWRRMQL--PEELRDEVTPK-NILMIGPTGVGKTEIAR 68
Query: 59 TLAKIINVPIIVVDATSFTEAGYVGDDVESIIQKL 93
LAK+ N P I V+AT FTE GYVG DVESII+ L
Sbjct: 69 RLAKLANAPFIKVEATKFTEVGYVGRDVESIIRDL 103
Score = 74.3 bits (184), Expect = 1e-15
Identities = 38/97 (39%), Positives = 54/97 (55%), Gaps = 24/97 (24%)
Query: 91 QKLLHECDYD------VELAEQS-IIYIDEIDKISKKTDVVSGKDVSGEGVQQSLLKLIE 143
KL+ D + +E EQ+ I++IDEIDKI+ + SG DVS EGVQ+ LL L+E
Sbjct: 231 AKLI---DMEEIKQEAIERVEQNGIVFIDEIDKIAARGGS-SGPDVSREGVQRDLLPLVE 286
Query: 144 GVNLSITSLAEKKNPSQNPQVFNIDTTNILFIAGGAF 180
G ++++ K + T +ILFIA GAF
Sbjct: 287 G-----STVSTKYGM--------VKTDHILFIASGAF 310
>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 = 99.9 bits (249), Expect = 2e-24
Identities = 46/92 (50%), Positives = 63/92 (68%)
Query: 2 ELDRHIIGQHETKKIVSVGVYNHYKRLFLLKSKNIYLEKSNILLVGPTGCGKTLMVKTLA 61
ELD++IIGQ E KK V++ + N Y+R L + + NIL++GPTG GKT + + LA
Sbjct: 9 ELDKYIIGQDEAKKSVAIALRNRYRRSQLPEELKDEVTPKNILMIGPTGVGKTEIARRLA 68
Query: 62 KIINVPIIVVDATSFTEAGYVGDDVESIIQKL 93
K+ N P I V+AT FTE GYVG DVES+++ L
Sbjct: 69 KLANAPFIKVEATKFTEVGYVGRDVESMVRDL 100
Score = 60.6 bits (147), Expect = 7e-11
Identities = 39/81 (48%), Positives = 49/81 (60%), Gaps = 15/81 (18%)
Query: 101 VELAEQS-IIYIDEIDKISKKTDVVSGKDVSGEGVQQSLLKLIEGVNLSITSLAEKKNPS 159
++ EQS II+IDEIDKI+KK + SG DVS EGVQ+ LL ++EG S K S
Sbjct: 242 IDRVEQSGIIFIDEIDKIAKKGES-SGADVSREGVQRDLLPIVEG------STVNTKYGS 294
Query: 160 QNPQVFNIDTTNILFIAGGAF 180
+ T +ILFIA GAF
Sbjct: 295 -------VKTDHILFIAAGAF 308
>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 = 72.6 bits (179), Expect = 2e-16
Identities = 31/106 (29%), Positives = 49/106 (46%), Gaps = 14/106 (13%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIINVPIIVVDATSFTEAGYVGDDVESIIQKLLHECDYDVE 102
+LL GP G GKT + K +AK + P I + + YVG+ + + + E
Sbjct: 1 LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVS-KYVGESEKRLRELF--------E 51
Query: 103 LAEQ---SIIYIDEIDKISKKTDVVSGKDVSGEGVQQSLLKLIEGV 145
A++ +I+IDEID ++ SG D V LL ++G
Sbjct: 52 AAKKLAPCVIFIDEIDALAGSRG--SGGDSESRRVVNQLLTELDGF 95
>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 = 66.4 bits (162), Expect = 6e-14
Identities = 31/118 (26%), Positives = 53/118 (44%), Gaps = 19/118 (16%)
Query: 40 KSNILLVGPTGCGKTLMVKTLAKII---NVPIIVVDATSFTEAGYVGDDVESIIQKLLHE 96
N+LL GP G GKT + + +A + P + ++A+ E V + + +LL E
Sbjct: 19 PKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLFE 78
Query: 97 CDYDVELAEQSIIYIDEIDKISKKTDVVSGKDVSGEGVQQSLLKLIEGVNLSITSLAE 154
E A+ +++IDEID +S G Q +LL+++E +N
Sbjct: 79 ---LAEKAKPGVLFIDEIDSLS-------------RGAQNALLRVLETLNDLRIDREN 120
>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction
only].
Length = 329
Score = 60.1 bits (146), Expect = 9e-11
Identities = 23/129 (17%), Positives = 48/129 (37%), Gaps = 28/129 (21%)
Query: 1 MELDRHIIGQHETKKIVSVGVYNHYKRLFLLKSKNIYLEKSNILLVGPTGCGKTLMVKTL 60
EL++ ++G E ++ + + L ++LL GP G GKTL+ + L
Sbjct: 20 SELEKVVVGDEEVIELALLAL----------------LAGGHVLLEGPPGVGKTLLARAL 63
Query: 61 AKIINVPIIVVDATSFTEAGYVGDDVESIIQKLLHECDYDVE--------LAEQSIIYID 112
A+ + +P + + T + + A + I+ +D
Sbjct: 64 ARALGLPFVRIQCTPDLLPSDL--LGTYAYAA--LLLEPGEFRFVPGPLFAAVRVILLLD 119
Query: 113 EIDKISKKT 121
EI++ +
Sbjct: 120 EINRAPPEV 128
>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational
modification, protein turnover, chaperones].
Length = 494
Score = 60.2 bits (146), Expect = 1e-10
Identities = 37/122 (30%), Positives = 55/122 (45%), Gaps = 9/122 (7%)
Query: 25 YKRLFLLKSKNIYLEKSNILLVGPTGCGKTLMVKTLAKIINVPIIVVDATSFTEAGYVGD 84
KR L + + K +LL GP G GKTL+ K +A I V + + +VG
Sbjct: 262 LKRPELFRKLGLRPPKG-VLLYGPPGTGKTLLAKAVALESRSRFISVKGSELL-SKWVG- 318
Query: 85 DVESIIQKLLHECDYDVELAEQSIIYIDEIDKISKKTDVVSGKDVSGEGVQQSLLKLIEG 144
+ E I++L SII+IDEID ++ +D SG V LL ++G
Sbjct: 319 ESEKNIRELFE----KARKLAPSIIFIDEIDSLASGRG--PSEDGSGRRVVGQLLTELDG 372
Query: 145 VN 146
+
Sbjct: 373 IE 374
Score = 31.3 bits (71), Expect = 0.40
Identities = 33/123 (26%), Positives = 50/123 (40%), Gaps = 23/123 (18%)
Query: 31 LKSKNIYLEKSNILLVGPTGCGKTLMVKTLAKIINVPIIVVDATSFTEAGYVGDDVESII 90
L K +LL GP G GKTL+ + LA A ++ + I+
Sbjct: 9 LFKKLGIEPPKGVLLHGPPGTGKTLLARALA--------------NEGAEFLSINGPEIL 54
Query: 91 QKLLHECDY-------DVELAEQSIIYIDEIDKISKKTDVVSGKDVSGEGVQQSLLKLIE 143
K + E + + E SII+IDEID ++ K G+ V LL L++
Sbjct: 55 SKYVGESELRLRELFEEAEKLAPSIIFIDEIDALAPKRSSDQGE--VERRVVAQLLALMD 112
Query: 144 GVN 146
G+
Sbjct: 113 GLK 115
>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many
proteins may score above the trusted cutoff because an
internal.
Length = 364
Score = 57.9 bits (140), Expect = 6e-10
Identities = 38/104 (36%), Positives = 57/104 (54%), Gaps = 16/104 (15%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIINVPIIVVDATSFTEAGYVGDDVESIIQKLLHECDYDVE 102
+LL GP G GKTL+ K +A N I V + Y+G+ +L+ E E
Sbjct: 159 VLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELVRK-YIGEGA-----RLVREI---FE 209
Query: 103 LAEQ---SIIYIDEIDKI-SKKTDVVSGKDVSGEGVQQSLLKLI 142
LA++ SII+IDEID I +K+TD + D VQ++L++L+
Sbjct: 210 LAKEKAPSIIFIDEIDAIAAKRTDSGTSGD---REVQRTLMQLL 250
>gnl|CDD|224144 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 368
Score = 57.9 bits (140), Expect = 6e-10
Identities = 38/120 (31%), Positives = 53/120 (44%), Gaps = 29/120 (24%)
Query: 7 IIGQHETKKIVSVGVYNHYKRLFLLKSKNIYLEK---------SNILLVGPTGCGKTLMV 57
+IGQ E K+ + +++ YLE N+L GP G GKT+M
Sbjct: 123 VIGQEEAKRKCRL----------IME----YLENPERFGDWAPKNVLFYGPPGTGKTMMA 168
Query: 58 KTLAKIINVPIIVVDATSFTEAGYVGDDVESIIQKLLHECDYDVELAEQSIIYIDEIDKI 117
K LA VP+++V AT +VGD I HE A I++IDE+D I
Sbjct: 169 KALANEAKVPLLLVKATELI-GEHVGDGARRI-----HELYERARKAAPCIVFIDELDAI 222
>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 = 56.1 bits (135), Expect = 3e-09
Identities = 37/103 (35%), Positives = 53/103 (51%), Gaps = 8/103 (7%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIINVPIIVVDATSFTEAGYVGDDVESIIQKLLHECDYDVE 102
+LL GP G GKTL+ K +A I ++ + Y G+ E L E + E
Sbjct: 215 VLLYGPPGTGKTLLAKAVANEAGAYFISINGPEIM-SKYYGESEER-----LREIFKEAE 268
Query: 103 LAEQSIIYIDEIDKISKKTDVVSGKDVSGEGVQQSLLKLIEGV 145
SII+IDEID I+ K + V+G +V V Q LL L++G+
Sbjct: 269 ENAPSIIFIDEIDAIAPKREEVTG-EVEKRVVAQ-LLTLMDGL 309
Score = 38.7 bits (90), Expect = 0.002
Identities = 29/99 (29%), Positives = 45/99 (45%), Gaps = 6/99 (6%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIINVPIIVVDATSFTEAGYVGDDVESIIQKLLHECDYDVE 102
+LL GP G GKTL+ K +A I V + +VG+ E I+++ +
Sbjct: 490 VLLFGPPGTGKTLLAKAVATESGANFIAVRGPEIL-SKWVGES-EKAIREIFRK----AR 543
Query: 103 LAEQSIIYIDEIDKISKKTDVVSGKDVSGEGVQQSLLKL 141
A +II+ DEID I+ V+ V Q L ++
Sbjct: 544 QAAPAIIFFDEIDAIAPARGARFDTSVTDRIVNQLLTEM 582
>gnl|CDD|224143 COG1222, RPT1, ATP-dependent 26S proteasome regulatory subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 406
Score = 52.3 bits (126), Expect = 4e-08
Identities = 36/104 (34%), Positives = 56/104 (53%), Gaps = 16/104 (15%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIINVPIIVVDATSFTEAGYVGDDVESIIQKLLHECDYDVE 102
+LL GP G GKTL+ K +A + I V + + Y+G+ +L+ E E
Sbjct: 188 VLLYGPPGTGKTLLAKAVANQTDATFIRVVGSELVQK-YIGEG-----ARLVREL---FE 238
Query: 103 LAEQ---SIIYIDEIDKI-SKKTDVVSGKDVSGEGVQQSLLKLI 142
LA + SII+IDEID I +K+ D + D VQ+++L+L+
Sbjct: 239 LAREKAPSIIFIDEIDAIGAKRFDSGTSGDRE---VQRTMLELL 279
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 48.3 bits (116), Expect = 1e-06
Identities = 40/106 (37%), Positives = 59/106 (55%), Gaps = 18/106 (16%)
Query: 41 SNILLVGPTGCGKTLMVKTLAKIINVPIIVVDATSFTEAGYVGDDVESIIQKLLHECDYD 100
+LL GP G GKTL+ K +A N I V + + ++G+ +L+ E
Sbjct: 166 KGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELVQK-FIGEGA-----RLVREL--- 216
Query: 101 VELAEQ---SIIYIDEIDKI-SKKTDVVSGKDVSGEG-VQQSLLKL 141
ELA + SII+IDEID I +K+TD SG SG+ VQ++L++L
Sbjct: 217 FELAREKAPSIIFIDEIDAIAAKRTD--SG--TSGDREVQRTLMQL 258
>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 = 46.2 bits (109), Expect = 1e-06
Identities = 27/121 (22%), Positives = 46/121 (38%), Gaps = 14/121 (11%)
Query: 40 KSNILLVGPTGCGKTLMVKTLAKIINVP---IIVVDATSFTEAGYVGDDVESIIQKLLHE 96
IL+VGP G GKT + + LA+ + P +I +D E + + K
Sbjct: 2 GEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASG 61
Query: 97 CDYD-----VELAEQS---IIYIDEIDKISKKTDVVSGKDVSGEGVQQSLLKLIEGVNLS 148
+ LA + ++ +DEI + D + + LL L NL+
Sbjct: 62 SGELRLRLALALARKLKPDVLILDEITSL---LDAEQEALLLLLEELRLLLLLKSEKNLT 118
Query: 149 I 149
+
Sbjct: 119 V 119
>gnl|CDD|240423 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like
protein; Provisional.
Length = 398
Score = 47.5 bits (113), Expect = 2e-06
Identities = 37/108 (34%), Positives = 52/108 (48%), Gaps = 24/108 (22%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIINVPIIVVDATSFTEAGYVGDDVESIIQKLLHECDYDV- 101
+LL GP G GKT++ K +A I V + F +QK L E V
Sbjct: 182 VLLYGPPGTGKTMLAKAVAHHTTATFIRVVGSEF-------------VQKYLGEGPRMVR 228
Query: 102 ---ELAEQ---SIIYIDEIDKI-SKKTDVVSGKDVSGEGVQQSLLKLI 142
LA + SII+IDE+D I +K+ D +G D VQ+ LL+L+
Sbjct: 229 DVFRLARENAPSIIFIDEVDSIATKRFDAQTGAD---REVQRILLELL 273
>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 = 44.2 bits (105), Expect = 5e-06
Identities = 22/93 (23%), Positives = 36/93 (38%), Gaps = 24/93 (25%)
Query: 42 NILLVGPTGCGKTLMVKTLAKII-NVPIIVVDATSFTEAGYVGDDVESIIQKLLHECDYD 100
+LLVGP G GK+ + + LA + N P+ V T T +D++ + D
Sbjct: 1 GVLLVGPPGTGKSELAERLAAALSNRPVFYVQLTRDTTE----EDLKGRR-------NID 49
Query: 101 VELAEQS------------IIYIDEIDKISKKT 121
A I +DEI++ +
Sbjct: 50 PGGASWVDGPLVRAAREGEIAVLDEINRANPDV 82
>gnl|CDD|223616 COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ
chaperones [Posttranslational modification, protein
turnover, chaperones].
Length = 786
Score = 46.1 bits (110), Expect = 6e-06
Identities = 32/89 (35%), Positives = 49/89 (55%), Gaps = 16/89 (17%)
Query: 40 KSNILLVGPTGCGKTLMVKTLA-KIIN--VPIIVVDATSFT------EAG--YVGDDVES 88
K+N +LVG G GKT +V+ LA +I+N VP + D ++ AG Y G + E
Sbjct: 191 KNNPVLVGEPGVGKTAIVEGLAQRIVNGDVPESLKDKRIYSLDLGSLVAGAKYRG-EFEE 249
Query: 89 IIQKLLHECDYDVELAEQSIIYIDEIDKI 117
++ +L E VE ++ I++IDEI I
Sbjct: 250 RLKAVLKE----VEKSKNVILFIDEIHTI 274
Score = 43.0 bits (102), Expect = 7e-05
Identities = 36/135 (26%), Positives = 58/135 (42%), Gaps = 38/135 (28%)
Query: 2 ELDRHIIGQHETKKIVSVGVYNHYKRL-FLLKSKNIYLEKSNILLVGPTGCGKTLMVKTL 60
L + +IGQ E + VS + +R L N + + L +GPTG GKT + K L
Sbjct: 488 RLKKRVIGQDEAVEAVS----DAIRRARAGLGDPNRPI--GSFLFLGPTGVGKTELAKAL 541
Query: 61 AKIIN---VPIIVVDATSFTEA-----------GYVGDD-----VESIIQKLLHECDYDV 101
A+ + +I +D + + E GYVG + E++ +K
Sbjct: 542 AEALFGDEQALIRIDMSEYMEKHSVSRLIGAPPGYVGYEEGGQLTEAVRRK--------- 592
Query: 102 ELAEQSIIYIDEIDK 116
S+I +DEI+K
Sbjct: 593 ---PYSVILLDEIEK 604
>gnl|CDD|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed.
Length = 644
Score = 46.2 bits (109), Expect = 7e-06
Identities = 36/120 (30%), Positives = 59/120 (49%), Gaps = 11/120 (9%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIINVPIIVVDATSFTEAGYVGDDVESIIQKLLHECDYDVE 102
+L+VGP G GKTL+ K +A VP + + F E +VG S ++ + + +
Sbjct: 188 VLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDFVEM-FVGVGA-SRVRDMFEQ----AK 241
Query: 103 LAEQSIIYIDEIDKISKK--TDVVSGKDVSGEGVQQSLLKL--IEGVNLSITSLAEKKNP 158
A II+IDEID + ++ + G D + + Q L+++ EG N I +A P
Sbjct: 242 KAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEG-NEGIIVIAATNRP 300
>gnl|CDD|214386 CHL00176, ftsH, cell division protein; Validated.
Length = 638
Score = 45.8 bits (109), Expect = 9e-06
Identities = 28/103 (27%), Positives = 41/103 (39%), Gaps = 23/103 (22%)
Query: 29 FLLKSKNIYLEKSN-----ILLVGPTGCGKTLMVKTLAKIINVPIIVVDATSFTE----- 78
LK + +LLVGP G GKTL+ K +A VP + + F E
Sbjct: 200 SFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGEAEVPFFSISGSEFVEMFVGV 259
Query: 79 -AGYVGDDVESIIQKLLHECDYDVELAEQSIIYIDEIDKISKK 120
A V D + + C I++IDEID + ++
Sbjct: 260 GAARVRDLFKKAKEN--SPC----------IVFIDEIDAVGRQ 290
>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 = 43.4 bits (103), Expect = 4e-05
Identities = 29/90 (32%), Positives = 38/90 (42%), Gaps = 30/90 (33%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIINVPIIVVDATSFTE------AGYVGDDVESIIQKLLHE 96
+LLVGP G GKTL+ K +A VP + + F E A V D
Sbjct: 91 VLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEMFVGVGASRVRD------------ 138
Query: 97 CDYDVELAEQ------SIIYIDEIDKISKK 120
L EQ II+IDEID + ++
Sbjct: 139 ------LFEQAKKNAPCIIFIDEIDAVGRQ 162
>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like
protein; Provisional.
Length = 438
Score = 42.5 bits (100), Expect = 8e-05
Identities = 39/109 (35%), Positives = 59/109 (54%), Gaps = 26/109 (23%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIINVPIIVVDATSFTEAGYVGDDVESIIQKLLHECDYDV- 101
++L GP G GKTL+ K +A + TS T VG + +IQK L + V
Sbjct: 220 VILYGPPGTGKTLLAKAVA----------NETSATFLRVVGSE---LIQKYLGDGPKLVR 266
Query: 102 ---ELAEQ---SIIYIDEIDKI-SKKTDVVSGKDVSGEG-VQQSLLKLI 142
+AE+ SI++IDEID I +K+ D SG GE +Q+++L+L+
Sbjct: 267 ELFRVAEENAPSIVFIDEIDAIGTKRYDATSG----GEKEIQRTMLELL 311
>gnl|CDD|223401 COG0324, MiaA, tRNA delta(2)-isopentenylpyrophosphate transferase
[Translation, ribosomal structure and biogenesis].
Length = 308
Score = 41.1 bits (97), Expect = 2e-04
Identities = 13/30 (43%), Positives = 18/30 (60%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIINVPIIVVD 72
I++ GPT GKT + LAK + II +D
Sbjct: 6 IVIAGPTASGKTALAIALAKRLGGEIISLD 35
>gnl|CDD|233959 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit
clpA. [Protein fate, Degradation of proteins, peptides,
and glycopeptides].
Length = 730
Score = 40.8 bits (96), Expect = 3e-04
Identities = 19/53 (35%), Positives = 27/53 (50%), Gaps = 11/53 (20%)
Query: 42 NILLVGPTGCGKTLMVKTLAKIINVPIIVVDATSFTE-----------AGYVG 83
+ L VGPTG GKT + K LA+ + V ++ D + + E GYVG
Sbjct: 485 SFLFVGPTGVGKTELAKQLAEELGVHLLRFDMSEYMEKHTVSRLIGSPPGYVG 537
Score = 36.2 bits (84), Expect = 0.011
Identities = 31/89 (34%), Positives = 46/89 (51%), Gaps = 16/89 (17%)
Query: 40 KSNILLVGPTGCGKTLMVKTLAKII---NVPIIVVDATSFT------EAG--YVGDDVES 88
K+N LLVG G GKT +V+ LA I VP + +A ++ AG Y G D E
Sbjct: 202 KNNPLLVGEPGVGKTAIVEGLALRIAEGKVPERLKNAKIYSLDMGTLLAGTKYRG-DFEE 260
Query: 89 IIQKLLHECDYDVELAEQSIIYIDEIDKI 117
++ ++ E +E +I++IDEI I
Sbjct: 261 RLKAVVSE----IEKEPNAILFIDEIHTI 285
>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 = 38.7 bits (90), Expect = 5e-04
Identities = 14/58 (24%), Positives = 27/58 (46%)
Query: 39 EKSNILLVGPTGCGKTLMVKTLAKIINVPIIVVDATSFTEAGYVGDDVESIIQKLLHE 96
++LL GP+G GKT +++ L + + V D + ++++LL E
Sbjct: 23 GPPSVLLTGPSGTGKTSLLRELLEGLLVAAGKCDQAERNPPYAFSQALRELLRQLLRE 80
>gnl|CDD|225165 COG2256, MGS1, ATPase related to the helicase subunit of the
Holliday junction resolvase [DNA replication,
recombination, and repair].
Length = 436
Score = 39.1 bits (92), Expect = 0.001
Identities = 29/131 (22%), Positives = 60/131 (45%), Gaps = 29/131 (22%)
Query: 30 LLKSKNIYLEKSNILLVGPTGCGKTLMVKTLAKIINVPIIVVDATSFTEAGYVGDDVESI 89
+++ ++ +++L GP G GKT + + +A N + A + V D
Sbjct: 42 AVEAGHL----HSMILWGPPGTGKTTLARLIAGTTNAAFEALSAVTSG----VKD----- 88
Query: 90 IQKLLHECDYDVELAEQSIIYIDEIDKISKKTDVVSGKDVSGEGVQQSLLKLIEGVNLSI 149
+++++ E + L ++I+++DEI + +K Q +LL +E N +I
Sbjct: 89 LREIIEEARKNRLLGRRTILFLDEIHRFNKAQ-------------QDALLPHVE--NGTI 133
Query: 150 TSL-AEKKNPS 159
+ A +NPS
Sbjct: 134 ILIGATTENPS 144
>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 38.9 bits (92), Expect = 0.001
Identities = 33/148 (22%), Positives = 62/148 (41%), Gaps = 55/148 (37%)
Query: 7 IIGQHETKKIVSVGVYNHYKRLF-LLKSKNIYLEKSNILLVGPTGCGKTLMVKTLAKIIN 65
++GQ + ++ G K L ++++ + S+++L GP G GKT TLA+II
Sbjct: 14 VVGQ---EHLLGPG-----KPLRRMIEAGRL----SSMILWGPPGTGKT----TLARII- 56
Query: 66 VPIIVVDATSFTEAGYVGDDVESI---------IQKLLHECDYDVELAEQSIIYIDEIDK 116
AG E++ +++++ E ++I++IDEI +
Sbjct: 57 -------------AGATDAPFEALSAVTSGVKDLREVIEEARQRRSAGRRTILFIDEIHR 103
Query: 117 ISKKTDVVSGKDVSGEGVQQ-SLLKLIE 143
+K QQ +LL +E
Sbjct: 104 FNKA--------------QQDALLPHVE 117
>gnl|CDD|234626 PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate
transferase; Reviewed.
Length = 307
Score = 38.6 bits (91), Expect = 0.001
Identities = 16/32 (50%), Positives = 22/32 (68%), Gaps = 2/32 (6%)
Query: 43 ILLVGPTGCGKT-LMVKTLAKIINVPIIVVDA 73
I++VGPT GKT L ++ LAK +N II D+
Sbjct: 7 IVIVGPTASGKTALAIE-LAKRLNGEIISADS 37
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 36.9 bits (86), Expect = 0.002
Identities = 21/99 (21%), Positives = 41/99 (41%), Gaps = 24/99 (24%)
Query: 39 EKSNILLVGPTGCGKTLMVKTLAK-IINVPIIVVDATSFTEAGYVGDDVESIIQKLLHEC 97
+L G +G GKT +++ LA+ + N ++ V+A S + +++K+L
Sbjct: 3 GAGIGVLTGESGSGKTTLLRRLARQLPNRRVVYVEAPSLG-------TPKDLLRKILRAL 55
Query: 98 DYDV------ELAEQ----------SIIYIDEIDKISKK 120
+ EL E ++ IDE +S +
Sbjct: 56 GLPLSGGTTAELLEAILDALKRRGRPLLIIDEAQHLSLE 94
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 36.9 bits (85), Expect = 0.002
Identities = 20/82 (24%), Positives = 38/82 (46%), Gaps = 2/82 (2%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIINVPIIVVDATSFTEAGYVGDDVESIIQKLLHECDYDVE 102
IL+ GP G GK+ + K LA+ + +P+I +D E DD + + + + E
Sbjct: 2 ILITGPPGSGKSTLAKKLAEKLGIPVISLDDLLREEGLAELDD--GELDDIDIDLELLEE 59
Query: 103 LAEQSIIYIDEIDKISKKTDVV 124
+ ++ ID + + T +
Sbjct: 60 ILDELAKQEWVIDGVRESTLEL 81
>gnl|CDD|223541 COG0465, HflB, ATP-dependent Zn proteases [Posttranslational
modification, protein turnover, chaperones].
Length = 596
Score = 38.5 bits (90), Expect = 0.002
Identities = 29/90 (32%), Positives = 41/90 (45%), Gaps = 18/90 (20%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIINVPIIVVDATSFTEAGYVGDDVESIIQKLLHECDYDVE 102
+LLVGP G GKTL+ K +A VP + + F E +VG + +
Sbjct: 186 VLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEM-FVGVGASRV-----------RD 233
Query: 103 LAEQ------SIIYIDEIDKISKKTDVVSG 126
L EQ II+IDEID + ++ G
Sbjct: 234 LFEQAKKNAPCIIFIDEIDAVGRQRGAGLG 263
>gnl|CDD|236828 PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit;
Provisional.
Length = 758
Score = 37.5 bits (87), Expect = 0.005
Identities = 33/89 (37%), Positives = 49/89 (55%), Gaps = 16/89 (17%)
Query: 40 KSNILLVGPTGCGKTLMVKTLA-KII--NVPIIVVDATSFT------EAG--YVGDDVES 88
K+N LLVG +G GKT + + LA +I+ +VP ++ D T ++ AG Y G D E
Sbjct: 207 KNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRG-DFEK 265
Query: 89 IIQKLLHECDYDVELAEQSIIYIDEIDKI 117
+ LL + + D SI++IDEI I
Sbjct: 266 RFKALLKQLEQD----TNSILFIDEIHTI 290
Score = 34.0 bits (78), Expect = 0.061
Identities = 22/89 (24%), Positives = 39/89 (43%), Gaps = 28/89 (31%)
Query: 44 LLVGPTGCGKTLMVKTLAKIINVPIIVVDATSFTE-----------AGYVGDD-----VE 87
L GPTG GKT + L+K + + ++ D + + E GYVG D +
Sbjct: 492 LFAGPTGVGKTEVTVQLSKALGIELLRFDMSEYMERHTVSRLIGAPPGYVGFDQGGLLTD 551
Query: 88 SIIQKLLHECDYDVELAEQSIIYIDEIDK 116
++I+ +++ +DEI+K
Sbjct: 552 AVIKH------------PHAVLLLDEIEK 568
>gnl|CDD|177094 CHL00195, ycf46, Ycf46; Provisional.
Length = 489
Score = 36.9 bits (86), Expect = 0.007
Identities = 51/187 (27%), Positives = 83/187 (44%), Gaps = 47/187 (25%)
Query: 5 RHIIGQHE-------TKKIVSVGVYNHYKRLFLLKSKNIYLEKS---------NILLVGP 48
+ II Q E +KI +G ++ K +L K + +++ +LLVG
Sbjct: 209 KQIISQTEILEFYSVNEKISDIGGLDNLKD-WLKKRSTSFSKQASNYGLPTPRGLLLVGI 267
Query: 49 TGCGKTLMVKTLAKIINVPIIVVDATSFTEAGYVGDDVESIIQKLLHECDYDVELAEQS- 107
G GK+L K +A +P++ +D G VG+ ES ++++ + +AE
Sbjct: 268 QGTGKSLTAKAIANDWQLPLLRLDVGKLF-GGIVGES-ESRMRQM-------IRIAEALS 318
Query: 108 --IIYIDEIDKISKKTDVVSGKDVSGE-GVQQSLLKLIEGVNLSITSLAEKKNPSQNPQV 164
I++IDEIDK S + G+ G +L IT L+EKK+P V
Sbjct: 319 PCILWIDEIDK------AFSNSESKGDSGTTNRVLATF------ITWLSEKKSP-----V 361
Query: 165 FNIDTTN 171
F + T N
Sbjct: 362 FVVATAN 368
>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 = 35.2 bits (82), Expect = 0.011
Identities = 11/34 (32%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 29 FLLKSKNIYLE-KSNILLVGPTGCGKTLMVKTLA 61
LLK + ++ +L+ GP+G GK+ + + LA
Sbjct: 15 VLLKDLSFEIKPGDRLLITGPSGTGKSSLFRALA 48
>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 = 35.7 bits (83), Expect = 0.012
Identities = 33/140 (23%), Positives = 58/140 (41%), Gaps = 36/140 (25%)
Query: 8 IGQHETKKIVSVGVYNHYKRLFLLKSKNIYLEKSNILLVGPTGCGKTLMVKTLAKIINVP 67
IGQ + K+ + +LF+ +K ++LL GP G GKT + +A + V
Sbjct: 7 IGQEKVKEQL---------QLFIEAAKMRQEALDHLLLYGPPGLGKTTLAHIIANEMGVN 57
Query: 68 IIVVDATSFTEAGYVGDDVESIIQKLLHECDYDVELAEQSIIYIDEIDKISK-------- 119
+ + + + G D+ +I+ L E +++IDEI ++S
Sbjct: 58 LKITSGPALEKPG----DLAAIL----------TNLEEGDVLFIDEIHRLSPAVEELLYP 103
Query: 120 -----KTDVVSGKDVSGEGV 134
+ D+V GK S V
Sbjct: 104 AMEDFRLDIVIGKGPSARSV 123
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 36.1 bits (84), Expect = 0.013
Identities = 23/86 (26%), Positives = 36/86 (41%), Gaps = 18/86 (20%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIINVPIIVVDATSFTEAGYVGDDVESIIQK------LLHE 96
+LL GP G GKT + LA +I ++A+ A D +E + + L
Sbjct: 42 LLLYGPPGVGKTSLAHALANDYGWEVIELNASDQRTA----DVIERVAGEAATSGSLFG- 96
Query: 97 CDYDVELAEQSIIYIDEIDKISKKTD 122
A + +I +DE+D I D
Sbjct: 97 -------ARRKLILLDEVDGIHGNED 115
>gnl|CDD|217429 pfam03215, Rad17, Rad17 cell cycle checkpoint protein.
Length = 490
Score = 35.0 bits (80), Expect = 0.022
Identities = 17/39 (43%), Positives = 26/39 (66%), Gaps = 3/39 (7%)
Query: 34 KNIYLEKSN---ILLVGPTGCGKTLMVKTLAKIINVPII 69
K ++LE + +LL GP+GCGK+ VK L+K + + II
Sbjct: 36 KAVFLESNKQLILLLTGPSGCGKSTTVKVLSKELGIEII 74
>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 = 34.4 bits (80), Expect = 0.025
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 42 NILLVGPTGCGKTLMVKTLAKI 63
N+L++GP G GKT++ K L I
Sbjct: 24 NLLMIGPPGSGKTMLAKRLPGI 45
>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 585
Score = 34.8 bits (80), Expect = 0.029
Identities = 27/100 (27%), Positives = 38/100 (38%), Gaps = 33/100 (33%)
Query: 44 LLVGPTGCGKTLMVKTLAKIIN-------------------------VPIIVVDATSFTE 78
L GP G GKT + LAK +N V +I +DA S T
Sbjct: 42 LFTGPRGVGKTSTARILAKAVNCTTNDPKGRPCGTCEMCRAIAEGSAVDVIEMDAASHTS 101
Query: 79 AGYVGDDVESIIQKLLHECDYDVELAEQSIIYIDEIDKIS 118
DD II+++ + LA + IDE+ +S
Sbjct: 102 V----DDAREIIERV----QFRPALARYKVYIIDEVHMLS 133
>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 = 33.3 bits (77), Expect = 0.029
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIIN 65
+LL G G KTL+ +TLA+ +
Sbjct: 2 VLLEGVPGLAKTLLARTLARSLG 24
>gnl|CDD|234232 TIGR03499, FlhF, flagellar biosynthetic protein FlhF. [Cellular
processes, Chemotaxis and motility].
Length = 283
Score = 34.6 bits (80), Expect = 0.030
Identities = 14/25 (56%), Positives = 15/25 (60%), Gaps = 3/25 (12%)
Query: 39 EKSNILLVGPTGCGKTLMVKTLAKI 63
I LVGPTG GKT TLAK+
Sbjct: 194 RGGVIALVGPTGVGKT---TTLAKL 215
>gnl|CDD|226359 COG3839, MalK, ABC-type sugar transport systems, ATPase
components [Carbohydrate transport and metabolism].
Length = 338
Score = 34.5 bits (80), Expect = 0.030
Identities = 13/43 (30%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 20 GVYNHYKRLFLLKSKNIYLEKSNIL-LVGPTGCGKTLMVKTLA 61
V + +LK N+ +E + L+GP+GCGK+ +++ +A
Sbjct: 8 NVRKSFGSFEVLKDVNLDIEDGEFVVLLGPSGCGKSTLLRMIA 50
>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 = 34.0 bits (79), Expect = 0.034
Identities = 14/46 (30%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 20 GVYNHYKRLFLLKSKNIYLEKSNIL-LVGPTGCGKTLMVKTLAKII 64
G+ Y + L ++ +E L L+GP+GCGKT +++ +A +
Sbjct: 5 GLSKTYGSVRALDDLSLTVEPGEFLALLGPSGCGKTTLLRLIAGLE 50
>gnl|CDD|220739 pfam10412, TrwB_AAD_bind, Type IV secretion-system coupling
protein DNA-binding domain. The plasmid conjugative
coupling protein TrwB forms hexamers from six
structurally very similar protomers. This hexamer
contains a central channel running from the cytosolic
pole (made up by the AADs) to the membrane pole ending
at the transmembrane pore shaped by 12 transmembrane
helices, rendering an overall mushroom-like structure.
The TrwB_AAD (all-alpha domain) domain appears to be
the DNA-binding domain of the structure. TrwB, a basic
integral inner-membrane nucleoside-triphosphate-binding
protein, is the structural prototype for the type IV
secretion system coupling proteins, a family of
proteins essential for macromolecular transport between
cells and export.
Length = 386
Score = 34.5 bits (80), Expect = 0.035
Identities = 20/59 (33%), Positives = 26/59 (44%), Gaps = 6/59 (10%)
Query: 36 IYLEKSNILLVGPTGCGKTLMVKTLAKIINV---PIIVVDAT-SFTEAGYVGDDVESII 90
E +IL+VG TG GKT ++ L I I+ D T +F E Y II
Sbjct: 11 RRSETQHILIVGTTGTGKTQALRELLDQIRARGDRAIIYDPTGTFVERFY--RPGGDII 67
>gnl|CDD|236982 PRK11784, PRK11784, tRNA 2-selenouridine synthase; Provisional.
Length = 345
Score = 34.4 bits (80), Expect = 0.035
Identities = 12/30 (40%), Positives = 18/30 (60%), Gaps = 3/30 (10%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIINVPIIVVD 72
++L G TG GKT +++ LA N V+D
Sbjct: 144 VVLGGNTGSGKTELLQALA---NAGAQVLD 170
>gnl|CDD|226646 COG4178, COG4178, ABC-type uncharacterized transport system,
permease and ATPase components [General function
prediction only].
Length = 604
Score = 34.6 bits (80), Expect = 0.038
Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 29 FLLKSKNIYLEKSNILLV-GPTGCGKTLMVKTLA 61
LL N + LL+ G +G GKT +++ LA
Sbjct: 407 TLLSELNFEVRPGERLLITGESGAGKTSLLRALA 440
>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 = 0.040
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 43 ILLVGPTGCGKTLMVKTLAKII 64
I L GP GCGK+ + K LA+ +
Sbjct: 1 IWLYGPPGCGKSTLAKYLARAL 22
>gnl|CDD|235570 PRK05703, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 424
Score = 34.1 bits (79), Expect = 0.042
Identities = 21/89 (23%), Positives = 31/89 (34%), Gaps = 42/89 (47%)
Query: 43 ILLVGPTGCGKTLMV--------------------------------KTLAKIINVPIIV 70
+ LVGPTG GKT + KT AKI+ +P+ V
Sbjct: 224 VALVGPTGVGKTTTLAKLAARYALLYGKKKVALITLDTYRIGAVEQLKTYAKIMGIPVEV 283
Query: 71 VDATSFTEAGYVGDDVESIIQKLLHECDY 99
V Y ++ +++L CD
Sbjct: 284 V---------YDPKELAKALEQLRD-CDV 302
>gnl|CDD|213192 cd03225, ABC_cobalt_CbiO_domain1, First domain of the ATP-binding
cassette component of cobalt transport system. Domain
I 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. This ABC transport
system of the CbiMNQO family is involved in cobalt
transport in association with the cobalamin (vitamin
B12) biosynthetic pathways. Most of 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 = 211
Score = 33.6 bits (78), Expect = 0.043
Identities = 10/23 (43%), Positives = 16/23 (69%), Gaps = 4/23 (17%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIIN 65
+L+VGP G GK+ TL +++N
Sbjct: 30 VLIVGPNGSGKS----TLLRLLN 48
>gnl|CDD|110723 pfam01745, IPT, Isopentenyl transferase. Isopentenyl transferase /
dimethylallyl transferase synthesises
isopentenyladensosine 5'-monophosphate, a cytokinin that
induces shoot formation on host plants infected with the
Ti plasmid.
Length = 232
Score = 33.5 bits (77), Expect = 0.049
Identities = 31/110 (28%), Positives = 41/110 (37%), Gaps = 19/110 (17%)
Query: 44 LLVGPTGCGKTLMVKTLAKIINVPIIVVD--------ATSF---TEAGYVGDDVESIIQK 92
L+ G T GKT LAK P+IV+D AT A G + +
Sbjct: 5 LIWGATCTGKTAEAIALAKETGWPVIVLDRVQCCSQLATGSGRPLPAELQGTRRIYLDNR 64
Query: 93 LLHECDYDVELAEQSIIYIDEIDKISKKTDVVSGKDVSGEGVQQSLLKLI 142
L E D E A + I E+ + V+ EG SLLK +
Sbjct: 65 PLSEGIIDAEEAHDRL--IAEVTSHKDEGGVIL------EGGSISLLKRM 106
>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 = 33.0 bits (76), Expect = 0.052
Identities = 12/45 (26%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 24 HYKRLFLLKSKNIYLEKSNIL-LVGPTGCGKTLMVKTLAKIINVP 67
Y L + ++ L+ I+ LVGP G GK+ +++ +A ++
Sbjct: 8 RYGGRTALDNVSLTLKAGEIVALVGPNGSGKSTLLRAIAGLLKPT 52
>gnl|CDD|182791 PRK10865, PRK10865, protein disaggregation chaperone; Provisional.
Length = 857
Score = 34.1 bits (78), Expect = 0.052
Identities = 36/130 (27%), Positives = 58/130 (44%), Gaps = 28/130 (21%)
Query: 2 ELDRHIIGQHETKKIVSVGVYNHYKRLFL-LKSKNIYLEKSNILLVGPTGCGKTLMVKTL 60
EL +IGQ+E + VS N +R L N + + L +GPTG GKT + K L
Sbjct: 565 ELHHRVIGQNEAVEAVS----NAIRRSRAGLSDPNRPI--GSFLFLGPTGVGKTELCKAL 618
Query: 61 AKII---NVPIIVVDATSFTEA-----------GYVGDDVESIIQKLLHECDYDVELAEQ 106
A + + ++ +D + F E GYVG + + + + Y
Sbjct: 619 ANFMFDSDDAMVRIDMSEFMEKHSVSRLVGAPPGYVGYEEGGYLTEAVRRRPY------- 671
Query: 107 SIIYIDEIDK 116
S+I +DE++K
Sbjct: 672 SVILLDEVEK 681
Score = 27.9 bits (62), Expect = 4.8
Identities = 16/31 (51%), Positives = 22/31 (70%), Gaps = 3/31 (9%)
Query: 40 KSNILLVGPTGCGKTLMVKTLA-KIIN--VP 67
K+N +L+G G GKT +V+ LA +IIN VP
Sbjct: 199 KNNPVLIGEPGVGKTAIVEGLAQRIINGEVP 229
>gnl|CDD|172375 PRK13851, PRK13851, type IV secretion system protein VirB11;
Provisional.
Length = 344
Score = 33.7 bits (77), Expect = 0.052
Identities = 14/22 (63%), Positives = 15/22 (68%)
Query: 43 ILLVGPTGCGKTLMVKTLAKII 64
+LL GPTG GKT M KTL I
Sbjct: 165 MLLCGPTGSGKTTMSKTLISAI 186
>gnl|CDD|224391 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA
replication, recombination, and repair /
Posttranslational modification, protein turnover,
chaperones].
Length = 366
Score = 33.9 bits (78), Expect = 0.060
Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 16/97 (16%)
Query: 40 KSNILLVGPTGCGKTLMVKTLAKIINVPIIVVDA---------TSFTEAGYVGDDVESII 90
SNI++ GPTG GKT VK + + + V+ T + + + + +
Sbjct: 42 PSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELRTPYQVLSKILNKLGKVP 101
Query: 91 QKLLHECDYDVELAE-------QSIIYIDEIDKISKK 120
+ L + I+ +DE+D + K
Sbjct: 102 LTGDSSLEILKRLYDNLSKKGKTVIVILDEVDALVDK 138
>gnl|CDD|234619 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed.
Length = 328
Score = 33.6 bits (78), Expect = 0.066
Identities = 25/81 (30%), Positives = 37/81 (45%), Gaps = 22/81 (27%)
Query: 43 ILLVGPTGCGKTLMVKTLAKII----NVPIIVVDATSFTEAGYVGDDVESIIQKLLHECD 98
+LL GP G GKT TLA II V I + + + G D+ +I+
Sbjct: 54 VLLYGPPGLGKT----TLANIIANEMGVNIRITSGPALEKPG----DLAAIL-------- 97
Query: 99 YDVELAEQSIIYIDEIDKISK 119
L E +++IDEI ++S
Sbjct: 98 --TNLEEGDVLFIDEIHRLSP 116
>gnl|CDD|225806 COG3267, ExeA, Type II secretory pathway, component ExeA
(predicted ATPase) [Intracellular trafficking and
secretion].
Length = 269
Score = 33.2 bits (76), Expect = 0.070
Identities = 13/61 (21%), Positives = 28/61 (45%), Gaps = 3/61 (4%)
Query: 23 NHYKRLFLLKSKNIYLEKSNILLVGPTGCGKTLMVKTLAKIIN---VPIIVVDATSFTEA 79
+ L+ I + + + G G GKT++ + L +N V ++V+D + ++A
Sbjct: 34 ADHNEALLMLHAAIADGQGILAVTGEVGSGKTVLRRALLASLNEDQVAVVVIDKPTLSDA 93
Query: 80 G 80
Sbjct: 94 T 94
>gnl|CDD|213512 TIGR00174, miaA, tRNA dimethylallyltransferase. Alternate names
include delta(2)-isopentenylpyrophosphate transferase,
IPP transferase, 2-methylthio-N6-isopentyladenosine
tRNA modification enzyme. Catalyzes the first step in
the modification of an adenosine near the anticodon to
2-methylthio-N6-isopentyladenosine. Understanding of
substrate specificity has changed [Protein synthesis,
tRNA and rRNA base modification].
Length = 287
Score = 33.1 bits (76), Expect = 0.075
Identities = 14/31 (45%), Positives = 20/31 (64%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIINVPIIVVDA 73
I L+GPT GK+ + LA+ +N II VD+
Sbjct: 2 IFLMGPTASGKSQLSIQLAQKLNAEIISVDS 32
>gnl|CDD|234063 TIGR02928, TIGR02928, orc1/cdc6 family replication initiation
protein. Members of this protein family are found
exclusively in the archaea. This set of DNA binding
proteins shows homology to the origin recognition
complex subunit 1/cell division control protein 6
family in eukaryotes. Several members may be found in
genome and interact with each other [DNA metabolism,
DNA replication, recombination, and repair].
Length = 365
Score = 33.4 bits (77), Expect = 0.078
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 41 SNILLVGPTGCGKTLMVKTLAKIIN 65
SN+ + G TG GKT + K + K +
Sbjct: 41 SNVFIYGKTGTGKTAVTKYVMKELE 65
>gnl|CDD|224292 COG1373, COG1373, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 398
Score = 33.5 bits (77), Expect = 0.081
Identities = 20/80 (25%), Positives = 39/80 (48%), Gaps = 8/80 (10%)
Query: 38 LEKSNILLVGPTGCGKTLMVKTLAKIINVPIIVVDATSFTEAGYVGDDVESIIQKLLHEC 97
L IL++GP GKT ++K L K + II + +F + ++ +++ +
Sbjct: 35 LRPFIILILGPRQVGKTTLLKLLIKGLLEEIIYI---NFDDLRLDRIELLDLLRAYIEL- 90
Query: 98 DYDVELAEQSIIYIDEIDKI 117
+ E+S I++DEI +
Sbjct: 91 ----KEREKSYIFLDEIQNV 106
>gnl|CDD|234041 TIGR02868, CydC, thiol reductant ABC exporter, CydC subunit. The
gene pair cydCD encodes an ABC-family transporter in
which each gene contains an N-terminal membrane-spanning
domain (pfam00664) and a C-terminal ATP-binding domain
(pfam00005). In E. coli these genes were discovered as
mutants which caused the terminal heme-copper oxidase
complex cytochrome bd to fail to assemble. Recent work
has shown that the transporter is involved in export of
redox-active thiol compounds such as cysteine and
glutathione. The linkage to assembly of the cytochrome
bd complex is further supported by the conserved operon
structure found outside the gammaproteobacteria
(cydABCD) containing both the transporter and oxidase
genes components. The genes used as the seed members for
this model are all either found in the
gammproteobacterial context or the CydABCD context. All
members of this family scoring above trusted at the time
of its creation were from genomes which encode a
cytochrome bd complex.
Length = 530
Score = 33.5 bits (77), Expect = 0.082
Identities = 8/22 (36%), Positives = 17/22 (77%)
Query: 43 ILLVGPTGCGKTLMVKTLAKII 64
+ ++GP+G GK+ ++ TLA ++
Sbjct: 364 VAILGPSGSGKSTLLATLAGLL 385
>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 = 33.5 bits (77), Expect = 0.083
Identities = 12/19 (63%), Positives = 15/19 (78%)
Query: 43 ILLVGPTGCGKTLMVKTLA 61
+LL GP GCGKTL+ K +A
Sbjct: 219 VLLYGPPGCGKTLIAKAVA 237
>gnl|CDD|184586 PRK14240, PRK14240, phosphate transporter ATP-binding protein;
Provisional.
Length = 250
Score = 33.1 bits (76), Expect = 0.086
Identities = 13/31 (41%), Positives = 23/31 (74%), Gaps = 1/31 (3%)
Query: 31 LKSKNIYLEKSNIL-LVGPTGCGKTLMVKTL 60
LK N+ +E++ + L+GP+GCGK+ ++TL
Sbjct: 19 LKKINLDIEENQVTALIGPSGCGKSTFLRTL 49
>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 = 32.1 bits (74), Expect = 0.10
Identities = 13/31 (41%), Positives = 21/31 (67%)
Query: 42 NILLVGPTGCGKTLMVKTLAKIINVPIIVVD 72
NI+L+G G GKT + + LAK + +P + +D
Sbjct: 1 NIVLIGMMGAGKTTVGRLLAKALGLPFVDLD 31
>gnl|CDD|237802 PRK14723, flhF, flagellar biosynthesis regulator FlhF; Provisional.
Length = 767
Score = 33.2 bits (76), Expect = 0.12
Identities = 16/39 (41%), Positives = 23/39 (58%), Gaps = 4/39 (10%)
Query: 26 KRLFLLKSKNIYLEKSNIL-LVGPTGCGKTLMVKTLAKI 63
L +L+ ++ L + +L LVGPTG GKT T AK+
Sbjct: 170 THLPVLRDEDALLAQGGVLALVGPTGVGKT---TTTAKL 205
>gnl|CDD|183044 PRK11231, fecE, iron-dicitrate transporter ATP-binding subunit;
Provisional.
Length = 255
Score = 32.3 bits (74), Expect = 0.14
Identities = 9/19 (47%), Positives = 15/19 (78%)
Query: 45 LVGPTGCGKTLMVKTLAKI 63
L+GP GCGK+ ++K A++
Sbjct: 33 LIGPNGCGKSTLLKCFARL 51
>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 100
Score = 31.0 bits (71), Expect = 0.14
Identities = 16/39 (41%), Positives = 19/39 (48%), Gaps = 4/39 (10%)
Query: 38 LEKSNILLVGPTGCGKTLM----VKTLAKIINVPIIVVD 72
LEK L+V TG GKTL + LAK + VV
Sbjct: 16 LEKKRGLIVMATGSGKTLTAAALIARLAKGKKKVLFVVP 54
>gnl|CDD|235335 PRK05057, aroK, shikimate kinase I; Reviewed.
Length = 172
Score = 32.0 bits (73), Expect = 0.14
Identities = 14/27 (51%), Positives = 19/27 (70%)
Query: 39 EKSNILLVGPTGCGKTLMVKTLAKIIN 65
EK NI LVGP G GK+ + + LA+ +N
Sbjct: 3 EKRNIFLVGPMGAGKSTIGRQLAQQLN 29
>gnl|CDD|215451 PLN02840, PLN02840, tRNA dimethylallyltransferase.
Length = 421
Score = 32.5 bits (74), Expect = 0.15
Identities = 19/46 (41%), Positives = 25/46 (54%), Gaps = 4/46 (8%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIINVPIIVVDATSFTEAGYVGDDVES 88
I++ GPTG GK+ + LAK +N II D+ Y G DV S
Sbjct: 24 IVISGPTGAGKSRLALELAKRLNGEIISADSVQV----YRGLDVGS 65
>gnl|CDD|238550 cd01130, VirB11-like_ATPase, Type IV secretory pathway component
VirB11, and related ATPases. The homohexamer, VirB11 is
one of eleven Vir proteins, which are required for
T-pilus biogenesis and virulence in the transfer of
T-DNA from the Ti (tumor-inducing) plasmid of bacterial
to plant cells. The pilus is a fibrous cell surface
organelle, which mediates adhesion between bacteria
during conjugative transfer or between bacteria and
host eukaryotic cells during infection. VirB11- related
ATPases include the archaeal flagella biosynthesis
protein and the pilus assembly proteins CpaF/TadA and
TrbB. This alignment contains the C-terminal domain,
which is the ATPase.
Length = 186
Score = 31.9 bits (73), Expect = 0.16
Identities = 11/32 (34%), Positives = 15/32 (46%)
Query: 34 KNIYLEKSNILLVGPTGCGKTLMVKTLAKIIN 65
+ NIL+ G TG GKT ++ L I
Sbjct: 19 WLAVEARKNILISGGTGSGKTTLLNALLAFIP 50
>gnl|CDD|184584 PRK14238, PRK14238, phosphate transporter ATP-binding protein;
Provisional.
Length = 271
Score = 32.1 bits (73), Expect = 0.19
Identities = 14/41 (34%), Positives = 29/41 (70%), Gaps = 2/41 (4%)
Query: 31 LKSKNIYLEKSNIL-LVGPTGCGKTLMVKTLAKII-NVPII 69
LK+ N+ + ++ + ++GP+GCGK+ +KTL +++ VP +
Sbjct: 40 LKNINLDIHENEVTAIIGPSGCGKSTYIKTLNRMVELVPSV 80
>gnl|CDD|221955 pfam13173, AAA_14, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily.
Length = 127
Score = 31.0 bits (71), Expect = 0.19
Identities = 16/77 (20%), Positives = 32/77 (41%), Gaps = 9/77 (11%)
Query: 42 NILLVGPTGCGKTLMVKTLAK-IINVPIIVVDATSFTEAGYVGDDVESIIQKLLHECDYD 100
I++ GP GKT ++ K +++ I+ ++ D+ KLL
Sbjct: 4 IIVITGPRQVGKTTLLLQFLKELLSENILYINLDDPRFLRLALLDLLEEFLKLLLP---- 59
Query: 101 VELAEQSIIYIDEIDKI 117
+ +++DEI K+
Sbjct: 60 ----GKKYLFLDEIQKV 72
>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 = 31.8 bits (73), Expect = 0.19
Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 5/45 (11%)
Query: 21 VYNHYKRLFLLKSKNIYLEKSNIL-LVGPTGCGKTLMVKTLAKII 64
+++ K +L ++ L I+ L G G GKT TLAKI+
Sbjct: 6 SFSYKKGTEILDDLSLDLYAGEIIALTGKNGAGKT----TLAKIL 46
>gnl|CDD|129690 TIGR00602, rad24, checkpoint protein rad24. All proteins in this
family for which functions are known are involved in DNA
damage tolerance (likely cell cycle checkpoints).This
family is based on the phylogenomic analysis of JA Eisen
(1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 637
Score = 32.2 bits (73), Expect = 0.19
Identities = 10/27 (37%), Positives = 19/27 (70%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIINVPII 69
+L+ GP+GCGK+ +K L+K + + +
Sbjct: 113 LLITGPSGCGKSTTIKILSKELGIQVQ 139
>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 = 32.1 bits (73), Expect = 0.19
Identities = 12/44 (27%), Positives = 23/44 (52%), Gaps = 1/44 (2%)
Query: 45 LVGPTGCGKTLMVKTLAKIINVPIIVVDATS-FTEAGYVGDDVE 87
L GP G GKT + +A+ + P+++++ + T + VG
Sbjct: 26 LRGPAGTGKTTLAMHVARKRDRPVMLINGDAELTTSDLVGSYAG 69
>gnl|CDD|224049 COG1124, DppF, ABC-type dipeptide/oligopeptide/nickel transport
system, ATPase component [Amino acid transport and
metabolism / Inorganic ion transport and metabolism].
Length = 252
Score = 31.9 bits (73), Expect = 0.20
Identities = 15/46 (32%), Positives = 26/46 (56%), Gaps = 6/46 (13%)
Query: 21 VYNHYKRLF-LLKSKNIYLEKSNIL-LVGPTGCGKTLMVKTLAKII 64
VY K F L + ++ +E+ L +VG +G GK+ TLA+++
Sbjct: 12 VYGGGKFAFHALNNVSLEIERGETLGIVGESGSGKS----TLARLL 53
>gnl|CDD|234654 PRK00131, aroK, shikimate kinase; Reviewed.
Length = 175
Score = 31.3 bits (72), Expect = 0.21
Identities = 13/36 (36%), Positives = 20/36 (55%)
Query: 38 LEKSNILLVGPTGCGKTLMVKTLAKIINVPIIVVDA 73
L+ NI+L+G G GK+ + + LAK + I D
Sbjct: 2 LKGPNIVLIGFMGAGKSTIGRLLAKRLGYDFIDTDH 37
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 32.3 bits (73), Expect = 0.22
Identities = 23/67 (34%), Positives = 33/67 (49%), Gaps = 1/67 (1%)
Query: 14 KKIVSVGVYNHYKRLFLLKSKNIYLEKSNILLVGPTGCGKTLMVKTLAKIINVPIIVVDA 73
K++ V RL L K + + K +LLVG TGCGKT + LA + +++A
Sbjct: 1148 KELSKVVWTEPMCRLERLVGKCL-VTKEPVLLVGETGCGKTTGCQVLADTFRRELNLMNA 1206
Query: 74 TSFTEAG 80
TE G
Sbjct: 1207 HQETENG 1213
Score = 31.1 bits (70), Expect = 0.50
Identities = 15/38 (39%), Positives = 23/38 (60%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIINVPIIVVDATSFTEAG 80
LLVG TG GKT M++ LA ++ + V++ + TE
Sbjct: 467 TLLVGETGTGKTTMIQYLALKLHFKLTVINKSQQTEMS 504
Score = 30.4 bits (68), Expect = 1.0
Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 5/52 (9%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIINVPIIVVDATSFTEAG-----YVGDDVESI 89
+L+ GPT GKT M+ LA+ + ++ T+ YV DD S+
Sbjct: 891 LLIQGPTSSGKTSMILYLARETGHKFVRINNHEHTDLQEYIGTYVTDDDGSL 942
>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 = 31.6 bits (73), Expect = 0.22
Identities = 23/81 (28%), Positives = 37/81 (45%), Gaps = 22/81 (27%)
Query: 43 ILLVGPTGCGKTLMVKTLAKII----NVPIIVVDATSFTEAGYVGDDVESIIQKLLHECD 98
+LL GP G GKT TLA II V I + + + G D+ +I+
Sbjct: 53 VLLYGPPGLGKT----TLANIIANEMGVNIRITSGPALEKPG----DLAAIL-------- 96
Query: 99 YDVELAEQSIIYIDEIDKISK 119
L +++IDEI ++++
Sbjct: 97 --TNLEPGDVLFIDEIHRLNR 115
>gnl|CDD|238554 cd01134, V_A-ATPase_A, V/A-type ATP synthase catalytic subunit A.
These ATPases couple ATP hydrolysis to the build up of a
H+ gradient, but V-type ATPases do not catalyze the
reverse reaction. The Vacuolar (V-type) ATPase is found
in the membranes of vacuoles, the golgi apparatus and in
other coated vesicles in eukaryotes. Archaea have a
protein which is similar in sequence to V-ATPases, but
functions like an F-ATPase (called A-ATPase). A similar
protein is also found in a few bacteria.
Length = 369
Score = 31.8 bits (73), Expect = 0.24
Identities = 11/24 (45%), Positives = 18/24 (75%)
Query: 47 GPTGCGKTLMVKTLAKIINVPIIV 70
GP GCGKT++ ++L+K N I++
Sbjct: 164 GPFGCGKTVIQQSLSKYSNSDIVI 187
>gnl|CDD|225323 COG2603, COG2603, Predicted ATPase [General function prediction
only].
Length = 334
Score = 31.7 bits (72), Expect = 0.24
Identities = 13/42 (30%), Positives = 24/42 (57%)
Query: 26 KRLFLLKSKNIYLEKSNILLVGPTGCGKTLMVKTLAKIINVP 67
R F +++ + + + +L G TGCGKT +V+ L I++
Sbjct: 126 LRTFAIQATIKEIAQKDFILCGCTGCGKTELVEQLPNAIDLE 167
>gnl|CDD|224045 COG1120, FepC, ABC-type cobalamin/Fe3+-siderophores transport
systems, ATPase components [Inorganic ion transport and
metabolism / Coenzyme metabolism].
Length = 258
Score = 31.4 bits (72), Expect = 0.26
Identities = 12/42 (28%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 25 YKRLFLLKSKNIYLEKSNIL-LVGPTGCGKTLMVKTLAKIIN 65
Y +L + + K I ++GP G GK+ ++K LA ++
Sbjct: 12 YGGKPILDDLSFSIPKGEITGILGPNGSGKSTLLKCLAGLLK 53
>gnl|CDD|226372 COG3854, SpoIIIAA, ncharacterized protein conserved in bacteria
[Function unknown].
Length = 308
Score = 31.7 bits (72), Expect = 0.28
Identities = 19/114 (16%), Positives = 43/114 (37%), Gaps = 23/114 (20%)
Query: 40 KSNILLVGPTGCGKTLMVKTLAKIINVPI--------IVVDATSFTEAGYVGDDVESIIQ 91
N L++GP GKT +++ +A++++ I ++D S G +
Sbjct: 137 WLNTLIIGPPQVGKTTLLRDIARLLSDGINQFLPKKVGIIDERSEIAGCLNGVPQHGRGR 196
Query: 92 KL--LHECDYDVELAEQSIIYIDE--------IDKISKKTDVVSGKDVSGEGVQ 135
++ L C + ++ +D+I + D ++ GV+
Sbjct: 197 RMDVLDPC-----PKAEGMMMAIRSMSPEVIIVDEIGTEEDALAILTALHAGVK 245
>gnl|CDD|236861 PRK11147, PRK11147, ABC transporter ATPase component; Reviewed.
Length = 635
Score = 31.8 bits (73), Expect = 0.28
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 43 ILLVGPTGCGKTLMVKTL 60
I L+GP GCGKT ++K +
Sbjct: 348 IALIGPNGCGKTTLLKLM 365
>gnl|CDD|225164 COG2255, RuvB, Holliday junction resolvasome, helicase subunit [DNA
replication, recombination, and repair].
Length = 332
Score = 31.8 bits (73), Expect = 0.28
Identities = 24/81 (29%), Positives = 37/81 (45%), Gaps = 22/81 (27%)
Query: 43 ILLVGPTGCGKTLMVKTLAKII----NVPIIVVDATSFTEAGYVGDDVESIIQKLLHECD 98
+LL GP G GKT TLA II V + + + + G D+ +I+
Sbjct: 55 VLLFGPPGLGKT----TLAHIIANELGVNLKITSGPALEKPG----DLAAIL-------- 98
Query: 99 YDVELAEQSIIYIDEIDKISK 119
L E +++IDEI ++S
Sbjct: 99 --TNLEEGDVLFIDEIHRLSP 117
>gnl|CDD|213268 cd03301, ABC_MalK_N, The N-terminal ATPase domain of the maltose
transporter, MalK. ATP binding cassette (ABC) proteins
function from bacteria to human, mediating the
translocation of substances into and out of cells or
organelles. ABC transporters contain two
transmembrane-spanning domains (TMDs) or subunits and
two nucleotide binding domains (NBDs) or subunits that
couple transport to the hydrolysis of ATP. In the
maltose transport system, the periplasmic maltose
binding protein (MBP) stimulates the ATPase activity of
the membrane-associated transporter, which consists of
two transmembrane subunits, MalF and MalG, and two
copies of the ATP binding subunit, MalK, and becomes
tightly bound to the transporter in the catalytic
transition state, ensuring that maltose is passed to
the transporter as ATP is hydrolyzed.
Length = 213
Score = 31.1 bits (71), Expect = 0.29
Identities = 12/50 (24%), Positives = 24/50 (48%), Gaps = 1/50 (2%)
Query: 16 IVSVGVYNHYKRLFLLKSKNIYLEKSNIL-LVGPTGCGKTLMVKTLAKII 64
+ V + + L N+ + + L+GP+GCGKT ++ +A +
Sbjct: 1 VELENVTKRFGNVTALDDLNLDIADGEFVVLLGPSGCGKTTTLRMIAGLE 50
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 31.6 bits (72), Expect = 0.32
Identities = 8/33 (24%), Positives = 16/33 (48%)
Query: 39 EKSNILLVGPTGCGKTLMVKTLAKIINVPIIVV 71
+ ++V PTG GKT++ + +V+
Sbjct: 54 TERRGVIVLPTGAGKTVVAAEAIAELKRSTLVL 86
>gnl|CDD|213227 cd03260, ABC_PstB_phosphate_transporter, ATP-binding cassette
domain of the phosphate transport system. Phosphate
uptake is of fundamental importance in the cell
physiology of bacteria because phosphate is required as
a nutrient. The Pst system of E. coli comprises four
distinct subunits encoded by the pstS, pstA, pstB, and
pstC genes. The PstS protein is a phosphate-binding
protein located in the periplasmic space. PstA and PstC
are hydrophobic and they form the transmembrane portion
of the Pst system. PstB is the catalytic subunit, which
couples the energy of ATP hydrolysis to the import of
phosphate across cellular membranes through the Pst
system, often referred as ABC-protein. PstB belongs to
one of the largest superfamilies of proteins
characterized by a highly conserved adenosine
triphosphate (ATP) binding cassette (ABC), which is
also a nucleotide binding domain (NBD).
Length = 227
Score = 31.0 bits (71), Expect = 0.32
Identities = 8/20 (40%), Positives = 16/20 (80%)
Query: 45 LVGPTGCGKTLMVKTLAKII 64
L+GP+GCGK+ +++ L ++
Sbjct: 31 LIGPSGCGKSTLLRLLNRLN 50
>gnl|CDD|213260 cd03293, ABC_NrtD_SsuB_transporters, ATP-binding cassette domain
of the nitrate and sulfonate transporters. NrtD and
SsuB are the ATP-binding subunits of the bacterial
ABC-type nitrate and sulfonate transport systems,
respectively. 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 = 220
Score = 31.3 bits (72), Expect = 0.32
Identities = 12/20 (60%), Positives = 15/20 (75%), Gaps = 4/20 (20%)
Query: 45 LVGPTGCGKTLMVKTLAKII 64
LVGP+GCGK+ TL +II
Sbjct: 35 LVGPSGCGKS----TLLRII 50
>gnl|CDD|234132 TIGR03167, tRNA_sel_U_synt, tRNA 2-selenouridine synthase. The
Escherichia coli YbbB protein was shown to encode a
selenophosphate-dependent tRNA 2-selenouridine synthase,
essential for modification of some tRNAs to replace a
sulfur atom with selenium. This enzyme works with SelD,
the selenium donor protein, which also acts in
selenocysteine incorporation. Although the members of
this protein family show a fairly deep split, sequences
from both sides of the split are supported by
co-occurence with, and often proximity to, the selD gene
[Protein synthesis, tRNA and rRNA base modification].
Length = 311
Score = 31.4 bits (72), Expect = 0.33
Identities = 14/43 (32%), Positives = 22/43 (51%)
Query: 20 GVYNHYKRLFLLKSKNIYLEKSNILLVGPTGCGKTLMVKTLAK 62
G Y Y+R + + + + I+L G TG GKT ++ LA
Sbjct: 107 GGYKAYRRFVIDQLEELPQPFPLIVLGGMTGSGKTELLHALAN 149
>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 = 30.6 bits (70), Expect = 0.35
Identities = 12/44 (27%), Positives = 25/44 (56%), Gaps = 1/44 (2%)
Query: 20 GVYNHYKRLFLLKSKNIYLEKSNIL-LVGPTGCGKTLMVKTLAK 62
V Y + +L ++ +E I+ L+GP+G GK+ +++ +A
Sbjct: 5 NVSKRYGQKTVLNDVSLNIEAGEIVALLGPSGSGKSTLLRCIAG 48
>gnl|CDD|213195 cd03228, ABCC_MRP_Like, ATP-binding cassette domain of multidrug
resistance protein-like transporters. The MRP
(Multidrug Resistance Protein)-like transporters are
involved in drug, peptide, and lipid export. They
belong to the subfamily C of the ATP-binding cassette
(ABC) superfamily of transport proteins. The ABCC
subfamily contains transporters with a diverse
functional spectrum that includes ion transport, cell
surface receptor, and toxin secretion activities. The
MRP-like family, similar to all ABC proteins, have a
common four-domain core structure constituted by two
membrane-spanning domains, each composed of six
transmembrane (TM) helices, and two nucleotide-binding
domains (NBD). 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 = 171
Score = 30.8 bits (71), Expect = 0.35
Identities = 9/22 (40%), Positives = 15/22 (68%), Gaps = 4/22 (18%)
Query: 43 ILLVGPTGCGKTLMVKTLAKII 64
+ +VGP+G GK+ TL K++
Sbjct: 31 VAIVGPSGSGKS----TLLKLL 48
>gnl|CDD|237182 PRK12727, PRK12727, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 559
Score = 31.5 bits (71), Expect = 0.36
Identities = 12/20 (60%), Positives = 14/20 (70%)
Query: 43 ILLVGPTGCGKTLMVKTLAK 62
I LVGPTG GKT + LA+
Sbjct: 353 IALVGPTGAGKTTTIAKLAQ 372
>gnl|CDD|184590 PRK14249, PRK14249, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 251
Score = 31.2 bits (70), Expect = 0.37
Identities = 16/50 (32%), Positives = 31/50 (62%), Gaps = 1/50 (2%)
Query: 15 KIVSVGVYNHYKRLFLLKSKNI-YLEKSNILLVGPTGCGKTLMVKTLAKI 63
KI GV Y + +LK+ N+ + E+ ++GP+GCGK+ +++ L ++
Sbjct: 4 KIKIRGVNFFYHKHQVLKNINMDFPERQITAIIGPSGCGKSTLLRALNRM 53
>gnl|CDD|224337 COG1419, FlhF, Flagellar GTP-binding protein [Cell motility and
secretion].
Length = 407
Score = 31.2 bits (71), Expect = 0.37
Identities = 18/38 (47%), Positives = 24/38 (63%), Gaps = 4/38 (10%)
Query: 26 KRLFLLKSKNIYLEKS-NILLVGPTGCGKTLMVKTLAK 62
++L L +N+ +E+ I LVGPTG GKT TLAK
Sbjct: 188 RKLLLSLIENLIVEQKRVIALVGPTGVGKT---TTLAK 222
>gnl|CDD|226361 COG3842, PotA, ABC-type spermidine/putrescine transport systems,
ATPase components [Amino acid transport and
metabolism].
Length = 352
Score = 31.1 bits (71), Expect = 0.38
Identities = 13/46 (28%), Positives = 24/46 (52%), Gaps = 5/46 (10%)
Query: 20 GVYNHYKRLFLLKSKNIYLEKSNIL-LVGPTGCGKTLMVKTLAKII 64
V + + ++ ++K + L+GP+GCGKT TL ++I
Sbjct: 10 NVSKSFGDFTAVDDISLDIKKGEFVTLLGPSGCGKT----TLLRMI 51
>gnl|CDD|224048 COG1123, COG1123, ATPase components of various ABC-type transport
systems, contain duplicated ATPase [General function
prediction only].
Length = 539
Score = 31.4 bits (72), Expect = 0.38
Identities = 10/20 (50%), Positives = 14/20 (70%), Gaps = 4/20 (20%)
Query: 45 LVGPTGCGKTLMVKTLAKII 64
LVG +G GK+ TLA+I+
Sbjct: 322 LVGESGSGKS----TLARIL 337
Score = 28.3 bits (64), Expect = 3.6
Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 5/49 (10%)
Query: 17 VSVGVYNHYKRLFLLKSKNIYLEKSNIL-LVGPTGCGKTLMVKTLAKII 64
++V R+ ++ + +E IL +VG +G GK+ TLA +
Sbjct: 11 LTVEFATDGGRVPAVRDVSFEVEPGEILGIVGESGSGKS----TLALAL 55
>gnl|CDD|215947 pfam00493, MCM, MCM2/3/5 family.
Length = 327
Score = 31.0 bits (71), Expect = 0.39
Identities = 23/90 (25%), Positives = 42/90 (46%), Gaps = 17/90 (18%)
Query: 40 KSNILLVGPTGCGKTLMVKTLAKIINVPIIVVDATSFTEAG---YVGDDVESIIQKLLHE 96
N+LLVG G K+ ++K +AK+ + S + AG V D ++
Sbjct: 57 DINVLLVGDPGTAKSQLLKYVAKLAPRAVYTSGKGS-SAAGLTAAVVRDPDTG------- 108
Query: 97 CDYDVE-----LAEQSIIYIDEIDKISKKT 121
++ +E LA+ + IDE DK++++
Sbjct: 109 -EWTLEAGALVLADGGVCCIDEFDKMNEED 137
>gnl|CDD|226970 COG4619, COG4619, ABC-type uncharacterized transport system,
ATPase component [General function prediction only].
Length = 223
Score = 31.0 bits (70), Expect = 0.39
Identities = 10/22 (45%), Positives = 17/22 (77%)
Query: 43 ILLVGPTGCGKTLMVKTLAKII 64
I + GP+GCGK+ ++K +A +I
Sbjct: 32 IAITGPSGCGKSTLLKIVASLI 53
>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 = 30.5 bits (70), Expect = 0.39
Identities = 16/50 (32%), Positives = 29/50 (58%), Gaps = 5/50 (10%)
Query: 17 VSVGVYNHYKRLFLLKSKNIYLEKSNIL-LVGPTGCGKTLMVKTLAKIIN 65
+SVG Y +L ++ +E I+ ++GP G GK+ ++KTLA ++
Sbjct: 5 LSVG----YGGRTVLDDLSLSIEAGEIVGILGPNGAGKSTLLKTLAGLLK 50
>gnl|CDD|236947 PRK11650, ugpC, glycerol-3-phosphate transporter ATP-binding
subunit; Provisional.
Length = 356
Score = 31.0 bits (71), Expect = 0.42
Identities = 15/24 (62%), Positives = 18/24 (75%), Gaps = 3/24 (12%)
Query: 43 ILLVGPTGCGK-TL--MVKTLAKI 63
I+LVGP+GCGK TL MV L +I
Sbjct: 33 IVLVGPSGCGKSTLLRMVAGLERI 56
>gnl|CDD|221803 pfam12846, AAA_10, AAA-like domain. This family of domains
contain a P-loop motif that is characteristic of the
AAA superfamily. Many of the proteins in this family
are conjugative transfer proteins.
Length = 316
Score = 30.9 bits (70), Expect = 0.42
Identities = 14/34 (41%), Positives = 22/34 (64%), Gaps = 3/34 (8%)
Query: 42 NILLVGPTGCGKTLMVKTLAK---IINVPIIVVD 72
N+L+VGP+G GK+ ++K LA +IV+D
Sbjct: 3 NMLIVGPSGSGKSTLLKLLALRLLARGGRVIVID 36
>gnl|CDD|237651 PRK14266, PRK14266, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 250
Score = 30.7 bits (69), Expect = 0.44
Identities = 13/38 (34%), Positives = 29/38 (76%), Gaps = 1/38 (2%)
Query: 30 LLKSKNIYLEKSNIL-LVGPTGCGKTLMVKTLAKIINV 66
+LK+ N+ + K+++ L+GP+GCGK+ ++TL ++ ++
Sbjct: 18 ILKNVNLDIPKNSVTALIGPSGCGKSTFIRTLNRMNDL 55
>gnl|CDD|172762 PRK14274, PRK14274, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 259
Score = 31.0 bits (70), Expect = 0.44
Identities = 13/37 (35%), Positives = 26/37 (70%), Gaps = 1/37 (2%)
Query: 31 LKSKNIYLEKSNIL-LVGPTGCGKTLMVKTLAKIINV 66
LK+ N+ + ++ + ++GP+GCGK+ +KTL +I +
Sbjct: 28 LKNINLSIPENEVTAIIGPSGCGKSTFIKTLNLMIQM 64
>gnl|CDD|172751 PRK14263, PRK14263, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 261
Score = 30.8 bits (69), Expect = 0.47
Identities = 10/40 (25%), Positives = 25/40 (62%), Gaps = 1/40 (2%)
Query: 25 YKRLFLLKSKNIYLEKSNIL-LVGPTGCGKTLMVKTLAKI 63
Y ++ ++ + K+ I +GP+GCGK+ ++++L ++
Sbjct: 18 YGNFMAVRDSHVPIRKNEITGFIGPSGCGKSTVLRSLNRM 57
>gnl|CDD|215920 pfam00437, T2SE, Type II/IV secretion system protein. This family
contains both type II and type IV pathway secretion
proteins from bacteria. VirB11 ATPase is a subunit of
the Agrobacterium tumefaciens transfer DNA (T-DNA)
transfer system, a type IV secretion pathway required
for delivery of T-DNA and effector proteins to plant
cells during infection.
Length = 273
Score = 30.7 bits (70), Expect = 0.47
Identities = 12/24 (50%), Positives = 15/24 (62%)
Query: 42 NILLVGPTGCGKTLMVKTLAKIIN 65
NIL+ G TG GKT ++ L IN
Sbjct: 131 NILVSGGTGSGKTTLLYALLNEIN 154
>gnl|CDD|224050 COG1125, OpuBA, ABC-type proline/glycine betaine transport
systems, ATPase components [Amino acid transport and
metabolism].
Length = 309
Score = 30.7 bits (70), Expect = 0.48
Identities = 16/46 (34%), Positives = 23/46 (50%), Gaps = 5/46 (10%)
Query: 21 VYNHYKRLFLLKSKNIYLEKSNIL-LVGPTGCGKTLMVKTLAKIIN 65
V Y + N+ +E+ L L+GP+G GKT T K+IN
Sbjct: 7 VSKRYGNKKAVDDVNLTIEEGEFLVLIGPSGSGKT----TTLKMIN 48
>gnl|CDD|224077 COG1155, NtpA, Archaeal/vacuolar-type H+-ATPase subunit A [Energy
production and conversion].
Length = 588
Score = 31.1 bits (71), Expect = 0.48
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 47 GPTGCGKTLMVKTLAKIINVPIIVVDA 73
GP G GKT+ TL+K+ + I++
Sbjct: 231 GPFGSGKTVSQHTLSKLADGDIVIYVG 257
>gnl|CDD|223775 COG0703, AroK, Shikimate kinase [Amino acid transport and
metabolism].
Length = 172
Score = 30.3 bits (69), Expect = 0.48
Identities = 14/34 (41%), Positives = 21/34 (61%)
Query: 40 KSNILLVGPTGCGKTLMVKTLAKIINVPIIVVDA 73
NI+L+G G GK+ + + LAK +N+P I D
Sbjct: 2 NMNIVLIGFMGAGKSTIGRALAKALNLPFIDTDQ 35
>gnl|CDD|225364 COG2805, PilT, Tfp pilus assembly protein, pilus retraction ATPase
PilT [Cell motility and secretion / Intracellular
trafficking and secretion].
Length = 353
Score = 30.7 bits (70), Expect = 0.51
Identities = 12/23 (52%), Positives = 16/23 (69%), Gaps = 3/23 (13%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIIN 65
IL+ GPTG GK+ TLA +I+
Sbjct: 128 ILVTGPTGSGKS---TTLAAMID 147
>gnl|CDD|181235 PRK08118, PRK08118, topology modulation protein; Reviewed.
Length = 167
Score = 30.0 bits (68), Expect = 0.55
Identities = 11/31 (35%), Positives = 21/31 (67%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIINVPIIVVDA 73
I+L+G G GK+ + + L + +N+P+ +DA
Sbjct: 4 IILIGSGGSGKSTLARQLGEKLNIPVHHLDA 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 = 30.3 bits (69), Expect = 0.56
Identities = 16/46 (34%), Positives = 23/46 (50%), Gaps = 7/46 (15%)
Query: 21 VYNHYKRLFLLKSKNIYLEKSNIL-LVGPTGCGKTLMVKTLAKIIN 65
Y K + + N+ + K L L+GP+G GKT T K+IN
Sbjct: 9 RYGGGK--KAVNNLNLEIAKGEFLVLIGPSGSGKT----TTMKMIN 48
>gnl|CDD|214940 smart00962, SRP54, SRP54-type protein, GTPase domain. This entry
represents the GTPase domain of the 54 kDa SRP54
component, a GTP-binding protein that interacts with
the signal sequence when it emerges from the ribosome.
SRP54 of the signal recognition particle has a
three-domain structure: an N-terminal helical bundle
domain, a GTPase domain, and the M-domain that binds
the 7s RNA and also binds the signal sequence. The
extreme C-terminal region is glycine-rich and lower in
complexity and poorly conserved between species. The
GTPase domain is evolutionary related to P-loop NTPase
domains found in a variety of other proteins.
Length = 197
Score = 30.1 bits (69), Expect = 0.58
Identities = 13/21 (61%), Positives = 15/21 (71%), Gaps = 3/21 (14%)
Query: 43 ILLVGPTGCGKTLMVKTLAKI 63
ILLVGP G GKT T+AK+
Sbjct: 4 ILLVGPNGVGKT---TTIAKL 21
>gnl|CDD|131806 TIGR02759, TraD_Ftype, type IV conjugative transfer system coupling
protein TraD. The TraD protein performs an essential
coupling function in conjugative type IV secretion
systems. This protein sits at the inner membrane in
contact with the assembled pilus and its scaffold as
well as the relaxosome-plasmid DNA complex (through
TraM).
Length = 566
Score = 30.8 bits (70), Expect = 0.64
Identities = 17/66 (25%), Positives = 29/66 (43%), Gaps = 9/66 (13%)
Query: 37 YLEKSNILLVGPTGCGKTLMVKTLAKIINV---PIIVVDAT-SFTEAGYVGDDVESIIQK 92
E +IL+ G TG GK++ ++ L + I I+ D +FT Y +
Sbjct: 173 GSETQHILIHGTTGSGKSVAIRKLLRWIRQRGDRAIIYDKGCTFTSRFY-----DPSQDV 227
Query: 93 LLHECD 98
+L+ D
Sbjct: 228 ILNPFD 233
>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 = 29.9 bits (68), Expect = 0.65
Identities = 14/65 (21%), Positives = 29/65 (44%), Gaps = 15/65 (23%)
Query: 45 LVGPTGCGKTLMVKTLAKII-----NVPIIVVDATSFTEA------GYVGDDVE----SI 89
++GP+G GK+ + + + ++ V + D + + GY+ D E SI
Sbjct: 33 IIGPSGSGKSTLARLILGLLRPTSGRVRLDGADISQWDPNELGDHVGYLPQDDELFSGSI 92
Query: 90 IQKLL 94
+ +L
Sbjct: 93 AENIL 97
>gnl|CDD|224162 COG1241, MCM2, Predicted ATPase involved in replication control,
Cdc46/Mcm family [DNA replication, recombination, and
repair].
Length = 682
Score = 30.8 bits (70), Expect = 0.66
Identities = 22/90 (24%), Positives = 43/90 (47%), Gaps = 13/90 (14%)
Query: 41 SNILLVGPTGCGKTLMVKTLAKIINVPI-IVVDATSFTEAGYVGDDVESIIQKLLHECDY 99
+ILLVG G K+ ++K +AK+ P + + AG +++ + ++
Sbjct: 320 IHILLVGDPGTAKSQLLKYVAKLA--PRGVYTSGKGSSAAG----LTAAVV-RDKVTGEW 372
Query: 100 DVE-----LAEQSIIYIDEIDKISKKTDVV 124
+E LA+ + IDE DK++++ V
Sbjct: 373 VLEAGALVLADGGVCCIDEFDKMNEEDRVA 402
>gnl|CDD|215427 PLN02796, PLN02796, D-glycerate 3-kinase.
Length = 347
Score = 30.5 bits (69), Expect = 0.67
Identities = 11/26 (42%), Positives = 15/26 (57%), Gaps = 3/26 (11%)
Query: 44 LLVG---PTGCGKTLMVKTLAKIINV 66
L++G P GCGKT +V L + N
Sbjct: 101 LVIGISAPQGCGKTTLVFALVYLFNA 126
>gnl|CDD|215832 pfam00270, DEAD, DEAD/DEAH box helicase. Members of this family
include the DEAD and DEAH box helicases. Helicases are
involved in unwinding nucleic acids. The DEAD box
helicases are involved in various aspects of RNA
metabolism, including nuclear transcription, pre mRNA
splicing, ribosome biogenesis, nucleocytoplasmic
transport, translation, RNA decay and organellar gene
expression.
Length = 169
Score = 29.9 bits (68), Expect = 0.67
Identities = 12/39 (30%), Positives = 19/39 (48%), Gaps = 5/39 (12%)
Query: 38 LEKSNILLVGPTGCGKTL-----MVKTLAKIINVPIIVV 71
L ++L+ PTG GKTL +++ L P +V
Sbjct: 12 LSGKDVLVQAPTGSGKTLAFLLPILQALLPKKGGPQALV 50
>gnl|CDD|213266 cd03299, ABC_ModC_like, ATP-binding cassette domain similar to
the molybdate transporter. Archaeal protein closely
related to ModC. ModC is an ABC-type transporter and
the ATPase component of a molybdate transport system
that also includes the periplasmic binding protein ModA
and the membrane protein ModB. 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 = 235
Score = 30.0 bits (68), Expect = 0.69
Identities = 13/37 (35%), Positives = 27/37 (72%), Gaps = 1/37 (2%)
Query: 29 FLLKSKNIYLEKSNIL-LVGPTGCGKTLMVKTLAKII 64
F LK+ ++ +E+ + ++GPTG GK+++++T+A I
Sbjct: 13 FKLKNVSLEVERGDYFVILGPTGSGKSVLLETIAGFI 49
>gnl|CDD|140006 PRK13949, PRK13949, shikimate kinase; Provisional.
Length = 169
Score = 29.7 bits (67), Expect = 0.72
Identities = 19/65 (29%), Positives = 27/65 (41%), Gaps = 13/65 (20%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIINVPIIVVD-----------ATSFTEAGYVGDDVESIIQ 91
I LVG G GKT + K LA+ + + I +D F E G + +
Sbjct: 4 IFLVGYMGAGKTTLGKALARELGLSFIDLDFFIENRFHKTVGDIFAERGEAV--FRELER 61
Query: 92 KLLHE 96
+LHE
Sbjct: 62 NMLHE 66
>gnl|CDD|214361 CHL00095, clpC, Clp protease ATP binding subunit.
Length = 821
Score = 30.4 bits (69), Expect = 0.73
Identities = 24/64 (37%), Positives = 28/64 (43%), Gaps = 7/64 (10%)
Query: 1 MELDRH--IIGQHETKKIVSVGVYNHYKRLFLLKSKNIYLEKSNILLVGPTGCGKTLMVK 58
ME H IIGQ E VS + L KN ++ L GPTG GKT + K
Sbjct: 503 MEETLHKRIIGQDEAVVAVSKAIRRARVGL-----KNPNRPIASFLFSGPTGVGKTELTK 557
Query: 59 TLAK 62
LA
Sbjct: 558 ALAS 561
>gnl|CDD|206669 cd01882, BMS1, Bms1, an essential GTPase, promotes assembly of
preribosomal RNA processing complexes. Bms1 is an
essential, evolutionarily conserved, nucleolar protein.
Its depletion interferes with processing of the 35S
pre-rRNA at sites A0, A1, and A2, and the formation of
40S subunits. Bms1, the putative endonuclease Rc11, and
the essential U3 small nucleolar RNA form a stable
subcomplex that is believed to control an early step in
the formation of the 40S subumit. The C-terminal domain
of Bms1 contains a GTPase-activating protein (GAP) that
functions intramolecularly. It is believed that Rc11
activates Bms1 by acting as a guanine-nucleotide
exchange factor (GEF) to promote GDP/GTP exchange, and
that activated (GTP-bound) Bms1 delivers Rc11 to the
preribosomes.
Length = 231
Score = 30.0 bits (68), Expect = 0.74
Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 15/60 (25%)
Query: 43 ILLVGPTGCGKTLMVKTLAK--------IINVPIIVVDATS----FTEAGYVGDDVESII 90
+++VGP G GK+ ++++L K I PI +V F E +D+ S+I
Sbjct: 42 VVVVGPPGVGKSTLIRSLIKRYTKQNLSDIKGPITIVTGKKRRLTFIE---CPNDINSMI 98
>gnl|CDD|224041 COG1116, TauB, ABC-type nitrate/sulfonate/bicarbonate transport
system, ATPase component [Inorganic ion transport and
metabolism].
Length = 248
Score = 30.2 bits (69), Expect = 0.75
Identities = 15/46 (32%), Positives = 28/46 (60%), Gaps = 5/46 (10%)
Query: 20 GVYNHYKRLFLLKSKNIYLEKSNIL-LVGPTGCGKTLMVKTLAKII 64
GV + + +L+ N+ +EK + ++GP+GCGK+ TL ++I
Sbjct: 8 GVSKSFGGVEVLEDINLSVEKGEFVAILGPSGCGKS----TLLRLI 49
>gnl|CDD|213264 cd03297, ABC_ModC_molybdenum_transporter, ATP-binding cassette
domain of the molybdenum transport system. ModC is an
ABC-type transporter and the ATPase component of a
molybdate transport system that also includes the
periplasmic binding protein ModA and the membrane
protein ModB. 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 = 214
Score = 30.0 bits (68), Expect = 0.77
Identities = 8/32 (25%), Positives = 18/32 (56%), Gaps = 2/32 (6%)
Query: 45 LVGPTGCGKTLMVKTLAKIINVP--IIVVDAT 74
+ G +G GK+ +++ +A + IV++ T
Sbjct: 28 IFGASGAGKSTLLRCIAGLEKPDGGTIVLNGT 59
>gnl|CDD|226905 COG4525, TauB, ABC-type taurine transport system, ATPase
component [Inorganic ion transport and metabolism].
Length = 259
Score = 30.1 bits (68), Expect = 0.79
Identities = 9/36 (25%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 30 LLKSKNIYLEKSNIL-LVGPTGCGKTLMVKTLAKII 64
L+ ++ + ++ ++GP+GCGKT ++ +A +
Sbjct: 20 ALEDVSLTIASGELVVVLGPSGCGKTTLLNLIAGFV 55
>gnl|CDD|235153 PRK03731, aroL, shikimate kinase II; Reviewed.
Length = 171
Score = 29.5 bits (67), Expect = 0.79
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIIN 65
+ LVG GCGKT + LA+ +
Sbjct: 5 LFLVGARGCGKTTVGMALAQALG 27
>gnl|CDD|236333 PRK08691, PRK08691, DNA polymerase III subunits gamma and tau;
Validated.
Length = 709
Score = 30.4 bits (68), Expect = 0.80
Identities = 25/92 (27%), Positives = 39/92 (42%), Gaps = 16/92 (17%)
Query: 44 LLVGPTGCGKTLMVKTLAKIINV-------PIIVVDATSFTEAGYVGDDVE--------- 87
LL G G GKT + + LAK +N P V + + +AG D +E
Sbjct: 42 LLTGTRGVGKTTIARILAKSLNCENAQHGEPCGVCQSCTQIDAGRYVDLLEIDAASNTGI 101
Query: 88 SIIQKLLHECDYDVELAEQSIIYIDEIDKISK 119
I+++L Y + + IDE+ +SK
Sbjct: 102 DNIREVLENAQYAPTAGKYKVYIIDEVHMLSK 133
>gnl|CDD|172748 PRK14260, PRK14260, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 259
Score = 30.0 bits (67), Expect = 0.81
Identities = 13/31 (41%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 33 SKNIYLEKSNILLVGPTGCGKTLMVKTLAKI 63
S +IY ++GP+GCGK+ +KTL +I
Sbjct: 27 SMDIY-RNKVTAIIGPSGCGKSTFIKTLNRI 56
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 30.4 bits (69), Expect = 0.88
Identities = 12/32 (37%), Positives = 17/32 (53%), Gaps = 5/32 (15%)
Query: 36 IYLEKSNILLVGPTGCGKTL-----MVKTLAK 62
L N+L+ PTG GKTL ++ TL +
Sbjct: 43 GLLSDENVLISAPTGSGKTLIALLAILSTLLE 74
>gnl|CDD|223679 COG0606, COG0606, Predicted ATPase with chaperone activity
[Posttranslational modification, protein turnover,
chaperones].
Length = 490
Score = 30.3 bits (69), Expect = 0.92
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 42 NILLVGPTGCGKTLMVKTLAKI 63
N+LLVGP G GKT++ L +
Sbjct: 200 NLLLVGPPGTGKTMLASRLPGL 221
>gnl|CDD|182336 PRK10253, PRK10253, iron-enterobactin transporter ATP-binding
protein; Provisional.
Length = 265
Score = 30.0 bits (67), Expect = 0.93
Identities = 8/20 (40%), Positives = 18/20 (90%)
Query: 45 LVGPTGCGKTLMVKTLAKII 64
++GP GCGK+ +++TL++++
Sbjct: 38 IIGPNGCGKSTLLRTLSRLM 57
>gnl|CDD|213224 cd03257, ABC_NikE_OppD_transporters, ATP-binding cassette domain
of nickel/oligopeptides specific transporters. The ABC
transporter subfamily specific for the transport of
dipeptides, oligopeptides (OppD), and nickel (NikDE).
The NikABCDE system of E. coli belongs to this family
and is composed of the periplasmic binding protein
NikA, two integral membrane components (NikB and NikC),
and two ATPase (NikD and NikE). The NikABCDE
transporter is synthesized under anaerobic conditions
to meet the increased demand for nickel resulting from
hydrogenase synthesis. The molecular mechanism of
nickel uptake in many bacteria and most archaea is not
known. Many other members of this ABC family are also
involved in the uptake of dipeptides and oligopeptides.
The oligopeptide transport system (Opp) is a
five-component ABC transport composed of a
membrane-anchored substrate binding proteins (SRP),
OppA, two transmembrane proteins, OppB and OppC, and
two ATP-binding domains, OppD and OppF.
Length = 228
Score = 29.8 bits (68), Expect = 0.93
Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 5/49 (10%)
Query: 17 VSVGVYNHYKRLFLLKSKNIYLEKSNIL-LVGPTGCGKTLMVKTLAKII 64
+SV + L + ++K L LVG +G GK+ TLA+ I
Sbjct: 7 LSVSFPTGGGSVKALDDVSFSIKKGETLGLVGESGSGKS----TLARAI 51
>gnl|CDD|223521 COG0444, DppD, ABC-type dipeptide/oligopeptide/nickel transport
system, ATPase component [Amino acid transport and
metabolism / Inorganic ion transport and metabolism].
Length = 316
Score = 29.8 bits (68), Expect = 0.94
Identities = 13/52 (25%), Positives = 26/52 (50%), Gaps = 1/52 (1%)
Query: 17 VSVGVYNHYKRLFLLKSKNIYLEKSNIL-LVGPTGCGKTLMVKTLAKIINVP 67
+SV + + + L+K IL +VG +G GK+++ K + ++ P
Sbjct: 7 LSVSFPTDAGVVKAVDGVSFELKKGEILGIVGESGSGKSVLAKAIMGLLPKP 58
>gnl|CDD|224047 COG1122, CbiO, ABC-type cobalt transport system, ATPase component
[Inorganic ion transport and metabolism].
Length = 235
Score = 29.9 bits (68), Expect = 0.94
Identities = 11/23 (47%), Positives = 16/23 (69%), Gaps = 4/23 (17%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIIN 65
+LL+GP G GK+ TL K++N
Sbjct: 33 VLLIGPNGSGKS----TLLKLLN 51
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 29.4 bits (66), Expect = 1.0
Identities = 10/41 (24%), Positives = 20/41 (48%), Gaps = 5/41 (12%)
Query: 36 IYLEKSNILLVGPTGCGKTL-----MVKTLAKIINVPIIVV 71
+ +++L PTG GKTL ++ L + ++V+
Sbjct: 20 LLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVL 60
>gnl|CDD|213231 cd03264, ABC_drug_resistance_like, ABC-type multidrug transport
system, ATPase component. The biological function of
this family is not well characterized, but display ABC
domains similar to members of ABCA subfamily. 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 = 211
Score = 29.5 bits (67), Expect = 1.0
Identities = 12/45 (26%), Positives = 21/45 (46%)
Query: 20 GVYNHYKRLFLLKSKNIYLEKSNILLVGPTGCGKTLMVKTLAKII 64
+ Y + L ++ L L+GP G GKT +++ LA +
Sbjct: 5 NLTKRYGKKRALDGVSLTLGPGMYGLLGPNGAGKTTLMRILATLT 49
>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 = 30.0 bits (68), Expect = 1.1
Identities = 12/22 (54%), Positives = 16/22 (72%), Gaps = 4/22 (18%)
Query: 43 ILLVGPTGCGKTLMVKTLAKII 64
+ L+GP+GCGKT TL +II
Sbjct: 33 VCLLGPSGCGKT----TLLRII 50
>gnl|CDD|234172 TIGR03345, VI_ClpV1, type VI secretion ATPase, ClpV1 family.
Members of this protein family are homologs of ClpB, an
ATPase associated with chaperone-related functions.
These ClpB homologs, designated ClpV1, are a key
component of the bacterial pathogenicity-associated type
VI secretion system [Protein fate, Protein and peptide
secretion and trafficking, Cellular processes,
Pathogenesis].
Length = 852
Score = 29.9 bits (68), Expect = 1.1
Identities = 19/54 (35%), Positives = 27/54 (50%), Gaps = 14/54 (25%)
Query: 44 LLVGPTGCGKTLMVKTLAKII---NVPIIVVDATSFTEA-----------GYVG 83
LLVGP+G GKT LA+++ +I ++ + F EA GYVG
Sbjct: 600 LLVGPSGVGKTETALALAELLYGGEQNLITINMSEFQEAHTVSRLKGSPPGYVG 653
>gnl|CDD|213228 cd03261, ABC_Org_Solvent_Resistant, ATP-binding cassette
transport system involved in resistant to organic
solvents. 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 = 235
Score = 29.4 bits (67), Expect = 1.1
Identities = 10/46 (21%), Positives = 27/46 (58%), Gaps = 1/46 (2%)
Query: 20 GVYNHYKRLFLLKSKNIYLEKSNIL-LVGPTGCGKTLMVKTLAKII 64
G+ + +LK ++ + + IL ++GP+G GK+ +++ + ++
Sbjct: 5 GLTKSFGGRTVLKGVDLDVRRGEILAIIGPSGSGKSTLLRLIVGLL 50
>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 = 1.1
Identities = 10/35 (28%), Positives = 16/35 (45%), Gaps = 1/35 (2%)
Query: 43 ILLVGPTGCGKT-LMVKTLAKIINVPIIVVDATSF 76
+LL G G GKT L L ++ ++ +D
Sbjct: 15 VLLGGQPGAGKTELARALLEELGGGNVVRIDPDEL 49
>gnl|CDD|162242 TIGR01187, potA, spermidine/putrescine ABC transporter
ATP-binding subunit. This model describes
spermidine/putrescine ABC transporter, ATP binding
subunit in bacteria and its equivalents in archaea.
This transport system belong to the larger ATP-Binding
Cassette (ABC) transporter superfamily. The
characteristic feature of these transporter is the
obligatory coupling of ATP hydrolysis to substrate
translocation. The minimal configuration of bacterial
ABC transport system: an ATPase or ATP binding subunit;
An integral membrane protein; a hydrophilic
polypetpide, which likely functions as substrate
binding protein. Polyamines like spermidine and
putrescine play vital role in cell proliferation,
differentiation, and ion homeostasis. The concentration
of polyamines within the cell are regulated by
biosynthesis, degradation and transport (uptake and
efflux included) [Transport and binding proteins, Amino
acids, peptides and amines].
Length = 325
Score = 29.8 bits (67), Expect = 1.2
Identities = 13/36 (36%), Positives = 20/36 (55%), Gaps = 2/36 (5%)
Query: 45 LVGPTGCGKTLMVKTLAKIINVPI--IVVDATSFTE 78
L+GP+GCGKT +++ LA I++D T
Sbjct: 1 LLGPSGCGKTTLLRLLAGFEQPDSGSIMLDGEDVTN 36
>gnl|CDD|224166 COG1245, COG1245, Predicted ATPase, RNase L inhibitor (RLI) homolog
[General function prediction only].
Length = 591
Score = 30.0 bits (68), Expect = 1.2
Identities = 13/38 (34%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 29 FLLKSKNIYLEKSNIL-LVGPTGCGKTLMVKTLAKIIN 65
F L+ + + ++ ++GP G GKT VK LA +I
Sbjct: 355 FKLEVEEGEIYDGEVIGILGPNGIGKTTFVKLLAGVIK 392
>gnl|CDD|182893 PRK11000, PRK11000, maltose/maltodextrin transporter ATP-binding
protein; Provisional.
Length = 369
Score = 29.6 bits (67), Expect = 1.2
Identities = 12/32 (37%), Positives = 22/32 (68%), Gaps = 3/32 (9%)
Query: 33 SKNIYLEKSN---ILLVGPTGCGKTLMVKTLA 61
SK+I L+ ++ VGP+GCGK+ +++ +A
Sbjct: 19 SKDINLDIHEGEFVVFVGPSGCGKSTLLRMIA 50
>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 = 29.8 bits (67), Expect = 1.2
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 42 NILLVGPTGCGKTLMVKTLAKII 64
N+LL GP G GKT++ L I+
Sbjct: 213 NLLLFGPPGSGKTMLASRLQGIL 235
>gnl|CDD|225369 COG2812, DnaX, DNA polymerase III, gamma/tau subunits [DNA
replication, recombination, and repair].
Length = 515
Score = 29.7 bits (67), Expect = 1.2
Identities = 33/128 (25%), Positives = 47/128 (36%), Gaps = 51/128 (39%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIIN------------------------VPIIVVDATSFTE 78
L GP G GKT + + LAK +N + +I +DA S T
Sbjct: 41 YLFSGPRGVGKTTIARILAKALNCENGPTAEPCGKCISCKEINEGSLIDVIEIDAASNT- 99
Query: 79 AGYVGDDVESIIQKLLH---ECDYDVELAEQSIIYIDEIDKISKKTDVVSGKDVSGEGVQ 135
DD+ II+K+ + E Y V IDE+ +SK
Sbjct: 100 ---GVDDIREIIEKVNYAPSEGRYKV-------YIIDEVHMLSK-------------QAF 136
Query: 136 QSLLKLIE 143
+LLK +E
Sbjct: 137 NALLKTLE 144
>gnl|CDD|214863 smart00859, Semialdhyde_dh, Semialdehyde dehydrogenase, NAD binding
domain. The semialdehyde dehydrogenase family is found
in N-acetyl-glutamine semialdehyde dehydrogenase (AgrC),
which is involved in arginine biosynthesis, and
aspartate-semialdehyde dehydrogenase, an enzyme involved
in the biosynthesis of various amino acids from
aspartate. This family is also found in yeast and fungal
Arg5,6 protein, which is cleaved into the enzymes
N-acety-gamma-glutamyl-phosphate reductase and
acetylglutamate kinase. These are also involved in
arginine biosynthesis. All proteins in this entry
contain a NAD binding region of semialdehyde
dehydrogenase.
Length = 123
Score = 28.7 bits (65), Expect = 1.3
Identities = 13/71 (18%), Positives = 29/71 (40%), Gaps = 4/71 (5%)
Query: 42 NILLVGPTGCGKTLMVKTLAKIINVPIIVVDATSFTEAGYVGDDVESIIQKLLHECDYDV 101
+ +VG TG +++ LA+ + + + A+S G V L E ++
Sbjct: 1 KVAIVGATGYVGQELLRLLAEHPDFELTALAASS----RSAGKKVSEAGPHLKGEVVLEL 56
Query: 102 ELAEQSIIYID 112
+ + + +D
Sbjct: 57 DPPDFEELAVD 67
>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 = 28.8 bits (65), Expect = 1.3
Identities = 9/31 (29%), Positives = 16/31 (51%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIINVPIIVVDA 73
IL+VG G GK+ + L + + ++ D
Sbjct: 2 ILMVGLPGSGKSTFARRLLRELGAVVLSSDT 32
>gnl|CDD|184934 PRK14970, PRK14970, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 367
Score = 29.5 bits (66), Expect = 1.3
Identities = 21/82 (25%), Positives = 34/82 (41%), Gaps = 4/82 (4%)
Query: 41 SNILLVGPTGCGKTLMVKTLAKIINVPIIVVDATSFT----EAGYVGDDVESIIQKLLHE 96
+L GP G GKT + LA+ IN P F+ E ++ I+ L+ +
Sbjct: 40 QALLFCGPRGVGKTTCARILARKINQPGYDDPNEDFSFNIFELDAASNNSVDDIRNLIDQ 99
Query: 97 CDYDVELAEQSIIYIDEIDKIS 118
+ + I IDE+ +S
Sbjct: 100 VRIPPQTGKYKIYIIDEVHMLS 121
>gnl|CDD|223703 COG0630, VirB11, Type IV secretory pathway, VirB11 components, and
related ATPases involved in archaeal flagella
biosynthesis [Cell motility and secretion /
Intracellular trafficking and secretion].
Length = 312
Score = 29.6 bits (67), Expect = 1.3
Identities = 10/38 (26%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 39 EKSNILLVGPTGCGKTLMVKTLAKIIN--VPIIVVDAT 74
+ +I++ G T GKT ++ L I I+ ++ T
Sbjct: 142 ARKSIIICGGTASGKTTLLNALLDFIPPEERIVTIEDT 179
>gnl|CDD|148114 pfam06309, Torsin, Torsin. This family consists of several
eukaryotic torsin proteins. Torsion dystonia is an
autosomal dominant movement disorder characterized by
involuntary, repetitive muscle contractions and twisted
postures. The most severe early-onset form of dystonia
has been linked to mutations in the human DYT1 (TOR1A)
gene encoding a protein termed torsinA. While causative
genetic alterations have been identified, the function
of torsin proteins and the molecular mechanism
underlying dystonia remain unknown. Phylogenetic
analysis of the torsin protein family indicates these
proteins share distant sequence similarity with the
large and diverse family of (pfam00004) proteins. It
has been suggested that torsins play a role in
effectively managing protein folding and that possible
breakdown in a neuroprotective mechanism that is, in
part, mediated by torsins may be responsible for the
neuronal dysfunction associated with dystonia.
Length = 127
Score = 28.5 bits (64), Expect = 1.4
Identities = 18/65 (27%), Positives = 25/65 (38%), Gaps = 15/65 (23%)
Query: 2 ELDRHIIGQHETKKIVSVGVYNHYKRLFLLKSKNIYLEKSNILLV----GPTGCGKTLMV 57
+L R + GQH K++V V H K LV G TG GK +
Sbjct: 22 DLARRLFGQHLVKQLVVRSVKGH-----------WENPKPRKPLVLSFHGWTGTGKNFVA 70
Query: 58 KTLAK 62
+ +A
Sbjct: 71 EIIAD 75
>gnl|CDD|237354 PRK13341, PRK13341, recombination factor protein RarA/unknown
domain fusion protein; Reviewed.
Length = 725
Score = 29.6 bits (67), Expect = 1.4
Identities = 12/24 (50%), Positives = 16/24 (66%), Gaps = 4/24 (16%)
Query: 41 SNILLVGPTGCGKTLMVKTLAKII 64
+++L GP G GKT TLA+II
Sbjct: 53 GSLILYGPPGVGKT----TLARII 72
>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 = 29.2 bits (66), Expect = 1.4
Identities = 9/13 (69%), Positives = 11/13 (84%)
Query: 42 NILLVGPTGCGKT 54
N+LL+GP G GKT
Sbjct: 49 NLLLLGPPGVGKT 61
>gnl|CDD|237866 PRK14952, PRK14952, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 584
Score = 29.5 bits (66), Expect = 1.4
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 44 LLVGPTGCGKTLMVKTLAKIIN 65
L GP GCGKT + LA+ +N
Sbjct: 39 LFSGPRGCGKTSSARILARSLN 60
>gnl|CDD|234478 TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA
ligase-associated. Members of this protein family are
DEAD/DEAH box helicases found associated with a
bacterial ATP-dependent DNA ligase, part of a four-gene
system that occurs in about 12 % of prokaryotic
reference genomes. The actual motif in this family is
DE[VILW]H.
Length = 803
Score = 29.4 bits (67), Expect = 1.5
Identities = 11/19 (57%), Positives = 13/19 (68%)
Query: 37 YLEKSNILLVGPTGCGKTL 55
LE + LL+ PTG GKTL
Sbjct: 25 ALEGRSGLLIAPTGSGKTL 43
>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 = 29.5 bits (67), Expect = 1.5
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 44 LLVGPTGCGKTLMVKTLA 61
L +GPTG GKT + K LA
Sbjct: 599 LFLGPTGVGKTELAKALA 616
Score = 28.0 bits (63), Expect = 5.3
Identities = 29/87 (33%), Positives = 48/87 (55%), Gaps = 17/87 (19%)
Query: 40 KSNILLVGPTGCGKTLMVKTLA-KIIN--VP-------IIVVDATSFTE-AGYVGDDVES 88
K+N +L+G G GKT +V+ LA +I+N VP ++ +D + A Y G + E
Sbjct: 194 KNNPVLIGEPGVGKTAIVEGLAQRIVNGDVPESLKNKRLLALDMGALIAGAKYRG-EFEE 252
Query: 89 IIQKLLHECDYDVELAEQSII-YIDEI 114
++ +L+E V +E II +IDE+
Sbjct: 253 RLKAVLNE----VTKSEGQIILFIDEL 275
>gnl|CDD|234034 TIGR02858, spore_III_AA, stage III sporulation protein AA. Members
of this protein are the stage III sporulation protein
AA, encoded by one of several genes in the spoIIIA
locus. It seems that this protein is found in a species
if and only if that species is capable of endospore
formation [Cellular processes, Sporulation and
germination].
Length = 270
Score = 29.2 bits (66), Expect = 1.5
Identities = 10/23 (43%), Positives = 17/23 (73%)
Query: 42 NILLVGPTGCGKTLMVKTLAKII 64
N L++ P CGKT +++ LA+I+
Sbjct: 113 NTLIISPPQCGKTTLLRDLARIL 135
>gnl|CDD|172743 PRK14255, PRK14255, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 252
Score = 29.2 bits (65), Expect = 1.5
Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 5/79 (6%)
Query: 12 ETKKIV-SVGVYNHYKRLFLLKSKNIYLEKSNIL-LVGPTGCGKTLMVKTLAKIINVPII 69
E KKI+ S V+ Y + LK ++ ++ I L+GP+GCGK+ ++TL ++ + +
Sbjct: 1 EAKKIITSSDVHLFYGKFEALKGIDLDFNQNEITALIGPSGCGKSTYLRTLNRMND---L 57
Query: 70 VVDATSFTEAGYVGDDVES 88
+ T G ++ +
Sbjct: 58 IPGVTITGNVSLRGQNIYA 76
>gnl|CDD|130254 TIGR01186, proV, glycine betaine/L-proline transport ATP binding
subunit. This model describes the glycine
betaine/L-proline ATP binding subunit in bacteria and
its equivalents in archaea. This transport system
belong to the larger ATP-Binding Cassette (ABC)
transporter superfamily. The characteristic feature of
these transporter is the obligatory coupling of ATP
hydrolysis to substrate translocation. The minimal
configuration of bacterial ABC transport system: an
ATPase or ATP binding subunit; An integral membrane
protein; a hydrophilic polypetpide, which likely
functions as substrate binding protein. Functionally,
this transport system is involved in osmoregulation.
Under conditions of stress, the organism recruits these
transport system to accumulate glycine betaine and
other solutes which offer osmo-protection. It has been
demonstrated that glycine betaine uptake is accompanied
by symport with sodium ions. The locus has been named
variously as proU or opuA. A gene library from L.lactis
functionally complements an E.coli proU mutant. The
comlementing locus is similar to a opuA locus in
B.sutlis. This clarifies the differences in
nomenclature [Transport and binding proteins, Amino
acids, peptides and amines].
Length = 363
Score = 29.4 bits (66), Expect = 1.6
Identities = 7/22 (31%), Positives = 15/22 (68%)
Query: 43 ILLVGPTGCGKTLMVKTLAKII 64
+++G +G GK+ V+ L ++I
Sbjct: 22 FVIMGLSGSGKSTTVRMLNRLI 43
>gnl|CDD|235904 PRK06995, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 484
Score = 29.5 bits (67), Expect = 1.6
Identities = 11/18 (61%), Positives = 12/18 (66%), Gaps = 3/18 (16%)
Query: 45 LVGPTGCGKTLMVKTLAK 62
L+GPTG GKT T AK
Sbjct: 261 LMGPTGVGKT---TTTAK 275
>gnl|CDD|183702 PRK12723, PRK12723, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 388
Score = 29.1 bits (65), Expect = 1.7
Identities = 18/44 (40%), Positives = 24/44 (54%), Gaps = 9/44 (20%)
Query: 38 LEKSNILLVGPTGCGKTLMVKTLAKI---------INVPIIVVD 72
L+K +LVGPTG GKT + LA I +N+ II +D
Sbjct: 172 LKKRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITID 215
>gnl|CDD|238005 cd00046, DEXDc, DEAD-like helicases superfamily. A diverse family
of proteins involved in ATP-dependent RNA or DNA
unwinding. This domain contains the ATP-binding region.
Length = 144
Score = 28.5 bits (64), Expect = 1.8
Identities = 11/36 (30%), Positives = 20/36 (55%), Gaps = 5/36 (13%)
Query: 41 SNILLVGPTGCGKTL-----MVKTLAKIINVPIIVV 71
++LL PTG GKTL +++ L + ++V+
Sbjct: 1 RDVLLAAPTGSGKTLAALLPILELLDSLKGGQVLVL 36
>gnl|CDD|223542 COG0466, Lon, ATP-dependent Lon protease, bacterial type
[Posttranslational modification, protein turnover,
chaperones].
Length = 782
Score = 29.1 bits (66), Expect = 1.9
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIIN 65
+ LVGP G GKT + K++AK +
Sbjct: 353 LCLVGPPGVGKTSLGKSIAKALG 375
>gnl|CDD|214396 CHL00206, ycf2, Ycf2; Provisional.
Length = 2281
Score = 29.5 bits (66), Expect = 1.9
Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 3/48 (6%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIINVPIIVVDATSFTE---AGYVGDDVE 87
IL++G G G++ +VK LA VP I V F + G++ DD++
Sbjct: 1633 ILVIGSIGTGRSYLVKYLATNSYVPFITVFLNKFLDNKPKGFLIDDID 1680
>gnl|CDD|206733 cd04170, EF-G_bact, Elongation factor G (EF-G) family.
Translocation is mediated by EF-G (also called
translocase). The structure of EF-G closely resembles
that of the complex between EF-Tu and tRNA. This is an
example of molecular mimicry; a protein domain evolved
so that it mimics the shape of a tRNA molecule. EF-G in
the GTP form binds to the ribosome, primarily through
the interaction of its EF-Tu-like domain with the 50S
subunit. The binding of EF-G to the ribosome in this
manner stimulates the GTPase activity of EF-G. On GTP
hydrolysis, EF-G undergoes a conformational change that
forces its arm deeper into the A site on the 30S
subunit. To accommodate this domain, the peptidyl-tRNA
in the A site moves to the P site, carrying the mRNA
and the deacylated tRNA with it. The ribosome may be
prepared for these rearrangements by the initial
binding of EF-G as well. The dissociation of EF-G
leaves the ribosome ready to accept the next
aminoacyl-tRNA into the A site. This group contains
only bacterial members.
Length = 268
Score = 28.7 bits (65), Expect = 2.0
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 42 NILLVGPTGCGKTLMVKTLA 61
NI LVG +G GKT + + L
Sbjct: 1 NIALVGHSGSGKTTLAEALL 20
>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 = 29.2 bits (66), Expect = 2.0
Identities = 25/84 (29%), Positives = 36/84 (42%), Gaps = 14/84 (16%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIINVPIIVVDATSFTEAG--------YVGDDVESIIQKLL 94
+ LVGP G GKT + K++AK +N + + YVG IIQ L
Sbjct: 350 LCLVGPPGVGKTSLGKSIAKALNRKFVRFSLGGVRDEAEIRGHRRTYVGAMPGRIIQG-L 408
Query: 95 HECDYDVELAEQSIIYIDEIDKIS 118
+ + + +DEIDKI
Sbjct: 409 KKAK-----TKNPLFLLDEIDKIG 427
>gnl|CDD|213189 cd03222, ABC_RNaseL_inhibitor, ATP-binding cassette domain of
RNase L inhibitor. The ABC ATPase RNase L inhibitor
(RLI) is a key enzyme in ribosomal biogenesis,
formation of translation preinitiation complexes, and
assembly of HIV capsids. RLI's are not transport
proteins, and thus cluster with a group of soluble
proteins that lack the transmembrane components
commonly found in other members of the family.
Structurally, RLI's have an N-terminal Fe-S domain and
two nucleotide-binding domains, which are arranged to
form two composite active sites in their interface
cleft. RLI is one of the most conserved enzymes between
archaea and eukaryotes with a sequence identity more
than 48%. The high degree of evolutionary conservation
suggests that RLI performs a central role in archaeal
and eukaryotic physiology.
Length = 177
Score = 28.7 bits (64), Expect = 2.0
Identities = 12/19 (63%), Positives = 13/19 (68%)
Query: 43 ILLVGPTGCGKTLMVKTLA 61
I +VGP G GKT VK LA
Sbjct: 28 IGIVGPNGTGKTTAVKILA 46
>gnl|CDD|173762 cd08222, STKc_Nek11, Catalytic domain of the Protein
Serine/Threonine Kinase, Never In Mitosis gene A-related
kinase 11. Serine/Threonine Kinases (STKs), Never In
Mitosis gene A (NIMA)-related kinase 11 (Nek11)
subfamily, catalytic (c) domain. STKs catalyze the
transfer of the gamma-phosphoryl group from ATP to
serine/threonine residues on protein substrates. The
Nek11 subfamily is one of a family of 11 different Neks
(Nek1-11) that are involved in cell cycle control. The
Nek family is part of a larger superfamily that includes
the catalytic domains of other protein STKs, protein
tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and phosphoinositide
3-kinase. Nek11 is involved, through direct
phosphorylation, in regulating the degradation of Cdc25A
(Cell Division Cycle 25 homolog A), which plays a role
in cell cycle progression and in activating cyclin
dependent kinases. Nek11 is activated by CHK1
(CHeckpoint Kinase 1) and may be involved in the G2/M
checkpoint. Nek11 may also play a role in the S-phase
checkpoint as well as in DNA replication and genotoxic
stress responses.
Length = 260
Score = 28.7 bits (64), Expect = 2.0
Identities = 16/37 (43%), Positives = 24/37 (64%), Gaps = 3/37 (8%)
Query: 22 YNHYKRLFL--LKSKNIYLEKSNILLVGPTGCGKTLM 56
Y H +R+ LK+KNI+L K+N+L +G G + LM
Sbjct: 121 YMHQRRILHRDLKAKNIFL-KNNLLKIGDFGVSRLLM 156
>gnl|CDD|184596 PRK14267, PRK14267, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 253
Score = 28.7 bits (64), Expect = 2.1
Identities = 12/52 (23%), Positives = 33/52 (63%), Gaps = 1/52 (1%)
Query: 16 IVSVGVYNHYKRLFLLKSKNIYLEKSNIL-LVGPTGCGKTLMVKTLAKIINV 66
I +V + +Y ++K ++ + ++ + L+GP+GCGK+ +++T +++ +
Sbjct: 5 IETVNLRVYYGSNHVIKGVDLKIPQNGVFALMGPSGCGKSTLLRTFNRLLEL 56
>gnl|CDD|233406 TIGR01420, pilT_fam, pilus retraction protein PilT. This model
represents the PilT subfamily of proteins related to
GspE, a protein involved in type II secretion (also
called the General Secretion Pathway). PilT is an
apparent cytosolic ATPase associated with type IV pilus
systems. It is not required for pilin biogenesis, but is
required for twitching motility and social gliding
behaviors, shown in some species, powered by pilus
retraction. Members of this family may be found in some
species that type IV pili but have related structures
for DNA uptake and natural transformation [Cell
envelope, Surface structures, Cellular processes,
Chemotaxis and motility].
Length = 343
Score = 28.8 bits (65), Expect = 2.1
Identities = 12/23 (52%), Positives = 16/23 (69%), Gaps = 3/23 (13%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIIN 65
IL+ GPTG GK+ TLA +I+
Sbjct: 125 ILVTGPTGSGKS---TTLASMID 144
>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 = 28.4 bits (64), Expect = 2.1
Identities = 7/19 (36%), Positives = 13/19 (68%)
Query: 43 ILLVGPTGCGKTLMVKTLA 61
++L G G GKT +++ +A
Sbjct: 3 VILQGEAGSGKTTLLQKIA 21
>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 = 28.5 bits (64), Expect = 2.1
Identities = 8/27 (29%), Positives = 13/27 (48%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIINVPII 69
+L+G G GK+ + LA + I
Sbjct: 1 FVLMGVAGSGKSTIASALAHRLGAKFI 27
>gnl|CDD|213197 cd03230, ABC_DR_subfamily_A, ATP-binding cassette domain of the
drug resistance transporter and related proteins,
subfamily A. This family of ATP-binding proteins
belongs to a multi-subunit transporter involved in drug
resistance (BcrA and DrrA), nodulation, lipid
transport, and lantibiotic immunity. In bacteria and
archaea, these transporters usually include an
ATP-binding protein and one or two integral membrane
proteins. Eukaryotic systems of the ABCA subfamily
display ABC domains that are quite similar to this
family. The ATP-binding domain shows the highest
similarity between all members of the ABC transporter
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 = 173
Score = 28.5 bits (65), Expect = 2.1
Identities = 13/42 (30%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 24 HYKRLFLLKSKNIYLEKSNIL-LVGPTGCGKTLMVKTLAKII 64
Y + L ++ +EK I L+GP G GKT ++K + ++
Sbjct: 9 RYGKKTALDDISLTVEKGEIYGLLGPNGAGKTTLIKIILGLL 50
>gnl|CDD|213204 cd03237, ABC_RNaseL_inhibitor_domain2, The ATP-binding cassette
domain 2 of RNase L inhibitor. The ABC ATPase, RNase L
inhibitor (RLI), is a key enzyme in ribosomal
biogenesis, formation of translation preinitiation
complexes, and assembly of HIV capsids. RLI's are not
transport proteins and thus cluster with a group of
soluble proteins that lack the transmembrane components
commonly found in other members of the family.
Structurally, RLI's have an N-terminal Fe-S domain and
two nucleotide-binding domains which are arranged to
form two composite active sites in their interface
cleft. RLI is one of the most conserved enzymes between
archaea and eukaryotes with a sequence identity of more
than 48%. The high degree of evolutionary conservation
suggests that RLI performs a central role in archaeal
and eukaryotic physiology.
Length = 246
Score = 28.9 bits (65), Expect = 2.1
Identities = 18/58 (31%), Positives = 29/58 (50%), Gaps = 5/58 (8%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIINV----PIIVVDATSFTEAGYVGDDVESIIQKLLHE 96
I ++GP G GKT +K LA ++ I +D S+ + Y+ D E ++ LL
Sbjct: 28 IGILGPNGIGKTTFIKMLAGVLKPDEGDIEIELDTVSY-KPQYIKADYEGTVRDLLSS 84
>gnl|CDD|238927 cd01965, Nitrogenase_MoFe_beta_like, Nitrogenase_MoFe_beta_like:
Nitrogenase MoFe protein, beta subunit_like. The
nitrogenase enzyme catalyzes the ATP-dependent reduction
of dinitrogen (N2) to ammonia. This group contains the
beta subunits of component 1 of the three known
genetically distinct types of nitrogenase systems: a
molybdenum-dependent nitrogenase (Mo-nitrogenase), a
vanadium-dependent nitrogenase (V-nitrogenase), and an
iron-only nitrogenase (Fe-nitrogenase). These
nitrogenase systems consist of component 1 (MoFe
protein, VFe protein or, FeFe protein respectively) and,
component 2 (Fe protein). The most widespread and best
characterized of these systems is the Mo-nitrogenase.
MoFe is an alpha2beta2 tetramer, the alternative
nitrogenases are alpha2beta2delta2 hexamers having
alpha and beta subunits similar to the alpha and beta
subunits of MoFe. For MoFe, each alphabeta pair contains
one P-cluster (at the alphabeta interface) and, one
molecule of iron molybdenum cofactor (FeMoco) contained
within the alpha subunit. The Fe protein contains, a
single [4Fe-4S] cluster from which electrons are
transferred to the P-cluster of the MoFe and in turn,
to FeMoCo, the site of substrate reduction. The
V-nitrogenase requires an iron-vanadium cofactor
(FeVco), the iron only-nitrogenase an iron only cofactor
(FeFeco). These cofactors are analogous to the FeMoco.
The V-nitrogenase has P clusters identical to those of
MoFe. In addition to N2, nitrogenase also catalyzes the
reduction of a variety of other substrates such as
acetylene The V-nitrogenase differs from the
Mo-nitrogenase in that it produces free hydrazine, as a
minor product during N2-reduction and, ethane as a minor
product during acetylene reduction.
Length = 428
Score = 29.1 bits (66), Expect = 2.2
Identities = 12/37 (32%), Positives = 17/37 (45%), Gaps = 2/37 (5%)
Query: 57 VKTLAKIINVPIIVVDATSFTEAGYVGDDVESIIQKL 93
+K L +I V T TE +GDDV I++
Sbjct: 73 LKNLLSRYKPDVIGVLTTCLTET--IGDDVAGFIKEF 107
>gnl|CDD|236461 PRK09302, PRK09302, circadian clock protein KaiC; Reviewed.
Length = 509
Score = 29.1 bits (66), Expect = 2.3
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 41 SNILLVGPTGCGKTLMV 57
S IL+ G TG GKTL+
Sbjct: 274 SIILVSGATGTGKTLLA 290
>gnl|CDD|173763 cd08223, STKc_Nek4, Catalytic domain of the Protein
Serine/Threonine Kinase, Never In Mitosis gene A-related
kinase 4. Serine/Threonine Kinases (STKs), Never In
Mitosis gene A (NIMA)-related kinase 4 (Nek4) subfamily,
catalytic (c) domain. STKs catalyze the transfer of the
gamma-phosphoryl group from ATP to serine/threonine
residues on protein substrates. The Nek4 subfamily is
one of a family of 11 different Neks (Nek1-11). The Nek
family is part of a larger superfamily that includes the
catalytic domains of other protein STKs, protein
tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and phosphoinositide
3-kinase. Neks are involved in the regulation of
downstream processes following the activation of Cdc2,
and many of their functions are cell cycle-related. They
play critical roles in microtubule dynamics during
ciliogenesis and mitosis. Nek4 is highly abundant in the
testis. Its specific function is unknown.
Length = 257
Score = 28.8 bits (64), Expect = 2.3
Identities = 13/35 (37%), Positives = 21/35 (60%), Gaps = 5/35 (14%)
Query: 31 LKSKNIYLEKSNILLVGPTGCGKTL-----MVKTL 60
LK++N++L ++NI+ VG G + L M TL
Sbjct: 128 LKTQNVFLTRTNIIKVGDLGIARVLENQCDMASTL 162
>gnl|CDD|217025 pfam02421, FeoB_N, Ferrous iron transport protein B. Escherichia
coli has an iron(II) transport system (feo) which may
make an important contribution to the iron supply of the
cell under anaerobic conditions. FeoB has been
identified as part of this transport system. FeoB is a
large 700-800 amino acid integral membrane protein. The
N terminus contains a P-loop motif suggesting that iron
transport may be ATP dependent.
Length = 190
Score = 28.2 bits (64), Expect = 2.4
Identities = 12/60 (20%), Positives = 28/60 (46%), Gaps = 7/60 (11%)
Query: 57 VKTLAKIINVPIIVVDATSFTEAGYVGDDVESIIQKLLHECDYDVELAEQSIIYIDEIDK 116
+K L++++ VP++ A G+ ++ + ++ + V A I Y EI++
Sbjct: 127 IKKLSELLGVPVVPTSARK-------GEGIDELKDAIIEVAEGKVPPAPLRINYGPEIEE 179
>gnl|CDD|184594 PRK14264, PRK14264, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 305
Score = 28.6 bits (64), Expect = 2.4
Identities = 11/25 (44%), Positives = 18/25 (72%)
Query: 39 EKSNILLVGPTGCGKTLMVKTLAKI 63
EKS L+GP+GCGK+ ++ L ++
Sbjct: 70 EKSVTALIGPSGCGKSTFLRCLNRM 94
>gnl|CDD|238991 cd02034, CooC, The accessory protein CooC, which contains a
nucleotide-binding domain (P-loop) near the N-terminus,
participates in the maturation of the nickel center of
carbon monoxide dehydrogenase (CODH). CODH from
Rhodospirillum rubrum catalyzes the reversible
oxidation of CO to CO2. CODH contains a
nickel-iron-sulfur cluster (C-center) and an
iron-sulfur cluster (B-center). CO oxidation occurs at
the C-center. Three accessory proteins encoded by
cooCTJ genes are involved in nickel incorporation into
a nickel site. CooC functions as a nickel insertase
that mobilizes nickel to apoCODH using energy released
from ATP hydrolysis. CooC is a homodimer and has NTPase
activities. Mutation at the P-loop abolishs its
function.
Length = 116
Score = 27.6 bits (62), Expect = 2.4
Identities = 14/58 (24%), Positives = 25/58 (43%), Gaps = 14/58 (24%)
Query: 42 NILLVGPTGCGKTLMVKTLAKII---NVPIIVVDATSFTEAGYVGDDVESIIQKLLHE 96
I + G G GKT + LA+ + P++ +DA D + + ++L E
Sbjct: 1 KIAITGKGGVGKTTIAALLARYLAEKGKPVLAIDA-----------DPDDLPERLSVE 47
>gnl|CDD|233206 TIGR00954, 3a01203, Peroxysomal Fatty Acyl CoA Transporter (FAT)
Family protei. [Transport and binding proteins,
Carbohydrates, organic alcohols, and acids].
Length = 659
Score = 28.9 bits (65), Expect = 2.4
Identities = 9/23 (39%), Positives = 17/23 (73%)
Query: 41 SNILLVGPTGCGKTLMVKTLAKI 63
+N+L+ GP GCGK+ + + L ++
Sbjct: 479 NNLLICGPNGCGKSSLFRILGEL 501
>gnl|CDD|206737 cd04174, Rnd1_Rho6, Rnd1/Rho6 GTPases. Rnd1/Rho6 is a member of
the novel Rho subfamily Rnd, together with Rnd2/Rho7
and Rnd3/RhoE/Rho8. Rnd1/Rho6 binds GTP but does not
hydrolyze it to GDP, indicating that it is
constitutively active. In rat, Rnd1/Rho6 is highly
expressed in the cerebral cortex and hippocampus during
synapse formation, and plays a role in spine formation.
Rnd1/Rho6 is also expressed in the liver and in
endothelial cells, and is upregulated in uterine
myometrial cells during pregnancy. Like Rnd3/RhoE/Rho8,
Rnd1/Rho6 is believed to function as an antagonist to
RhoA. Most Rho proteins contain a lipid modification
site at the C-terminus, with a typical sequence motif
CaaX, where a = an aliphatic amino acid and X = any
amino acid. Lipid binding is essential for membrane
attachment, a key feature of most Rho proteins. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for
annotation.
Length = 232
Score = 28.5 bits (63), Expect = 2.4
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 40 KSNILLVGPTGCGKTLMVKTLAK 62
+ ++LVG CGKT M++ LAK
Sbjct: 13 RCKLVLVGDVQCGKTAMLQVLAK 35
>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 = 29.0 bits (65), Expect = 2.5
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 43 ILLVGPTGCGKTLMVKTLAKI 63
+L GP G GKT + + +AKI
Sbjct: 315 MLFAGPPGTGKTTIARVVAKI 335
>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 = 29.0 bits (65), Expect = 2.5
Identities = 15/58 (25%), Positives = 27/58 (46%), Gaps = 16/58 (27%)
Query: 7 IIGQHETKKIVSVGVYNHYKRLFLLKSKNIYLEKSNILLVGPTGCGKTLMVKTLAKII 64
+IGQ E +I+ K N+LL+G G GK+++ K +A+++
Sbjct: 20 VIGQEEAVEIIKKAAKQ----------------KRNVLLIGEPGVGKSMLAKAMAELL 61
>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 = 2.5
Identities = 9/28 (32%), Positives = 12/28 (42%)
Query: 34 KNIYLEKSNILLVGPTGCGKTLMVKTLA 61
K + LL G G GK+ + LA
Sbjct: 27 KGLLPRGGLTLLAGAPGTGKSTLALDLA 54
>gnl|CDD|183088 PRK11331, PRK11331, 5-methylcytosine-specific restriction enzyme
subunit McrB; Provisional.
Length = 459
Score = 28.9 bits (64), Expect = 2.6
Identities = 12/25 (48%), Positives = 17/25 (68%)
Query: 40 KSNILLVGPTGCGKTLMVKTLAKII 64
K NI+L GP G GKT + + LA ++
Sbjct: 194 KKNIILQGPPGVGKTFVARRLAYLL 218
>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 = 28.5 bits (64), Expect = 2.6
Identities = 8/19 (42%), Positives = 15/19 (78%)
Query: 43 ILLVGPTGCGKTLMVKTLA 61
+ L+GP+G GKT +++ +A
Sbjct: 31 VALLGPSGSGKTTLLRLIA 49
>gnl|CDD|182120 PRK09862, PRK09862, putative ATP-dependent protease; Provisional.
Length = 506
Score = 28.8 bits (64), Expect = 2.7
Identities = 9/23 (39%), Positives = 16/23 (69%)
Query: 42 NILLVGPTGCGKTLMVKTLAKII 64
N+LL+GP G GKT++ + ++
Sbjct: 212 NLLLIGPPGTGKTMLASRINGLL 234
>gnl|CDD|225114 COG2204, AtoC, Response regulator containing CheY-like receiver,
AAA-type ATPase, and DNA-binding domains [Signal
transduction mechanisms].
Length = 464
Score = 28.8 bits (65), Expect = 2.8
Identities = 17/88 (19%), Positives = 33/88 (37%), Gaps = 22/88 (25%)
Query: 41 SNILLVGPTGCGKTLMVKTL---AKIINVPIIVVDATSFT-----------EAGYVGDDV 86
+++L+ G +G GK L+ + + + P I V+ + E G +
Sbjct: 165 ASVLITGESGTGKELVARAIHQASPRAKGPFIAVNCAAIPENLLESELFGHEKGAFTGAI 224
Query: 87 ESIIQKLLHECDYDVELAEQSIIYIDEI 114
I + E A +++DEI
Sbjct: 225 TRRIGRF--------EQANGGTLFLDEI 244
>gnl|CDD|238551 cd01131, PilT, Pilus retraction ATPase PilT. PilT is a nucleotide
binding protein responsible for the retraction of type
IV pili, likely by pili disassembly. This retraction
provides the force required for travel of bacteria in
low water environments by a mechanism known as
twitching motility.
Length = 198
Score = 28.1 bits (63), Expect = 2.8
Identities = 11/23 (47%), Positives = 16/23 (69%), Gaps = 3/23 (13%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIIN 65
+L+ GPTG GK+ TLA +I+
Sbjct: 4 VLVTGPTGSGKS---TTLAAMID 23
>gnl|CDD|234751 PRK00411, cdc6, cell division control protein 6; Reviewed.
Length = 394
Score = 28.7 bits (65), Expect = 2.8
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 41 SNILLVGPTGCGKTLMVKTL 60
N+L+ GP G GKT VK +
Sbjct: 56 LNVLIYGPPGTGKTTTVKKV 75
>gnl|CDD|181681 PRK09183, PRK09183, transposase/IS protein; Provisional.
Length = 259
Score = 28.5 bits (64), Expect = 2.9
Identities = 9/13 (69%), Positives = 12/13 (92%)
Query: 42 NILLVGPTGCGKT 54
NI+L+GP+G GKT
Sbjct: 104 NIVLLGPSGVGKT 116
>gnl|CDD|226997 COG4650, RtcR, Sigma54-dependent transcription regulator containing
an AAA-type ATPase domain and a DNA-binding domain
[Transcription / Signal transduction mechanisms].
Length = 531
Score = 28.7 bits (64), Expect = 2.9
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 40 KSNILLVGPTGCGKTLMVK 58
++ ILL GPTG GK+ + +
Sbjct: 208 RAPILLNGPTGAGKSFLAR 226
>gnl|CDD|203290 pfam05621, TniB, Bacterial TniB protein. This family consists of
several bacterial TniB NTP-binding proteins. TniB is a
probable ATP-binding protein which is involved in Tn5053
mercury resistance transposition.
Length = 302
Score = 28.5 bits (63), Expect = 2.9
Identities = 15/43 (34%), Positives = 24/43 (55%), Gaps = 9/43 (20%)
Query: 42 NILLVGPTGCGKTLMVKTL---------AKIINVPIIVVDATS 75
N+LLVGPT GK+++V+ A ++P++VV S
Sbjct: 63 NLLLVGPTNNGKSMIVEKFRRAHPAGSDADQEHIPVLVVQMPS 105
>gnl|CDD|215758 pfam00158, Sigma54_activat, Sigma-54 interaction domain.
Length = 168
Score = 28.1 bits (64), Expect = 3.0
Identities = 8/24 (33%), Positives = 13/24 (54%), Gaps = 4/24 (16%)
Query: 41 SNILLVGPTGCGKTLMVKTLAKII 64
+ +L+ G +G GK L A+ I
Sbjct: 23 ATVLITGESGTGKEL----FARAI 42
>gnl|CDD|238547 cd01127, TrwB, Bacterial conjugation protein TrwB, ATP binding
domain. TrwB is a homohexamer encoded by conjugative
plasmids in Gram-negative bacteria. TrwB also has an
all alpha domain which has been hypothesized to be
responsible for DNA binding. TrwB is a component of
Type IV secretion and is responsible for the horizontal
transfer of DNA between bacteria.
Length = 410
Score = 28.5 bits (64), Expect = 3.0
Identities = 13/49 (26%), Positives = 22/49 (44%), Gaps = 4/49 (8%)
Query: 37 YLEKSNILLVGPTGCGKTLMVKTLAKII---NVPIIVVDAT-SFTEAGY 81
E+++ +++G TG GKT ++ L I I+ D F Y
Sbjct: 39 DAEEAHTMIIGTTGTGKTTQIRELLASIRARGDRAIIYDPNGGFVSKFY 87
>gnl|CDD|226124 COG3596, COG3596, Predicted GTPase [General function prediction
only].
Length = 296
Score = 28.2 bits (63), Expect = 3.0
Identities = 11/37 (29%), Positives = 19/37 (51%)
Query: 39 EKSNILLVGPTGCGKTLMVKTLAKIINVPIIVVDATS 75
E N+LL+G TG GK+ ++ L + + V +
Sbjct: 38 EPVNVLLMGATGAGKSSLINALFQGEVKEVSKVGVGT 74
>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 = 28.3 bits (63), Expect = 3.2
Identities = 18/68 (26%), Positives = 27/68 (39%), Gaps = 8/68 (11%)
Query: 45 LVGPTGCGKTLMVKTLAKIINVPIIVVDATSFTEAGYVGDDVESIIQKLLHECDYDVELA 104
++G GK+ +V LA + N A + E GD+ L DY ++A
Sbjct: 167 ILGGESTGKSTLVNKLAAVFNTTSAWEYAREYVEEKLGGDEA-------LQYSDYA-QIA 218
Query: 105 EQSIIYID 112
YID
Sbjct: 219 LGQQRYID 226
>gnl|CDD|237536 PRK13873, PRK13873, conjugal transfer ATPase TrbE; Provisional.
Length = 811
Score = 28.7 bits (65), Expect = 3.2
Identities = 9/18 (50%), Positives = 15/18 (83%)
Query: 44 LLVGPTGCGKTLMVKTLA 61
L+VGPTG GK++++ +A
Sbjct: 445 LVVGPTGAGKSVLLALMA 462
>gnl|CDD|226967 COG4608, AppF, ABC-type oligopeptide transport system, ATPase
component [Amino acid transport and metabolism].
Length = 268
Score = 28.3 bits (64), Expect = 3.4
Identities = 10/20 (50%), Positives = 14/20 (70%), Gaps = 4/20 (20%)
Query: 45 LVGPTGCGKTLMVKTLAKII 64
LVG +GCGK+ TL ++I
Sbjct: 44 LVGESGCGKS----TLGRLI 59
>gnl|CDD|151168 pfam10662, PduV-EutP, Ethanolamine utilisation - propanediol
utilisation. Members of this family function in
ethanolamine and propanediol degradation pathways,
however the exact roles of these proteins is poorly
understood.
Length = 143
Score = 27.6 bits (62), Expect = 3.6
Identities = 11/25 (44%), Positives = 16/25 (64%), Gaps = 4/25 (16%)
Query: 41 SNILLVGPTGCGKTLMVKTLAKIIN 65
I+L+G +GCGKT TL + +N
Sbjct: 2 KKIMLIGRSGCGKT----TLTQALN 22
>gnl|CDD|234015 TIGR02788, VirB11, P-type DNA transfer ATPase VirB11. The VirB11
protein is found in the vir locus of Agrobacterium Ti
plasmids where it is involved in the type IV secretion
system for DNA transfer. VirB11 is believed to be an
ATPase. VirB11 is a homolog of the P-like conjugation
system TrbB protein and the Flp pilus sytem protein
TadA.
Length = 308
Score = 28.1 bits (63), Expect = 3.6
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 38 LEKSNILLVGPTGCGKTLMVKTLAKII 64
+ NI++ G TG GKT +K+L I
Sbjct: 142 ASRKNIIISGGTGSGKTTFLKSLVDEI 168
>gnl|CDD|219856 pfam08477, Miro, Miro-like protein. Mitochondrial Rho proteins
(Miro-1, and Miro-2), are atypical Rho GTPases. They
have a unique domain organisation, with tandem
GTP-binding domains and two EF hand domains (pfam00036),
that may bind calcium. They are also larger than
classical small GTPases. It has been proposed that they
are involved in mitochondrial homeostasis and apoptosis.
Length = 116
Score = 27.0 bits (60), Expect = 3.7
Identities = 14/84 (16%), Positives = 26/84 (30%), Gaps = 10/84 (11%)
Query: 42 NILLVGPTGCGKTLMVKTLAKIINVPIIVVDATSFTEAGYVGDDVESIIQK-LLHECDYD 100
++++G G GK+ ++ L P + D +E LL+ D+
Sbjct: 1 KVVVIGDKGSGKSSLLSQLVGGEFPPEPLE----IQGDTLAVDTLEVDGDTGLLNIWDF- 55
Query: 101 VELAEQSIIYIDEIDKISKKTDVV 124
E K D +
Sbjct: 56 ----GGREELKFEHIIFMKWADAI 75
>gnl|CDD|206703 cd04131, Rnd, Rho family GTPase subfamily Rnd includes Rnd1/Rho6,
Rnd2/Rho7, and Rnd3/RhoE/Rho8. The Rnd subfamily
contains Rnd1/Rho6, Rnd2/Rho7, and Rnd3/RhoE/Rho8.
These novel Rho family proteins have substantial
structural differences compared to other Rho members,
including N- and C-terminal extensions relative to
other Rhos. Rnd3/RhoE is farnesylated at the C-terminal
prenylation site, unlike most other Rho proteins that
are geranylgeranylated. In addition, Rnd members are
unable to hydrolyze GTP and are resistant to GAP
activity. They are believed to exist only in the
GTP-bound conformation, and are antagonists of RhoA
activity. Most Rho proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Rho
proteins. Due to the presence of truncated sequences in
this CD, the lipid modification site is not available
for annotation.
Length = 176
Score = 27.8 bits (62), Expect = 3.8
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 43 ILLVGPTGCGKTLMVKTLAK 62
I+LVG + CGKT +++ AK
Sbjct: 4 IVLVGDSQCGKTALLQVFAK 23
>gnl|CDD|184377 PRK13894, PRK13894, conjugal transfer ATPase TrbB; Provisional.
Length = 319
Score = 28.2 bits (63), Expect = 3.9
Identities = 13/32 (40%), Positives = 16/32 (50%), Gaps = 3/32 (9%)
Query: 34 KNIYLEKSNILLVGPTGCGKTLMVKTLAKIIN 65
NIL++G TG GKT +V IIN
Sbjct: 142 IAAVRAHRNILVIGGTGSGKTTLVNA---IIN 170
>gnl|CDD|224557 COG1643, HrpA, HrpA-like helicases [DNA replication, recombination,
and repair].
Length = 845
Score = 28.4 bits (64), Expect = 3.9
Identities = 27/111 (24%), Positives = 41/111 (36%), Gaps = 37/111 (33%)
Query: 38 LEKSNIL-LVGPTGCGKTLMVKT--LAKI--INVPIIVVD-----ATS--------FTEA 79
+E++ ++ +VG TG GKT + L + I I A S E
Sbjct: 62 IEQNQVVIIVGETGSGKTTQLPQFLLEEGLGIAGKIGCTQPRRLAARSVAERVAEELGEK 121
Query: 80 GYVGDDV------ESIIQK-----------LLHECDYDVELAEQSIIYIDE 113
+G+ V ES + LL E D L+ S++ IDE
Sbjct: 122 --LGETVGYSIRFESKVSPRTRIKVMTDGILLREIQNDPLLSGYSVVIIDE 170
>gnl|CDD|163508 TIGR03796, NHLM_micro_ABC1, NHLM bacteriocin system ABC
transporter, peptidase/ATP-binding protein. This
protein describes a multidomain ABC transporter subunit
that is one of three protein families associated with
some regularity with a distinctive family of putative
bacteriocins. It includes a bacteriocin-processing
peptidase domain at the N-terminus. Model TIGR03793
describes a conserved propeptide region for this
bacteriocin family, unusual because it shows obvious
homology a region of the enzyme nitrile hydratase up to
the classic Gly-Gly cleavage motif. This family is
therefore predicted to be a subunit of a bacteriocin
processing and export system characteristic to this
system that we designate NHLM, Nitrile Hydratase Leader
Microcin [Transport and binding proteins, Amino acids,
peptides and amines, Cellular processes, Biosynthesis of
natural products].
Length = 710
Score = 28.4 bits (64), Expect = 3.9
Identities = 9/24 (37%), Positives = 15/24 (62%), Gaps = 4/24 (16%)
Query: 41 SNILLVGPTGCGKTLMVKTLAKII 64
+ LVG +G GK+ T+AK++
Sbjct: 506 QRVALVGGSGSGKS----TIAKLV 525
>gnl|CDD|182692 PRK10744, pstB, phosphate transporter ATP-binding protein;
Provisional.
Length = 260
Score = 28.1 bits (63), Expect = 3.9
Identities = 13/45 (28%), Positives = 23/45 (51%), Gaps = 8/45 (17%)
Query: 22 YNHYKRLFLLKSKNIYL---EKSNILLVGPTGCGKTLMVKTLAKI 63
Y + L KNI L + +GP+GCGK+ +++T ++
Sbjct: 23 YGKFHAL-----KNINLDIAKNQVTAFIGPSGCGKSTLLRTFNRM 62
>gnl|CDD|132302 TIGR03258, PhnT, 2-aminoethylphosphonate ABC transport system,
ATP-binding component PhnT. This ATP-binding component
of an ABC transport system is found in Salmonella and
Burkholderia lineages in the vicinity of enzymes for
the breakdown of 2-aminoethylphosphonate.
Length = 362
Score = 28.0 bits (62), Expect = 3.9
Identities = 11/36 (30%), Positives = 23/36 (63%), Gaps = 1/36 (2%)
Query: 30 LLKSKNIYLEKSNIL-LVGPTGCGKTLMVKTLAKII 64
+L ++ +E +L L+G +GCGKT +++ +A +
Sbjct: 20 VLDDLSLEIEAGELLALIGKSGCGKTTLLRAIAGFV 55
>gnl|CDD|233821 TIGR02322, phosphon_PhnN, phosphonate metabolism
protein/1,5-bisphosphokinase (PRPP-forming) PhnN.
Members of this family resemble PhnN of phosphonate
utilization operons, where different such operons
confer the ability to use somewhat different profiles
of C-P bond-containing compounds (see PMID:15231805),
including phosphites as well as phosphonates. PhnN in
E. coli shows considerable homology to guanylate
kinases (EC 2.7.4.8), and has actually been shown to
act as a ribose 1,5-bisphosphokinase (PRPP forming).
This suggests an analogous kinase reaction for
phosphonate metabolism, converting
5-phosphoalpha-1-(methylphosphono)ribose to
methylphosphono-PRPP [Central intermediary metabolism,
Phosphorus compounds].
Length = 179
Score = 27.7 bits (62), Expect = 4.0
Identities = 11/30 (36%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 43 ILLVGPTGCGK-TLMVKTLAKIINVPIIVV 71
I +VGP+G GK TL+ A++ P +
Sbjct: 4 IYVVGPSGAGKDTLLDYARARLAGDPRVHF 33
>gnl|CDD|134335 PRK00625, PRK00625, shikimate kinase; Provisional.
Length = 173
Score = 27.4 bits (61), Expect = 4.2
Identities = 12/31 (38%), Positives = 15/31 (48%)
Query: 42 NILLVGPTGCGKTLMVKTLAKIINVPIIVVD 72
I L G GKT K LAK +++P D
Sbjct: 2 QIFLCGLPTVGKTSFGKALAKFLSLPFFDTD 32
>gnl|CDD|172741 PRK14253, PRK14253, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 249
Score = 27.9 bits (62), Expect = 4.2
Identities = 8/19 (42%), Positives = 16/19 (84%)
Query: 45 LVGPTGCGKTLMVKTLAKI 63
L+GP+GCGK+ +++ L ++
Sbjct: 34 LIGPSGCGKSTLLRCLNRM 52
>gnl|CDD|237498 PRK13768, PRK13768, GTPase; Provisional.
Length = 253
Score = 27.9 bits (63), Expect = 4.3
Identities = 7/24 (29%), Positives = 11/24 (45%)
Query: 39 EKSNILLVGPTGCGKTLMVKTLAK 62
+ +G G GKT + K L+
Sbjct: 1 MMYIVFFLGTAGSGKTTLTKALSD 24
>gnl|CDD|236144 PRK08057, PRK08057, cobalt-precorrin-6x reductase; Reviewed.
Length = 248
Score = 27.9 bits (63), Expect = 4.3
Identities = 9/43 (20%), Positives = 19/43 (44%), Gaps = 5/43 (11%)
Query: 59 TLAKII-----NVPIIVVDATSFTEAGYVGDDVESIIQKLLHE 96
T AK+ +P++++ + A +DV ++ L H
Sbjct: 204 TEAKLEAARELGIPVVMIARPALPYADREFEDVAELVAWLRHL 246
>gnl|CDD|172761 PRK14273, PRK14273, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 254
Score = 27.7 bits (61), Expect = 4.5
Identities = 15/40 (37%), Positives = 26/40 (65%), Gaps = 1/40 (2%)
Query: 25 YKRLFLLKSKNIYLEKSNIL-LVGPTGCGKTLMVKTLAKI 63
Y L + NI + K++I L+GP+GCGK+ ++TL ++
Sbjct: 17 YTDFKALNNINIKILKNSITALIGPSGCGKSTFLRTLNRM 56
>gnl|CDD|224027 COG1102, Cmk, Cytidylate kinase [Nucleotide transport and
metabolism].
Length = 179
Score = 27.3 bits (61), Expect = 4.6
Identities = 8/27 (29%), Positives = 16/27 (59%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIINVPII 69
I + G G GKT + + LA+ + + ++
Sbjct: 3 ITISGLPGSGKTTVARELAEHLGLKLV 29
>gnl|CDD|225713 COG3172, NadR, Predicted ATPase/kinase involved in NAD metabolism
[Coenzyme metabolism].
Length = 187
Score = 27.4 bits (61), Expect = 4.6
Identities = 16/70 (22%), Positives = 25/70 (35%), Gaps = 8/70 (11%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIINVPIIVVDATSFTEAGYVGDDVESIIQKLLHECDYDVE 102
+ ++G GK+ +V LA I N + GD+ L DY +
Sbjct: 11 VAILGGESSGKSTLVNKLANIFNTTSAWEYGREYVFEHLGGDEA-------LQYSDYA-K 62
Query: 103 LAEQSIIYID 112
+A Y D
Sbjct: 63 IALGQAAYED 72
>gnl|CDD|183056 PRK11248, tauB, taurine transporter ATP-binding subunit;
Provisional.
Length = 255
Score = 27.7 bits (62), Expect = 4.7
Identities = 14/32 (43%), Positives = 22/32 (68%), Gaps = 1/32 (3%)
Query: 31 LKSKNIYLEKSNILLV-GPTGCGKTLMVKTLA 61
L+ N+ LE +L+V GP+GCGKT ++ +A
Sbjct: 17 LEDINLTLESGELLVVLGPSGCGKTTLLNLIA 48
>gnl|CDD|182912 PRK11028, PRK11028, 6-phosphogluconolactonase; Provisional.
Length = 330
Score = 27.6 bits (62), Expect = 4.7
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 2/41 (4%)
Query: 162 PQVFNIDTTNILFIAGGAFSGIENFIINRINQETNFLEKLN 202
P+ FNID + IA G S + + I+ ET L +L
Sbjct: 276 PRGFNIDHSGKYLIAAGQKSH--HISVYEIDGETGLLTELG 314
>gnl|CDD|223562 COG0488, Uup, ATPase components of ABC transporters with
duplicated ATPase domains [General function prediction
only].
Length = 530
Score = 28.0 bits (63), Expect = 4.8
Identities = 10/20 (50%), Positives = 12/20 (60%), Gaps = 4/20 (20%)
Query: 45 LVGPTGCGKTLMVKTLAKII 64
LVG G GK+ TL KI+
Sbjct: 34 LVGRNGAGKS----TLLKIL 49
>gnl|CDD|182331 PRK10247, PRK10247, putative ABC transporter ATP-binding protein
YbbL; Provisional.
Length = 225
Score = 27.4 bits (61), Expect = 5.0
Identities = 10/21 (47%), Positives = 17/21 (80%)
Query: 44 LLVGPTGCGKTLMVKTLAKII 64
L+ GP+GCGK+ ++K +A +I
Sbjct: 37 LITGPSGCGKSTLLKIVASLI 57
>gnl|CDD|184411 PRK13946, PRK13946, shikimate kinase; Provisional.
Length = 184
Score = 27.2 bits (61), Expect = 5.1
Identities = 11/32 (34%), Positives = 20/32 (62%)
Query: 38 LEKSNILLVGPTGCGKTLMVKTLAKIINVPII 69
L K ++LVG G GK+ + + LA ++ +P +
Sbjct: 8 LGKRTVVLVGLMGAGKSTVGRRLATMLGLPFL 39
>gnl|CDD|223637 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide
transport and metabolism].
Length = 178
Score = 27.2 bits (61), Expect = 5.2
Identities = 12/26 (46%), Positives = 18/26 (69%)
Query: 42 NILLVGPTGCGKTLMVKTLAKIINVP 67
IL++GP G GK+ + K LAK + +P
Sbjct: 2 RILILGPPGAGKSTLAKKLAKKLGLP 27
>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 = 27.2 bits (61), Expect = 5.2
Identities = 10/27 (37%), Positives = 18/27 (66%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIINVPII 69
I+++G +G GK+ + K LA+ + P I
Sbjct: 2 IVVMGVSGSGKSTVGKALAERLGAPFI 28
>gnl|CDD|172740 PRK14252, PRK14252, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 265
Score = 27.7 bits (61), Expect = 5.3
Identities = 13/41 (31%), Positives = 24/41 (58%), Gaps = 1/41 (2%)
Query: 24 HYKRLFLLKSKNIYL-EKSNILLVGPTGCGKTLMVKTLAKI 63
+Y LK+ N+ + EK L+GP+GCGK+ ++ ++
Sbjct: 25 YYGGYQALKNINMMVHEKQVTALIGPSGCGKSTFLRCFNRM 65
>gnl|CDD|237645 PRK14235, PRK14235, phosphate transporter ATP-binding protein;
Provisional.
Length = 267
Score = 27.4 bits (61), Expect = 5.5
Identities = 13/47 (27%), Positives = 23/47 (48%), Gaps = 1/47 (2%)
Query: 15 KIVSVGVYNHYKRLFLLKSKNI-YLEKSNILLVGPTGCGKTLMVKTL 60
K+ + V Y L ++ EK+ +GP+GCGK+ ++ L
Sbjct: 19 KMRARDVSVFYGEKQALFDVDLDIPEKTVTAFIGPSGCGKSTFLRCL 65
>gnl|CDD|130234 TIGR01166, cbiO, cobalt transport protein ATP-binding subunit.
This model describes the ATP binding subunit of the
multisubunit cobalt transporter in bacteria and its
equivalents in archaea. The model is restricted to ATP
subunit that is a part of the cobalt transporter, which
belongs to the ABC transporter superfamily (ATP Binding
Cassette). The model excludes ATP binding subunit that
are associated with other transporters belonging to ABC
transporter superfamily. This superfamily includes two
groups, one which catalyze the uptake of small
molecules, including ions from the external milieu and
the other group which is engaged in the efflux of small
molecular weight compounds and ions from within the
cell. Energy derived from the hydrolysis of ATP drive
the both the process of uptake and efflux [Transport
and binding proteins, Cations and iron carrying
compounds].
Length = 190
Score = 27.4 bits (61), Expect = 5.7
Identities = 11/35 (31%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 31 LKSKNIYLEKSNIL-LVGPTGCGKTLMVKTLAKII 64
LK N E+ +L L+G G GK+ ++ L ++
Sbjct: 8 LKGLNFAAERGEVLALLGANGAGKSTLLLHLNGLL 42
>gnl|CDD|182106 PRK09841, PRK09841, cryptic autophosphorylating protein tyrosine
kinase Etk; Provisional.
Length = 726
Score = 28.0 bits (62), Expect = 5.8
Identities = 10/27 (37%), Positives = 16/27 (59%), Gaps = 1/27 (3%)
Query: 39 EKSNILLVGPT-GCGKTLMVKTLAKII 64
E + +++ G T GKT + TLA +I
Sbjct: 530 ENNILMITGATPDSGKTFVSSTLAAVI 556
>gnl|CDD|184412 PRK13947, PRK13947, shikimate kinase; Provisional.
Length = 171
Score = 27.0 bits (60), Expect = 5.8
Identities = 12/32 (37%), Positives = 18/32 (56%)
Query: 42 NILLVGPTGCGKTLMVKTLAKIINVPIIVVDA 73
NI+L+G G GKT + K +A ++ I D
Sbjct: 3 NIVLIGFMGTGKTTVGKRVATTLSFGFIDTDK 34
>gnl|CDD|206652 cd01853, Toc34_like, Translocon at the Outer-envelope membrane of
Chloroplasts 34-like (Toc34-like). The Toc34-like
(Translocon at the Outer-envelope membrane of
Chloroplasts) family contains several Toc proteins,
including Toc34, Toc33, Toc120, Toc159, Toc86, Toc125,
and Toc90. The Toc complex at the outer envelope
membrane of chloroplasts is a molecular machine of ~500
kDa that contains a single Toc159 protein, four Toc75
molecules, and four or five copies of Toc34. Toc64 and
Toc12 are associated with the translocon, but do not
appear to be part of the core complex. The Toc
translocon initiates the import of nuclear-encoded
preproteins from the cytosol into the organelle. Toc34
and Toc159 are both GTPases, while Toc75 is a
beta-barrel integral membrane protein. Toc159 is equally
distributed between a soluble cytoplasmic form and a
membrane-inserted form, suggesting that assembly of the
Toc complex is dynamic. Toc34 and Toc75 act sequentially
to mediate docking and insertion of Toc159 resulting in
assembly of the functional translocon.
Length = 248
Score = 27.3 bits (61), Expect = 5.9
Identities = 22/104 (21%), Positives = 35/104 (33%), Gaps = 36/104 (34%)
Query: 42 NILLVGPTGCGKTLMVKTLAKIINVPIIVVDA-----TSFTE------------------ 78
IL++G TG GK+ T+ I + V A E
Sbjct: 33 TILVLGKTGVGKS---STINSIFGERKVSVSAFQSETLRPREVSRTVDGFKLNIIDTPGL 89
Query: 79 ----AGYVGDDVESIIQKLLHECDYDVELAEQSIIYIDEIDKIS 118
V + SII++ L + DV ++Y+D +D
Sbjct: 90 LESQDQRVNRKILSIIKRFLKKKTIDV------VLYVDRLDMYR 127
>gnl|CDD|188099 TIGR00972, 3a0107s01c2, phosphate ABC transporter, ATP-binding
protein. This model represents the ATP-binding protein
of a family of ABC transporters for inorganic
phosphate. In the model species Escherichia coli, a
constitutive transporter for inorganic phosphate, with
low affinity, is also present. The high affinity
transporter that includes this polypeptide is induced
when extracellular phosphate concentrations are low.
The proteins most similar to the members of this family
but not included appear to be amino acid transporters
[Transport and binding proteins, Anions].
Length = 247
Score = 27.3 bits (61), Expect = 6.0
Identities = 12/31 (38%), Positives = 24/31 (77%), Gaps = 1/31 (3%)
Query: 31 LKSKNIYLEKSNIL-LVGPTGCGKTLMVKTL 60
LK+ N+ + K+ + L+GP+GCGK+ ++++L
Sbjct: 17 LKNINLDIPKNQVTALIGPSGCGKSTLLRSL 47
>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 = 27.2 bits (61), Expect = 6.3
Identities = 9/17 (52%), Positives = 15/17 (88%)
Query: 45 LVGPTGCGKTLMVKTLA 61
L+GP+GCGKT +++ +A
Sbjct: 31 LLGPSGCGKTTLLRLIA 47
>gnl|CDD|107248 cd01391, Periplasmic_Binding_Protein_Type_1, Type 1 periplasmic
binding fold superfamily. Type 1 periplasmic binding
fold superfamily. This model and hierarchy represent the
ligand binding domains of the LacI family of
transcriptional regulators, periplasmic binding proteins
of the ABC-type transport systems, the family C
G-protein couples receptors (GPCRs), membrane bound
guanylyl cyclases including the family of natriuretic
peptide receptors (NPRs), and the N-terminal
leucine/isoleucine/valine- binding protein (LIVBP)-like
domains of the ionotropic glutamate receptors (iGluRs).
In LacI-like transcriptional regulator and the bacterial
periplasmic binding proteins the ligands are
monosaccharides including lactose, ribose, fructose,
xylose, arabinose, galactose/glucose, and other sugars,
with a few exceptions. Periplasmic sugar binding
proteins are one of the components of ABC transporters
and are involved in the active transport of
water-soluble ligands. The LacI family of proteins
consists of transcriptional regulators related to the
lac repressor. In this case, the sugar binding domain
binds a sugar which changes the DNA binding activity of
the repressor domain. The periplasmic binding proteins
are the primary receptors for chemotaxis and transport
of many sugar based solutes. The core structures of
periplasmic binding proteins are classified into two
types, and they differ in number and order of beta
strands: type 1 has six beta strands, while type 2 has
five beta strands per sub-domain. These two structural
folds are thought to be distantly related via a common
ancestor. Notably, while the N-terminal LIVBP-like
domain of iGluRs belongs to the type 1
periplasmic-binding fold protein superfamily, the
glutamate-binding domain of the iGluR is structurally
similar to the type 2 periplasmic-binding fold.
Length = 269
Score = 27.5 bits (61), Expect = 6.3
Identities = 19/73 (26%), Positives = 30/73 (41%), Gaps = 8/73 (10%)
Query: 44 LLVGPTGCGKTLMVKTLAKIINVPIIVVDATSFTEAGY-----VGDDVESIIQKLLHECD 98
++GP L V LA +P++ +DAT+ GY VG D E + +
Sbjct: 61 GIIGPPSSSSALAVVELAAAAGIPVVSLDATAPDLTGYPYVFRVGPDNEQAGEAAA---E 117
Query: 99 YDVELAEQSIIYI 111
Y E + + I
Sbjct: 118 YLAEKGWKRVALI 130
>gnl|CDD|227519 COG5192, BMS1, GTP-binding protein required for 40S ribosome
biogenesis [Translation, ribosomal structure and
biogenesis].
Length = 1077
Score = 27.8 bits (61), Expect = 6.3
Identities = 7/20 (35%), Positives = 15/20 (75%)
Query: 43 ILLVGPTGCGKTLMVKTLAK 62
+ +VGP G GK+ ++++L +
Sbjct: 72 VAVVGPPGTGKSTLIRSLVR 91
>gnl|CDD|206651 cd01852, AIG1, AvrRpt2-Induced Gene 1 (AIG1). This group
represents Arabidoposis protein AIG1 (avrRpt2-induced
gene 1) that appears to be involved in plant resistance
to bacteria. The Arabidopsis disease resistance gene
RPS2 is involved in recognition of bacterial pathogens
carrying the avirulence gene avrRpt2. AIG1 exhibits
RPS2- and avrRpt1-dependent induction early after
infection with Pseudomonas syringae carrying avrRpt2.
This subfamily also includes IAN-4 protein, which has
GTP-binding activity and shares sequence homology with
a novel family of putative GTP-binding proteins: the
immuno-associated nucleotide (IAN) family. The
evolutionary conservation of the IAN family provides a
unique example of a plant pathogen response gene
conserved in animals. The IAN/IMAP subfamily has been
proposed to regulate apoptosis in vertebrates and
angiosperm plants, particularly in relation to cancer,
diabetes, and infections. The human IAN genes were
renamed GIMAP (GTPase of the immunity associated
proteins).
Length = 201
Score = 27.1 bits (61), Expect = 6.3
Identities = 7/13 (53%), Positives = 10/13 (76%)
Query: 42 NILLVGPTGCGKT 54
++LVG TG GK+
Sbjct: 2 RLVLVGKTGNGKS 14
>gnl|CDD|145542 pfam02456, Adeno_IVa2, Adenovirus IVa2 protein. IVa2 protein can
interact with the adenoviral packaging signal and that
this interaction involves DNA sequences that have
previously been demonstrated to be required for
packaging. During the course of lytic infection, the
adenovirus major late promoter (MLP) is induced to high
levels after replication of viral DNA has started. IVa2
is a transcriptional activator of the major late
promoter.
Length = 370
Score = 27.3 bits (61), Expect = 6.5
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 31 LKSKNIYLEKSNILLVGPTGCGKTLMVKTL 60
L S N L+ ++ GPTGCGK+ +++ L
Sbjct: 78 LPSLNYGLQPVIGVVYGPTGCGKSQLLRNL 107
>gnl|CDD|215925 pfam00448, SRP54, SRP54-type protein, GTPase domain. This family
includes relatives of the G-domain of the SRP54 family
of proteins.
Length = 196
Score = 27.1 bits (61), Expect = 6.6
Identities = 12/21 (57%), Positives = 14/21 (66%), Gaps = 3/21 (14%)
Query: 43 ILLVGPTGCGKTLMVKTLAKI 63
ILLVG G GKT T+AK+
Sbjct: 4 ILLVGLQGSGKT---TTIAKL 21
>gnl|CDD|234011 TIGR02782, TrbB_P, P-type conjugative transfer ATPase TrbB. The
TrbB protein is found in the trb locus of Agrobacterium
Ti plasmids where it is involved in the type IV
secretion system for plasmid conjugative transfer. TrbB
is a homolog of the vir system VirB11 ATPase , and the
Flp pilus sytem ATPase TadA [Cellular processes,
Conjugation].
Length = 299
Score = 27.4 bits (61), Expect = 6.8
Identities = 17/42 (40%), Positives = 26/42 (61%), Gaps = 5/42 (11%)
Query: 38 LEKSNILLVGPTGCGKTLMVKT-LAKI-INVP---IIVVDAT 74
L + NIL+VG TG GKT + LA+I N P +++++ T
Sbjct: 130 LARKNILVVGGTGSGKTTLANALLAEIAKNDPTDRVVIIEDT 171
>gnl|CDD|227320 COG4987, CydC, ABC-type transport system involved in cytochrome bd
biosynthesis, fused ATPase and permease components
[Energy production and conversion / Posttranslational
modification, protein turnover, chaperones].
Length = 573
Score = 27.7 bits (62), Expect = 6.8
Identities = 10/33 (30%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 31 LKSKNIYLEK-SNILLVGPTGCGKTLMVKTLAK 62
LK+ N+ L + + ++G +G GK+ +++ LA
Sbjct: 354 LKNFNLTLAQGEKVAILGRSGSGKSTLLQLLAG 386
>gnl|CDD|218788 pfam05872, DUF853, Bacterial protein of unknown function
(DUF853). This family consists of several bacterial
proteins of unknown function. BMEI1370 is thought to be
an ATPase.
Length = 504
Score = 27.4 bits (61), Expect = 6.8
Identities = 12/32 (37%), Positives = 19/32 (59%), Gaps = 3/32 (9%)
Query: 44 LLVGPTGCGKTLMVKTLAK---IINVPIIVVD 72
L+ G TG GKT+ ++ LA+ VP+ + D
Sbjct: 25 LIAGATGTGKTVTLQVLAESFSDAGVPVFLAD 56
>gnl|CDD|172744 PRK14256, PRK14256, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 252
Score = 27.3 bits (60), Expect = 6.9
Identities = 8/25 (32%), Positives = 19/25 (76%)
Query: 39 EKSNILLVGPTGCGKTLMVKTLAKI 63
E S ++GP+GCGK+ +++++ ++
Sbjct: 29 ENSVTAIIGPSGCGKSTVLRSINRM 53
>gnl|CDD|226622 COG4138, BtuD, ABC-type cobalamin transport system, ATPase
component [Coenzyme metabolism].
Length = 248
Score = 27.1 bits (60), Expect = 7.1
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 45 LVGPTGCGKTLMVKTLAKII 64
LVGP G GK+ ++ +A +
Sbjct: 30 LVGPNGAGKSTLLARMAGMT 49
>gnl|CDD|224046 COG1121, ZnuC, ABC-type Mn/Zn transport systems, ATPase component
[Inorganic ion transport and metabolism].
Length = 254
Score = 27.2 bits (61), Expect = 7.1
Identities = 10/31 (32%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 35 NIYLEKSNIL-LVGPTGCGKTLMVKTLAKII 64
++ +EK I L+GP G GK+ ++K + ++
Sbjct: 24 SLSVEKGEITALIGPNGAGKSTLLKAILGLL 54
>gnl|CDD|172756 PRK14268, PRK14268, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 258
Score = 27.3 bits (60), Expect = 7.3
Identities = 11/34 (32%), Positives = 25/34 (73%), Gaps = 1/34 (2%)
Query: 31 LKSKNIYLEKSNIL-LVGPTGCGKTLMVKTLAKI 63
LK+ ++ + K+++ L+GP+GCGK+ ++ L ++
Sbjct: 28 LKNVSMQIPKNSVTALIGPSGCGKSTFIRCLNRM 61
>gnl|CDD|145634 pfam02595, Gly_kinase, Glycerate kinase family. This is family of
Glycerate kinases.
Length = 378
Score = 27.4 bits (61), Expect = 7.4
Identities = 13/41 (31%), Positives = 18/41 (43%), Gaps = 8/41 (19%)
Query: 52 GKT-LMVKTLAKIINVPIIVVDATSFTEAGYVGDDVESIIQ 91
GK + V AK N P+I + AG + DV + Q
Sbjct: 302 GKVPIGVAAAAKKFNKPVIGI-------AGQLSLDVSVVHQ 335
>gnl|CDD|234643 PRK00114, hslO, Hsp33-like chaperonin; Reviewed.
Length = 293
Score = 27.0 bits (61), Expect = 7.4
Identities = 9/37 (24%), Positives = 16/37 (43%), Gaps = 1/37 (2%)
Query: 74 TSFTEAGYVGDDVESIIQKLLHECDYDVELAEQSIIY 110
F+ G E ++ +L HE D + L Q + +
Sbjct: 201 ELFSLLLESGLTAEELLYRLYHEEDVKI-LEPQPVEF 236
>gnl|CDD|236865 PRK11160, PRK11160, cysteine/glutathione ABC transporter
membrane/ATP-binding component; Reviewed.
Length = 574
Score = 27.5 bits (62), Expect = 7.6
Identities = 9/15 (60%), Positives = 12/15 (80%), Gaps = 1/15 (6%)
Query: 43 ILLVGPTGCGK-TLM 56
+ L+G TGCGK TL+
Sbjct: 369 VALLGRTGCGKSTLL 383
>gnl|CDD|131580 TIGR02528, EutP, ethanolamine utilization protein, EutP. This
protein is found within operons which code for
polyhedral organelles containing the enzyme
ethanolamine ammonia lyase. The function of this gene
is unknown, although the presence of an N-terminal
GxxGxGK motif implies a GTP-binding site [Energy
metabolism, Amino acids and amines].
Length = 142
Score = 26.6 bits (59), Expect = 7.6
Identities = 8/18 (44%), Positives = 12/18 (66%)
Query: 43 ILLVGPTGCGKTLMVKTL 60
I+ +G GCGKT + + L
Sbjct: 3 IMFIGSVGCGKTTLTQAL 20
>gnl|CDD|218141 pfam04548, AIG1, AIG1 family. Arabidopsis protein AIG1 appears
to be involved in plant resistance to bacteria.
Length = 211
Score = 26.8 bits (60), Expect = 7.7
Identities = 8/12 (66%), Positives = 9/12 (75%)
Query: 42 NILLVGPTGCGK 53
I+LVG TG GK
Sbjct: 2 RIVLVGKTGNGK 13
>gnl|CDD|172739 PRK14251, PRK14251, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 251
Score = 26.9 bits (59), Expect = 7.7
Identities = 10/27 (37%), Positives = 18/27 (66%)
Query: 37 YLEKSNILLVGPTGCGKTLMVKTLAKI 63
+ EK L+GP+GCGK+ ++ L ++
Sbjct: 27 FEEKELTALIGPSGCGKSTFLRCLNRM 53
>gnl|CDD|216999 pfam02367, UPF0079, Uncharacterized P-loop hydrolase UPF0079.
This uncharacterized family contains a P-loop.
Length = 123
Score = 26.5 bits (59), Expect = 7.8
Identities = 14/35 (40%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIINVPIIVVDATSFT 77
+LL G G GKT V+ LA+ + + V T FT
Sbjct: 18 VLLSGDLGAGKTTFVRGLAQGLGITGNVTSPT-FT 51
>gnl|CDD|202036 pfam01902, ATP_bind_4, ATP-binding region. This family of proteins
probably binds ATP. This domain is about 200 amino acids
long with a strongly conserved motif SGGKD at the N
terminus.In some members of this family , this domain is
associated with pfam01042.
Length = 220
Score = 27.0 bits (60), Expect = 7.9
Identities = 18/102 (17%), Positives = 44/102 (43%), Gaps = 5/102 (4%)
Query: 56 MVKTLAKIINVPIIVVDATSFTEAGYVGDDVESIIQKLLHECDYDVELAEQSIIYIDEID 115
+ K A+ + +PII + E V +D+ ++ L + D V A S I+
Sbjct: 50 LTKLQAEALGIPIIKLYTKGEKE-KEV-EDLAGFLESL--DVDGLVAGAIYSEYQKSRIE 105
Query: 116 KISKKTDVVSGKDVSGEGVQQSLLKLI-EGVNLSITSLAEKK 156
+ ++ + + G ++ +++ EG ++I +++
Sbjct: 106 SVCRELGLKPFAPLWGRDPRKLAEEIVREGFEVAIVAVSAYG 147
>gnl|CDD|240426 PTZ00466, PTZ00466, actin-like protein; Provisional.
Length = 380
Score = 27.2 bits (60), Expect = 7.9
Identities = 10/28 (35%), Positives = 19/28 (67%)
Query: 63 IINVPIIVVDATSFTEAGYVGDDVESII 90
N PII+ + T + +AG+ G+DV +++
Sbjct: 10 YSNQPIIIDNGTGYIKAGFAGEDVPNLV 37
>gnl|CDD|172457 PRK13951, PRK13951, bifunctional shikimate
kinase/3-dehydroquinate synthase; Provisional.
Length = 488
Score = 27.2 bits (60), Expect = 8.1
Identities = 10/30 (33%), Positives = 20/30 (66%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIINVPIIVVD 72
I LVG G GK+ + K +++++++ I +D
Sbjct: 3 IFLVGMMGSGKSTIGKRVSEVLDLQFIDMD 32
>gnl|CDD|225183 COG2274, SunT, ABC-type bacteriocin/lantibiotic exporters, contain
an N-terminal double-glycine peptidase domain [Defense
mechanisms].
Length = 709
Score = 27.2 bits (61), Expect = 8.1
Identities = 8/22 (36%), Positives = 14/22 (63%), Gaps = 4/22 (18%)
Query: 43 ILLVGPTGCGKTLMVKTLAKII 64
+ +VG +G GK+ TL K++
Sbjct: 502 VAIVGRSGSGKS----TLLKLL 519
>gnl|CDD|172760 PRK14272, PRK14272, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 252
Score = 26.9 bits (59), Expect = 8.1
Identities = 8/19 (42%), Positives = 15/19 (78%)
Query: 45 LVGPTGCGKTLMVKTLAKI 63
L+GP+GCGKT ++ + ++
Sbjct: 35 LIGPSGCGKTTFLRAINRM 53
>gnl|CDD|223666 COG0593, DnaA, ATPase involved in DNA replication initiation [DNA
replication, recombination, and repair].
Length = 408
Score = 27.2 bits (61), Expect = 8.2
Identities = 19/83 (22%), Positives = 37/83 (44%), Gaps = 13/83 (15%)
Query: 43 ILLVGPTGCGKT-LM----VKTLAKIINVPIIVVDATSFTEAGYVGDDVESIIQKLLHEC 97
+ + G G GKT L+ + LA N ++ + + FT +V ++ ++K +
Sbjct: 116 LFIYGGVGLGKTHLLQAIGNEALANGPNARVVYLTSEDFTND-FVKALRDNEMEKFKEKY 174
Query: 98 DYDVELAEQSIIYIDEIDKISKK 120
D+ L ID+I ++ K
Sbjct: 175 SLDLLL-------IDDIQFLAGK 190
>gnl|CDD|237090 PRK12402, PRK12402, replication factor C small subunit 2;
Reviewed.
Length = 337
Score = 27.3 bits (61), Expect = 8.2
Identities = 19/61 (31%), Positives = 27/61 (44%), Gaps = 14/61 (22%)
Query: 2 ELDRHIIGQHETKKIVSVGVYNHYKRLFLLKSKNIYLEKSNILLVGPTGCGKTLMVKTLA 61
L I+GQ E V R + S N+ ++L+ GP G GKT V+ LA
Sbjct: 12 ALLEDILGQDE--------VVERLSRA--VDSPNL----PHLLVQGPPGSGKTAAVRALA 57
Query: 62 K 62
+
Sbjct: 58 R 58
>gnl|CDD|216401 pfam01267, F-actin_cap_A, F-actin capping protein alpha subunit.
Length = 269
Score = 26.9 bits (60), Expect = 8.3
Identities = 8/26 (30%), Positives = 14/26 (53%), Gaps = 1/26 (3%)
Query: 187 IINRINQ-ETNFLEKLNNNYNLICET 211
I+ I + E + LN N+N + +T
Sbjct: 215 IVKAIREAENEYQAALNENFNTLNDT 240
>gnl|CDD|235244 PRK04182, PRK04182, cytidylate kinase; Provisional.
Length = 180
Score = 26.7 bits (60), Expect = 8.5
Identities = 8/23 (34%), Positives = 14/23 (60%)
Query: 47 GPTGCGKTLMVKTLAKIINVPII 69
GP G GKT + + LA+ + + +
Sbjct: 7 GPPGSGKTTVARLLAEKLGLKHV 29
>gnl|CDD|130260 TIGR01192, chvA, glucan exporter ATP-binding protein. This model
describes glucan exporter ATP binding protein in
bacteria. It belongs to the larger ABC transporter
superfamily with the characteristic ATP binding motif.
The In general, this protein is in some ways implicated
in osmoregulation and suggested to participate in the
export of glucan from the cytoplasm to periplasm. The
cyclic beta-1,2-glucan in the bactrerial periplasmic
space is suggested to confer the property of high
osmolority. It has also been demonstrated that mutants
in this loci have lost functions of virulence and
motility. It is unclear as to how virulence and
osmoadaptaion are related [Transport and binding
proteins, Carbohydrates, organic alcohols, and acids].
Length = 585
Score = 27.2 bits (60), Expect = 8.5
Identities = 9/21 (42%), Positives = 15/21 (71%)
Query: 43 ILLVGPTGCGKTLMVKTLAKI 63
+ +VGPTG GKT ++ L ++
Sbjct: 364 VAIVGPTGAGKTTLINLLQRV 384
>gnl|CDD|183521 PRK12422, PRK12422, chromosomal replication initiation protein;
Provisional.
Length = 445
Score = 27.1 bits (60), Expect = 8.7
Identities = 13/39 (33%), Positives = 19/39 (48%), Gaps = 3/39 (7%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIIN---VPIIVVDATSFTE 78
I L GP G GKT +++ + I+ V + FTE
Sbjct: 144 IYLFGPEGSGKTHLMQAAVHALRESGGKILYVRSELFTE 182
>gnl|CDD|178596 PLN03025, PLN03025, replication factor C subunit; Provisional.
Length = 319
Score = 27.0 bits (60), Expect = 8.7
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 42 NILLVGPTGCGKTLMVKTLA 61
N++L GP G GKT + LA
Sbjct: 36 NLILSGPPGTGKTTSILALA 55
>gnl|CDD|222290 pfam13654, AAA_32, AAA domain. This family includes a wide
variety of AAA domains including some that have lost
essential nucleotide binding residues in the P-loop.
Length = 509
Score = 27.0 bits (61), Expect = 8.8
Identities = 7/21 (33%), Positives = 13/21 (61%)
Query: 42 NILLVGPTGCGKTLMVKTLAK 62
NI ++G G G+T +V+ +
Sbjct: 32 NIFVLGEPGTGRTTLVRRYLE 52
>gnl|CDD|213218 cd03251, ABCC_MsbA, ATP-binding cassette domain of the bacterial
lipid flippase and related proteins, subfamily C. MsbA
is an essential ABC transporter, closely related to
eukaryotic MDR proteins. 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 = 234
Score = 26.8 bits (60), Expect = 8.9
Identities = 10/22 (45%), Positives = 14/22 (63%), Gaps = 4/22 (18%)
Query: 43 ILLVGPTGCGKTLMVKTLAKII 64
+ LVGP+G GK+ TL +I
Sbjct: 31 VALVGPSGSGKS----TLVNLI 48
>gnl|CDD|227321 COG4988, CydD, ABC-type transport system involved in cytochrome bd
biosynthesis, ATPase and permease components [Energy
production and conversion / Posttranslational
modification, protein turnover, chaperones].
Length = 559
Score = 27.2 bits (61), Expect = 9.0
Identities = 7/23 (30%), Positives = 11/23 (47%)
Query: 40 KSNILLVGPTGCGKTLMVKTLAK 62
LVG +G GK+ ++ L
Sbjct: 347 GQLTALVGASGAGKSTLLNLLLG 369
>gnl|CDD|183703 PRK12724, PRK12724, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 432
Score = 27.2 bits (60), Expect = 9.0
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 43 ILLVGPTGCGKTLMVKTLA 61
+ VGPTG GKT + LA
Sbjct: 226 VFFVGPTGSGKTTSIAKLA 244
>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 614
Score = 27.0 bits (60), Expect = 9.0
Identities = 11/22 (50%), Positives = 12/22 (54%)
Query: 44 LLVGPTGCGKTLMVKTLAKIIN 65
L GP G GKT + AK IN
Sbjct: 43 LFCGPRGVGKTTCARIFAKTIN 64
>gnl|CDD|233914 TIGR02538, type_IV_pilB, type IV-A pilus assembly ATPase PilB.
This model describes a protein of type IV pilus
biogenesis designated PilB in Pseudomonas aeruginosa but
PilF in Neisseria gonorrhoeae; the more common usage,
reflected here, is PilB. This protein is an ATPase
involved in protein export for pilin assembly and is
closely related to GspE (TIGR02533) of type II
secretion, also called the main terminal branch of the
general secretion pathway. Note that type IV pilus
systems are often divided into type IV-A and IV-B, with
the latter group including bundle-forming pilus,
mannose-sensitive hemagglutinin, etc. Members of this
family are found in type IV-A systems [Cell envelope,
Surface structures, Protein fate, Protein and peptide
secretion and trafficking].
Length = 564
Score = 26.9 bits (60), Expect = 9.1
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIINVP 67
+L+ GPTG GKT+ + T I+N
Sbjct: 319 VLVTGPTGSGKTVSLYTALNILNTE 343
>gnl|CDD|201257 pfam00485, PRK, Phosphoribulokinase / Uridine kinase family. In
Arabidopsis the region carries two binding domains, a
phosphoribosylpyrophosphate-binding domain and, at the
very C-terminus, a uracil-binding domain.
Length = 197
Score = 26.6 bits (59), Expect = 9.2
Identities = 12/38 (31%), Positives = 18/38 (47%), Gaps = 3/38 (7%)
Query: 43 ILLVGPTGCGKTLMVKTLAKIIN---VPIIVVDATSFT 77
I + G +G GKT + +T I VP ++ SF
Sbjct: 2 IGVTGSSGAGKTTVARTFVSIFGREGVPAAGIEGDSFH 39
>gnl|CDD|224719 COG1806, COG1806, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 273
Score = 26.8 bits (60), Expect = 9.3
Identities = 11/37 (29%), Positives = 20/37 (54%), Gaps = 4/37 (10%)
Query: 37 YLEKSNILLVGPTGCGKTLMVKTLA----KIINVPII 69
L++++++LVG + KT LA K N P++
Sbjct: 141 NLDEADVILVGVSRTSKTPTSLYLALQGIKAANYPLV 177
>gnl|CDD|184037 PRK13409, PRK13409, putative ATPase RIL; Provisional.
Length = 590
Score = 27.1 bits (61), Expect = 9.3
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 46 VGPTGCGKTLMVKTLAKIIN 65
VGP G GKT K LA ++
Sbjct: 371 VGPNGIGKTTFAKLLAGVLK 390
>gnl|CDD|184587 PRK14241, PRK14241, phosphate transporter ATP-binding protein;
Provisional.
Length = 258
Score = 26.6 bits (59), Expect = 9.5
Identities = 8/15 (53%), Positives = 14/15 (93%)
Query: 46 VGPTGCGKTLMVKTL 60
+GP+GCGK+ +++TL
Sbjct: 36 IGPSGCGKSTVLRTL 50
>gnl|CDD|238540 cd01120, RecA-like_NTPases, RecA-like NTPases. This family
includes the NTP binding domain of F1 and V1 H+ATPases,
DnaB and related helicases as well as bacterial RecA
and related eukaryotic and archaeal recombinases. This
group also includes bacterial conjugation proteins and
related DNA transfer proteins involved in type II and
type IV secretion.
Length = 165
Score = 26.3 bits (58), Expect = 9.5
Identities = 14/35 (40%), Positives = 18/35 (51%), Gaps = 3/35 (8%)
Query: 42 NILLVGPTGCGKTLMVKTLAKIINVP---IIVVDA 73
IL+ GPTG GKT + LA I ++ VD
Sbjct: 1 LILVFGPTGSGKTTLALQLALNIATKGGKVVYVDI 35
>gnl|CDD|213234 cd03267, ABC_NatA_like, ATP-binding cassette domain of an
uncharacterized transporter similar in sequence to
NatA. NatA is the ATPase component of a bacterial
ABC-type Na+ transport system called NatAB, which
catalyzes ATP-dependent electrogenic Na+ extrusion
without mechanically coupled to proton or K+ uptake.
NatB possess six putative membrane spanning regions at
its C-terminus. In B. subtilis, NatAB is inducible by
agents such as ethanol and protonophores, which lower
the proton-motive force across the membrane. The
closest sequence similarity to NatA is exhibited by
DrrA of the two-component daunorubicin- and
doxorubicin-efflux system. Hence, the functional NatAB
is presumably assembled with two copies of the single
ATP-binding protein and the single integral membrane
protein.
Length = 236
Score = 26.5 bits (59), Expect = 9.8
Identities = 13/35 (37%), Positives = 21/35 (60%), Gaps = 1/35 (2%)
Query: 31 LKSKNIYLEKSNIL-LVGPTGCGKTLMVKTLAKII 64
LK + +EK I+ +GP G GKT +K L+ ++
Sbjct: 37 LKGISFTIEKGEIVGFIGPNGAGKTTTLKILSGLL 71
>gnl|CDD|172750 PRK14262, PRK14262, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 250
Score = 26.8 bits (59), Expect = 9.9
Identities = 10/46 (21%), Positives = 27/46 (58%), Gaps = 1/46 (2%)
Query: 45 LVGPTGCGKTLMVKTLAKI-INVPIIVVDATSFTEAGYVGDDVESI 89
++GP+GCGKT +++++ ++ ++P V+ + + + D +
Sbjct: 34 IIGPSGCGKTTLLRSINRMNDHIPGFRVEGKIYFKGQDIYDPQLDV 79
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
0.317 0.138 0.380
Gapped
Lambda K H
0.267 0.0889 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,407,585
Number of extensions: 1090298
Number of successful extensions: 2260
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2193
Number of HSP's successfully gapped: 421
Length of query: 225
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 132
Effective length of database: 6,812,680
Effective search space: 899273760
Effective search space used: 899273760
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 57 (25.4 bits)