RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11425
(672 letters)
>gnl|CDD|234612 PRK00072, hemC, porphobilinogen deaminase; Reviewed.
Length = 295
Score = 400 bits (1031), Expect = e-136
Identities = 147/287 (51%), Positives = 196/287 (68%), Gaps = 5/287 (1%)
Query: 374 RLAIWQAEYVRKKIIELYPWCKVEILGITTKGDKIFEKVPL-KINEKGLFTKELEMAIIK 432
+LA+WQAE+V+ ++ +P +VE++ I TKGDKI VPL KI KGLF KELE A+++
Sbjct: 13 KLALWQAEWVKDRLKAAHPGLEVELVPIKTKGDKIL-DVPLAKIGGKGLFVKELEEALLE 71
Query: 433 GKADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFISNDYISLSTLPKNAVVGTNSLRR 492
G+ D+AVHSLKD+P LP G +L AI +REDPRDA +S DY SL LP+ AVVGT+SLRR
Sbjct: 72 GEIDIAVHSLKDVPTELPEGLVLAAIPEREDPRDALVSRDYKSLDDLPEGAVVGTSSLRR 131
Query: 493 KVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILAAAGLKRLNLQKRIRMLFSPNQI 552
+ + + P L IK LRGN+DTRL KLD+GEY AIILAAAGLKRL L+ RI P ++
Sbjct: 132 QAQLLALRPDLEIKPLRGNVDTRLRKLDEGEYDAIILAAAGLKRLGLEDRITEYLDPEEM 191
Query: 553 LPAPGQGAIAIEILDNRKELMEMLIPLNHYFSEQTVKAERAVSRNFNGSCKISLAAFAMV 612
LPAPGQGA+ IE + +E++E+L PLNH + V AERA R G C++ + A+A
Sbjct: 192 LPAPGQGALGIECRADDEEILELLAPLNHEETRLRVTAERAFLRALEGGCQVPIGAYA-- 249
Query: 613 NNFNESEINLRAIITNPNGLKIITAEVNGPIDTPETVGLYAAELLKK 659
E+ LR ++ +P+G +II AE+ GP E +G+ AE L
Sbjct: 250 -ELEGDELRLRGLVGSPDGSEIIRAEIEGPAADAEELGIELAEELLA 295
>gnl|CDD|223259 COG0181, HemC, Porphobilinogen deaminase [Coenzyme metabolism].
Length = 307
Score = 366 bits (942), Expect = e-122
Identities = 146/294 (49%), Positives = 199/294 (67%), Gaps = 2/294 (0%)
Query: 374 RLAIWQAEYVRKKIIELYPWCKVEILGITTKGDKIFEKVPLKINEKGLFTKELEMAIIKG 433
+LA+ QA V +++ YP +VEI+ I TKGD+I +K KI KGLFTKELE A+++G
Sbjct: 12 KLALAQANEVIERLKAAYPDLEVEIVTIKTKGDRILDKPLSKIGGKGLFTKELEQALLEG 71
Query: 434 KADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFISNDYISLSTLPKNAVVGTNSLRRK 493
+ D+AVHSLKD+P LP G +L AI +REDPRDA +S D L LP+ AVVGT+SLRR+
Sbjct: 72 EIDIAVHSLKDVPTELPEGLVLAAIPEREDPRDALVSRDGYDLEELPEGAVVGTSSLRRQ 131
Query: 494 VLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILAAAGLKRLNLQKRIRMLFSPNQIL 553
+K+ P L I+ LRGN+DTRL KLD+GEY AIILAAAGLKRL L+ RI + P + L
Sbjct: 132 AQLKALRPDLKIEPLRGNVDTRLRKLDEGEYDAIILAAAGLKRLGLENRITEILDPEEFL 191
Query: 554 PAPGQGAIAIEILDNRKELMEMLIPLNHYFSEQTVKAERAVSRNFNGSCKISLAAFAMVN 613
PAPGQGA+AIE ++++E+L LN + V AERA R G C++ + A+A +
Sbjct: 192 PAPGQGALAIECRAGDEKVLELLAELNDEDTRICVTAERAFLRELEGGCQVPIGAYAELT 251
Query: 614 NFNESEINLRAIITNPNGLKIITAEVNGPIDTPETVGLYAAELLKKKGAIEIIK 667
E+ LRA++ +P+G +II AE+ G + E +G AE L +KGA EI++
Sbjct: 252 --GGGELRLRALVGSPDGSQIIKAEIRGDAEDAEELGKELAEELLEKGAKEILE 303
>gnl|CDD|238276 cd00494, HMBS, Hydroxymethylbilane synthase (HMBS), also known as
porphobilinogen deaminase (PBGD), is an intermediate
enzyme in the biosynthetic pathway of tetrapyrrolic ring
systems, such as heme, chlorophylls, and vitamin B12.
HMBS catalyzes the conversion of porphobilinogen (PBG)
into hydroxymethylbilane (HMB). HMBS consists of three
domains, and is believed to bind substrate through a
hinge-bending motion of domains I and II. HMBS is found
in all organisms except viruses.
Length = 292
Score = 353 bits (908), Expect = e-118
Identities = 144/287 (50%), Positives = 188/287 (65%), Gaps = 4/287 (1%)
Query: 374 RLAIWQAEYVRKKIIELYPWCKVEILGITTKGDKIFEKVPL-KINEKGLFTKELEMAIIK 432
+LA+ Q V +K+ EL P +VEI+ I T GDKI +K PL KI KGLFTKELE A++
Sbjct: 9 KLALIQTNKVIEKLKELCPGIEVEIVIIKTTGDKILDK-PLAKIGGKGLFTKELEEALLN 67
Query: 433 GKADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFISNDYISLSTLPKNAVVGTNSLRR 492
G+ DLAVHSLKD+P LP G +L AI KREDPRDA +S + SL LP +VVGT+SLRR
Sbjct: 68 GEIDLAVHSLKDVPTELPEGLVLGAIPKREDPRDALVSRNGSSLEDLPAGSVVGTSSLRR 127
Query: 493 KVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILAAAGLKRLNLQKRIRMLFSPNQI 552
+ +K P L + LRGN+DTRL KLD+GEY AIILAAAGLKRL L+ RI SP +
Sbjct: 128 QAQLKRKRPDLKFEPLRGNVDTRLRKLDEGEYDAIILAAAGLKRLGLEDRITQYLSPEVM 187
Query: 553 LPAPGQGAIAIEILDNRKELMEMLIPLNHYFSEQTVKAERAVSRNFNGSCKISLAAFAMV 612
LPA GQGA+AIE +EL+ +L PLNH + V AERA R G C++ + +A +
Sbjct: 188 LPAVGQGALAIECRKGDEELLALLKPLNHEETALCVLAERAFLRELEGGCQVPIGVYAEL 247
Query: 613 NNFNESEINLRAIITNPNGLKIITAEVNGPIDTPETVGLYAAELLKK 659
+ E+ L+ ++ +P+G ++I EV G I+ E +G AE L
Sbjct: 248 D--GGEELKLKGLVGSPDGKRLIEGEVRGNIEDAEELGKKLAEELLA 292
>gnl|CDD|232876 TIGR00212, hemC, porphobilinogen deaminase. Alternate name
hydroxymethylbilane synthase Biosynthesis of cofactors,
prosthetic groups, and carriers: Heme and porphyrin
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Heme, porphyrin, and cobalamin].
Length = 292
Score = 326 bits (839), Expect = e-107
Identities = 137/286 (47%), Positives = 184/286 (64%), Gaps = 3/286 (1%)
Query: 374 RLAIWQAEYVRKKIIELYPWCKVEILGITTKGDKIFEKVPLKINEKGLFTKELEMAIIKG 433
+LA+ QA VR+++ +YP EI+ I T GDKI +K I KGLFTKELE A++ G
Sbjct: 9 KLALAQANLVREQLKAVYPELDTEIVIIKTTGDKIQDKPLYDIGGKGLFTKELEQALLDG 68
Query: 434 KADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFISNDYISLSTLPKNAVVGTNSLRRK 493
+ DLAVHSLKD+P LP G + A+LKREDPRD +S Y+SL +LP+ A VGT+SLRRK
Sbjct: 69 EIDLAVHSLKDVPTVLPEGLEIAAVLKREDPRDVLVSRKYLSLDSLPQGAKVGTSSLRRK 128
Query: 494 VLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILAAAGLKRLNLQKRIRMLFSPNQIL 553
+K+ P L I+ LRGNIDTRL KLD+GEY AIILA AGLKRL L+ I + P +L
Sbjct: 129 AQLKAIRPDLKIEPLRGNIDTRLRKLDEGEYDAIILAEAGLKRLGLEDVITEVLDPEVML 188
Query: 554 PAPGQGAIAIEILDNRKELMEMLIPLNHYFSEQTVKAERAVSRNFNGSCKISLAAFAMVN 613
PAPGQGAIA+E + E+ E+L +NH + AERA + G C+ + A+A N
Sbjct: 189 PAPGQGAIAVECRKDDTEIKEILKEINHPPTRVEATAERAFLKELGGGCQTPIGAYAEYN 248
Query: 614 NFNESEINLRAIITNPNGLKIITAEVNGPIDTPETVGLYAAELLKK 659
+++ L A++ + +G ++I E G I+ E A ELLK+
Sbjct: 249 G---NKLTLIAMVADLDGKEVIREEKEGNIEDAELGTEVAEELLKR 291
>gnl|CDD|234719 PRK00300, gmk, guanylate kinase; Provisional.
Length = 205
Score = 295 bits (757), Expect = 2e-96
Identities = 94/188 (50%), Positives = 139/188 (73%)
Query: 127 GNIFIISAPSGAGKSTLVNELLKKDHKIKLSISTTTRPMRPGEKNGREYYFTNIDNFKKL 186
G + ++S PSGAGKSTLV LL++D ++LS+S TTR RPGE +G +Y+F + + F+++
Sbjct: 5 GLLIVLSGPSGAGKSTLVKALLERDPNLQLSVSATTRAPRPGEVDGVDYFFVSKEEFEEM 64
Query: 187 QKSGKFLEWAEVHGNFYGTSFFPIVREIKSNVDILLEIDFQGAKQIKKKFPNAIGIFILP 246
++G+FLEWAEV GN+YGT P+ + + D+LLEID+QGA+Q+KKK P+A+ IFILP
Sbjct: 65 IENGEFLEWAEVFGNYYGTPRSPVEEALAAGKDVLLEIDWQGARQVKKKMPDAVSIFILP 124
Query: 247 PSLDSLKERLYKRGQDKYDVISRRILSANKEISYANKFDYIIINNKFSKALLQLKAIINA 306
PSL+ L+ RL RG D +VI+RR+ A +EI++A+++DY+I+N+ AL +LKAII A
Sbjct: 125 PSLEELERRLRGRGTDSEEVIARRLAKAREEIAHASEYDYVIVNDDLDTALEELKAIIRA 184
Query: 307 NRCFMARV 314
R +R
Sbjct: 185 ERLRRSRQ 192
>gnl|CDD|216465 pfam01379, Porphobil_deam, Porphobilinogen deaminase, dipyromethane
cofactor binding domain.
Length = 213
Score = 290 bits (745), Expect = 1e-94
Identities = 115/202 (56%), Positives = 146/202 (72%)
Query: 375 LAIWQAEYVRKKIIELYPWCKVEILGITTKGDKIFEKVPLKINEKGLFTKELEMAIIKGK 434
LA+ QAEYV++K+ +LYP + EI+ I T GDKI +K KI KGLFTKELE A++ +
Sbjct: 11 LALIQAEYVKEKLKKLYPDIEFEIVTIKTTGDKILDKPLAKIGGKGLFTKELEEALLNNE 70
Query: 435 ADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFISNDYISLSTLPKNAVVGTNSLRRKV 494
D+AVHSLKD+P LP G +L AI KREDPRDA +S++ SL LP +VVGT+SLRR
Sbjct: 71 IDIAVHSLKDVPTELPEGLVLGAIPKREDPRDALVSSNGKSLEDLPAGSVVGTSSLRRSA 130
Query: 495 LIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILAAAGLKRLNLQKRIRMLFSPNQILP 554
+K P L +SLRGN+DTRL KLD+GEY AIILAAAGLKRL L+ RI SP+ +LP
Sbjct: 131 QLKRKRPDLKFESLRGNVDTRLRKLDEGEYDAIILAAAGLKRLGLEDRITQSLSPDDMLP 190
Query: 555 APGQGAIAIEILDNRKELMEML 576
A GQGA+ IE KE++++L
Sbjct: 191 AVGQGALGIECRKGDKEMLDLL 212
>gnl|CDD|213788 TIGR03263, guanyl_kin, guanylate kinase. Members of this family
are the enzyme guanylate kinase, also called GMP kinase.
This enzyme transfers a phosphate from ATP to GMP,
yielding ADP and GDP [Purines, pyrimidines, nucleosides,
and nucleotides, Nucleotide and nucleoside
interconversions].
Length = 179
Score = 272 bits (698), Expect = 4e-88
Identities = 98/179 (54%), Positives = 136/179 (75%)
Query: 128 NIFIISAPSGAGKSTLVNELLKKDHKIKLSISTTTRPMRPGEKNGREYYFTNIDNFKKLQ 187
+ +IS PSGAGKSTLV LL++D +K SIS TTR RPGE +G +Y+F + + F+++
Sbjct: 1 LLIVISGPSGAGKSTLVKALLEEDPNLKFSISATTRKPRPGEVDGVDYFFVSKEEFEEMI 60
Query: 188 KSGKFLEWAEVHGNFYGTSFFPIVREIKSNVDILLEIDFQGAKQIKKKFPNAIGIFILPP 247
K+G+FLEWAEVHGN+YGT P+ + + D+LLEID QGA+Q+KKKFP+A+ IFILPP
Sbjct: 61 KAGEFLEWAEVHGNYYGTPKSPVEEALAAGKDVLLEIDVQGARQVKKKFPDAVSIFILPP 120
Query: 248 SLDSLKERLYKRGQDKYDVISRRILSANKEISYANKFDYIIINNKFSKALLQLKAIINA 306
SL+ L+ RL KRG D +VI RR+ A KEI++A++FDY+I+N+ KA+ +LK+II A
Sbjct: 121 SLEELERRLRKRGTDSEEVIERRLAKAKKEIAHADEFDYVIVNDDLEKAVEELKSIILA 179
>gnl|CDD|223272 COG0194, Gmk, Guanylate kinase [Nucleotide transport and
metabolism].
Length = 191
Score = 257 bits (660), Expect = 2e-82
Identities = 98/194 (50%), Positives = 137/194 (70%), Gaps = 4/194 (2%)
Query: 125 SFGNIFIISAPSGAGKSTLVNELLKKDHKIKLSISTTTRPMRPGEKNGREYYFTNIDNFK 184
S G + ++S PSG GKSTLV LL+ D K++ S+S TTR RPGE +G +Y+F + F+
Sbjct: 2 SKGLLIVLSGPSGVGKSTLVKALLE-DDKLRFSVSATTRKPRPGEVDGVDYFFVTEEEFE 60
Query: 185 KLQKSGKFLEWAEVHGNFYGTSFFPIVREIKSNVDILLEIDFQGAKQIKKKFPNAIGIFI 244
+L + +FLEWAE HGN+YGTS P+ + + D++L+ID QGA Q+KKK PNA+ IFI
Sbjct: 61 ELIERDEFLEWAEYHGNYYGTSREPVEQALAEGKDVILDIDVQGALQVKKKMPNAVSIFI 120
Query: 245 LPPSLDSLKERLYKRGQDKYDVISRRILSANKEISYANKFDYIIINNKFSKALLQLKAII 304
LPPSL+ L+ RL RG D +VI+RR+ +A KEIS+A++FDY+I+N+ KAL +LK+II
Sbjct: 121 LPPSLEELERRLKGRGTDSEEVIARRLENAKKEISHADEFDYVIVNDDLEKALEELKSII 180
Query: 305 NANRCFMARVTIED 318
A R R I +
Sbjct: 181 LAERL---RRDINE 191
>gnl|CDD|215373 PLN02691, PLN02691, porphobilinogen deaminase.
Length = 351
Score = 230 bits (588), Expect = 1e-69
Identities = 113/295 (38%), Positives = 165/295 (55%), Gaps = 9/295 (3%)
Query: 375 LAIWQAEYVRKKIIELYPWC----KVEILGITTKGDKIFEKVPLKINEKGLFTKELEMAI 430
LA+ QA R + +P +EI+ I T GDKI ++ I KGLFTKE++ A+
Sbjct: 53 LALAQAYETRDLLKAAHPELAEEGALEIVIIKTTGDKILDQPLADIGGKGLFTKEIDDAL 112
Query: 431 IKGKADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFISNDYISLSTLPKNAVVGTNSL 490
+ G+ D+AVHS+KD+P LP G IL L RED RDAFIS SL+ LP +VVGT SL
Sbjct: 113 LSGRIDIAVHSMKDVPTYLPEGTILPCNLPREDVRDAFISLKAKSLAELPAGSVVGTASL 172
Query: 491 RRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILAAAGLKRLNLQKRIRMLFSPN 550
RR+ I +P L + + RGN+ TRL KL +G A +LA AGLKRL++ + + S +
Sbjct: 173 RRQSQILHKYPHLKVVNFRGNVQTRLRKLQEGVVDATLLALAGLKRLDMTEHATSILSTD 232
Query: 551 QILPAPGQGAIAIEILDNRKELMEMLIPLNHYFSEQTVKAERAVSRNFNGSCKISLAAFA 610
++LPA QGAI I + +++E L LNH + V ERA +GSC+ +A +A
Sbjct: 233 EMLPAVAQGAIGIACRTDDDKMLEYLASLNHEETRLAVACERAFLAALDGSCRTPIAGYA 292
Query: 611 MVNNFNESEINLRAIITNPNGLKIITAEVNGPIDTPETVGL---YAAELLKKKGA 662
+ + + R ++ +P+G +++ GP + V + EL K G
Sbjct: 293 RRD--KDGNCDFRGLVASPDGKQVLETSRKGPYVIDDAVAMGKDAGKELKSKAGP 345
>gnl|CDD|201353 pfam00625, Guanylate_kin, Guanylate kinase.
Length = 183
Score = 176 bits (448), Expect = 1e-51
Identities = 70/181 (38%), Positives = 112/181 (61%), Gaps = 1/181 (0%)
Query: 127 GNIFIISAPSGAGKSTLVNELLKKD-HKIKLSISTTTRPMRPGEKNGREYYFTNIDNFKK 185
++S PSG GKS + LL + K S+S TTRP RPGE +G++Y+F + + +
Sbjct: 2 RRPIVLSGPSGVGKSHIKKALLDEYPEKFGYSVSHTTRPPRPGEVDGKDYHFVSKEEMEN 61
Query: 186 LQKSGKFLEWAEVHGNFYGTSFFPIVREIKSNVDILLEIDFQGAKQIKKKFPNAIGIFIL 245
+ +FLE+AE +GN+YGTS I + +S +L++D QG KQ++K + I +FI
Sbjct: 62 DISANEFLEYAEFNGNYYGTSKEAIEQIAESGKICILDVDIQGVKQLRKAELSPISVFIK 121
Query: 246 PPSLDSLKERLYKRGQDKYDVISRRILSANKEISYANKFDYIIINNKFSKALLQLKAIIN 305
PPSL L+ RL +RG ++ + I++R+ +A +E + FDYII+N+ +A +LK I+
Sbjct: 122 PPSLKVLQRRLKRRGTEQEEKINKRMEAAEQEFQHYALFDYIIVNDDLDEAYKKLKEILE 181
Query: 306 A 306
A
Sbjct: 182 A 182
>gnl|CDD|238026 cd00071, GMPK, Guanosine monophosphate kinase (GMPK, EC 2.7.4.8),
also known as guanylate kinase (GKase), catalyzes the
reversible phosphoryl transfer from adenosine
triphosphate (ATP) to guanosine monophosphate (GMP) to
yield adenosine diphosphate (ADP) and guanosine
diphosphate (GDP). It plays an essential role in the
biosynthesis of guanosine triphosphate (GTP). This
enzyme is also important for the activation of some
antiviral and anticancer agents, such as acyclovir,
ganciclovir, carbovir, and thiopurines.
Length = 137
Score = 173 bits (442), Expect = 3e-51
Identities = 65/174 (37%), Positives = 96/174 (55%), Gaps = 38/174 (21%)
Query: 129 IFIISAPSGAGKSTLVNELLKKDH-KIKLSISTTTRPMRPGEKNGREYYFTNIDNFKKLQ 187
+ ++S PSG GKSTL+ LL++ S+S TTR RPGE +G +Y+F + + F++L
Sbjct: 1 LIVLSGPSGVGKSTLLKRLLEEFDPNFGFSVSHTTRKPRPGEVDGVDYHFVSKEEFERLI 60
Query: 188 KSGKFLEWAEVHGNFYGTSFFPIVREIKSNVDILLEIDFQGAKQIKKKFPNAIGIFILPP 247
++G+FLEWAE HGN+YGTS + + ++LEID QGA+Q+KK +P+A+ IFILPP
Sbjct: 61 ENGEFLEWAEFHGNYYGTSKAAVEEALAEGKIVILEIDVQGARQVKKSYPDAVSIFILPP 120
Query: 248 SLDSLKERLYKRGQDKYDVISRRILSANKEISYANKFDYIIINNKFSKALLQLK 301
DY+I+N+ KA +LK
Sbjct: 121 -------------------------------------DYVIVNDDLEKAYEELK 137
>gnl|CDD|173199 PRK14737, gmk, guanylate kinase; Provisional.
Length = 186
Score = 171 bits (435), Expect = 9e-50
Identities = 83/178 (46%), Positives = 111/178 (62%), Gaps = 1/178 (0%)
Query: 128 NIFIISAPSGAGKSTLVNELLKKDHKIKLSISTTTRPMRPGEKNGREYYFTNIDNFKKLQ 187
+FIIS+ +G GKST++ LL++ SIS TTR RPG++ G+ Y+F I+ FKK
Sbjct: 5 KLFIISSVAGGGKSTIIQALLEEHPDFLFSISCTTRAPRPGDEEGKTYFFLTIEEFKKGI 64
Query: 188 KSGKFLEWAEVHGNFYGTSFFPIVREIKSNVDILLEIDFQGAKQIKKKFPNAI-GIFILP 246
G+FLEWAEVH N+YGT I K +++ID QGAK IK+KFP I IFI P
Sbjct: 65 ADGEFLEWAEVHDNYYGTPKAFIEDAFKEGRSAIMDIDVQGAKIIKEKFPERIVTIFIEP 124
Query: 247 PSLDSLKERLYKRGQDKYDVISRRILSANKEISYANKFDYIIINNKFSKALLQLKAII 304
PS + +ERL RG D + I +RI + E+ AN+FDY IIN+ A+ L+AII
Sbjct: 125 PSEEEWEERLIHRGTDSEESIEKRIENGIIELDEANEFDYKIINDDLEDAIADLEAII 182
>gnl|CDD|214504 smart00072, GuKc, Guanylate kinase homologues. Active enzymes
catalyze ATP-dependent phosphorylation of GMP to GDP.
Structure resembles that of adenylate kinase. So-called
membrane-associated guanylate kinase homologues (MAGUKs)
do not possess guanylate kinase activities; instead at
least some possess protein-binding functions.
Length = 174
Score = 169 bits (430), Expect = 3e-49
Identities = 73/173 (42%), Positives = 103/173 (59%), Gaps = 3/173 (1%)
Query: 136 SGAGKSTLVNELLKKDHKIKL--SISTTTRPMRPGEKNGREYYFTNIDNFKKLQKSGKFL 193
SG GK TL+ EL+++ +S TTRP RPGE NG +Y+F + + F+ KSG FL
Sbjct: 1 SGVGKGTLLAELIQE-IPDAFERVVSHTTRPPRPGEVNGVDYHFVSKEEFEDDIKSGLFL 59
Query: 194 EWAEVHGNFYGTSFFPIVREIKSNVDILLEIDFQGAKQIKKKFPNAIGIFILPPSLDSLK 253
EW E GN+YGTS I + + LL+ID QG KQ++K I IFI PPS + L+
Sbjct: 60 EWGEYEGNYYGTSKETIRQVAEKGKHCLLDIDPQGVKQLRKAQLYPIVIFIAPPSSEELE 119
Query: 254 ERLYKRGQDKYDVISRRILSANKEISYANKFDYIIINNKFSKALLQLKAIINA 306
RL +RG + + I +R+ +A KE + FDY+I+N+ A +LK I+ A
Sbjct: 120 RRLRQRGTETSERIQKRLAAAQKEAQEYHLFDYVIVNDDLEDAYEELKEILEA 172
>gnl|CDD|237809 PRK14738, gmk, guanylate kinase; Provisional.
Length = 206
Score = 155 bits (393), Expect = 2e-43
Identities = 64/181 (35%), Positives = 111/181 (61%), Gaps = 2/181 (1%)
Query: 131 IISAPSGAGKSTLVNELLKKDHKIKLSISTTTRPMRPGEKNGREYYFTNIDNFKKLQKSG 190
+IS PSG GK ++ + ++ ++ TTRP RPGE +G +Y+F + F+++
Sbjct: 17 VISGPSGVGKDAVLARMRERKLPFHFVVTATTRPKRPGEIDGVDYHFVTPEEFREMISQN 76
Query: 191 KFLEWAEVHGNFYGTSFFPIVREIKSNVDILLEIDFQGAKQIKKKFPNAIGIFILPPSLD 250
+ LEWAEV+GN+YG P+ + + S D+++++D QGA IK+ P A+ IF+ PPS+D
Sbjct: 77 ELLEWAEVYGNYYGVPKAPVRQALASGRDVIVKVDVQGAASIKRLVPEAVFIFLAPPSMD 136
Query: 251 SLKERLYKRGQDKYDVISRRILSANKEISYANKFDYIIIN--NKFSKALLQLKAIINANR 308
L RL R + + + RR+ +A E+ +FDY+++N ++ +A+ Q+ AII+A +
Sbjct: 137 ELTRRLELRRTESPEELERRLATAPLELEQLPEFDYVVVNPEDRLDEAVAQIMAIISAEK 196
Query: 309 C 309
Sbjct: 197 S 197
>gnl|CDD|131473 TIGR02420, dksA, RNA polymerase-binding protein DksA. The model
that is the basis for this family describes a small,
pleiotropic protein, DksA (DnaK suppressor A),
originally named as a multicopy suppressor of
temperature sensitivity of dnaKJ mutants. DksA mutants
are defective in quorum sensing, virulence, etc. DksA is
now understood to bind RNA polymerase directly and
modulate its response to small molecules to control the
level of transcription of rRNA. Nearly all members of
this family are in the Proteobacteria. Whether the
closest homologs outside the Proteobacteria function
equivalently is unknown. The low value set for the noise
cutoff allows identification of possible DksA proteins
from outside the proteobacteria. TIGR02419 describes a
closely related family of short sequences usually found
in prophage regions of proteobacterial genomes or in
known phage [Transcription, Transcription factors,
Regulatory functions, Small molecule interactions].
Length = 110
Score = 143 bits (364), Expect = 1e-40
Identities = 53/110 (48%), Positives = 75/110 (68%), Gaps = 1/110 (0%)
Query: 7 MNEEQLAFFKFRLKKLENDLLKNIVKTTEYLRE-TILVPDPADRATIEEENTLELRARDR 65
M+E QL F+ L + + +LL+ KT E+L+E + PDPADRAT EEE LELR RDR
Sbjct: 1 MSEAQLEHFRKILLRWKQELLEEADKTLEHLQEESENFPDPADRATQEEERALELRTRDR 60
Query: 66 ERKLLIKIQQSIINIDKKEYGWCKDTGEPIGILRLLAKPMATLSLEAQQR 115
ERKL+ KI +++ I+ EYG+C++ GE IG+ RL A+P ATL ++ +
Sbjct: 61 ERKLIKKIDEALKRIEDGEYGYCEECGEEIGLRRLEARPTATLCIDCKTL 110
>gnl|CDD|167150 PRK01066, PRK01066, porphobilinogen deaminase; Provisional.
Length = 231
Score = 131 bits (331), Expect = 9e-35
Identities = 70/210 (33%), Positives = 112/210 (53%), Gaps = 13/210 (6%)
Query: 375 LAIWQAEYVRKKIIELYPWCKVEILGITTKGDKIFEKVPLKINEK-GLFTKELEMAIIKG 433
LA+ Q + + +P +I TT+GD +K PL + E G FT +++ ++ G
Sbjct: 27 LAVAQVHECLRLLRSFFPKLWFQISTTTTQGDLD-QKTPLHLVENTGFFTDDVDFLVLSG 85
Query: 434 KADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFISNDYISLSTLPKNAVVGTNSLRRK 493
+ DLA+HS KD+P P + AI DPRD + + LP+ +G++SLRR+
Sbjct: 86 QCDLAIHSAKDLPE--PPKLTVVAITAGLDPRDLLVYAEKYLSQPLPRRPRIGSSSLRRE 143
Query: 494 VLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILAAAGLKRLNLQKRIRMLFSPNQIL 553
L+K FPS II +RG I+ RL L++ +Y AI++A A + RL L R+ ++ + L
Sbjct: 144 ELLKLLFPSGIILDIRGTIEERLKLLEEKKYDAIVVAKAAVLRLGL----RLPYT--KEL 197
Query: 554 PAP---GQGAIAIEILDNRKELMEMLIPLN 580
P P QG +AI + + + +PL
Sbjct: 198 PPPYHPLQGRLAITASKHIRSWKGLFLPLG 227
>gnl|CDD|224648 COG1734, DksA, DnaK suppressor protein [Signal transduction
mechanisms].
Length = 120
Score = 122 bits (308), Expect = 6e-33
Identities = 59/118 (50%), Positives = 80/118 (67%), Gaps = 1/118 (0%)
Query: 7 MNEEQLAFFKFRLKKLENDLLKNIVKTTEYLR-ETILVPDPADRATIEEENTLELRARDR 65
MN+EQL FK +L + + DLL+ + +T E+L+ E PDPADRAT EEE LELR RDR
Sbjct: 1 MNKEQLEHFKNKLLEWKKDLLEELEQTEEHLQDENEASPDPADRATQEEERELELRLRDR 60
Query: 66 ERKLLIKIQQSIINIDKKEYGWCKDTGEPIGILRLLAKPMATLSLEAQQRHELKKKSF 123
ERKLL KI+ ++ I++ YG C++ GEPI RL A+P A L +E Q+R E ++K
Sbjct: 61 ERKLLRKIESALDRIEEGTYGICEECGEPIPEARLEARPTARLCIECQERAERREKQR 118
>gnl|CDD|215414 PLN02772, PLN02772, guanylate kinase.
Length = 398
Score = 127 bits (321), Expect = 8e-32
Identities = 69/181 (38%), Positives = 102/181 (56%), Gaps = 4/181 (2%)
Query: 131 IISAPSGAGKSTLVNELLKK-DHKIKLSISTTTRPMRPGEKNGREYYFTNIDNFKKLQKS 189
+IS PSG GK TL++ L+K+ S+S TTR R EK+G Y+FT +K K
Sbjct: 139 VISGPSGVGKGTLISMLMKEFPSMFGFSVSHTTRAPREMEKDGVHYHFTERSVMEKEIKD 198
Query: 190 GKFLEWAEVHGNFYGTSFFPIVREIKSNVDILLEIDFQGAKQIKKKFPNAIGIFILPPSL 249
GKFLE+A VHGN YGTS + S +L+ID QGA+ ++ AI IFI PPS+
Sbjct: 199 GKFLEFASVHGNLYGTSIEAVEVVTDSGKRCILDIDVQGARSVRASSLEAIFIFICPPSM 258
Query: 250 DSLKERLYKRGQDKYDVISRRILSANKEISYANK---FDYIIINNKFSKALLQLKAIINA 306
+ L++RL RG + + I +R+ +A E+ FD+I+ N+ + LK ++
Sbjct: 259 EELEKRLRARGTETEEQIQKRLRNAEAELEQGKSSGIFDHILYNDNLEECYKNLKKLLGL 318
Query: 307 N 307
+
Sbjct: 319 D 319
>gnl|CDD|182722 PRK10778, dksA, RNA polymerase-binding transcription factor;
Provisional.
Length = 151
Score = 97.9 bits (243), Expect = 6e-24
Identities = 50/119 (42%), Positives = 78/119 (65%), Gaps = 1/119 (0%)
Query: 4 KDYMNEEQLAFFKFRLKKLENDLLKNIVKTTEYLR-ETILVPDPADRATIEEENTLELRA 62
++YMNE QLA FK L+ N L + +T +++ E PDP DRA EEE +LELR
Sbjct: 29 EEYMNEAQLAHFKRILEAWRNQLRDEVDRTVTHMQDEAANFPDPVDRAAQEEEFSLELRN 88
Query: 63 RDRERKLLIKIQQSIINIDKKEYGWCKDTGEPIGILRLLAKPMATLSLEAQQRHELKKK 121
RDRERKL+ KI++++ ++ +++G+C+ G IGI RL A+P A L ++ + E+++K
Sbjct: 89 RDRERKLIKKIEKTLKKVEDEDFGYCESCGVEIGIRRLEARPTADLCIDCKTLAEIREK 147
>gnl|CDD|234744 PRK00392, rpoZ, DNA-directed RNA polymerase subunit omega;
Reviewed.
Length = 69
Score = 76.9 bits (190), Expect = 2e-17
Identities = 34/63 (53%), Positives = 43/63 (68%), Gaps = 1/63 (1%)
Query: 311 MARVTIEDGLKKINNRFKLTLCAVYRARQLLKGHTKKIIGCDNDKVTVIALREISHGKIG 370
MAR TIED L+K++NR++L L A RARQL G K + +DK VIALREI+ GK+
Sbjct: 1 MARPTIEDLLEKVDNRYELVLLAAKRARQLRAGA-KPPVDKSSDKPVVIALREIAEGKVT 59
Query: 371 VEI 373
EI
Sbjct: 60 YEI 62
>gnl|CDD|224672 COG1758, RpoZ, DNA-directed RNA polymerase, subunit K/omega
[Transcription].
Length = 74
Score = 61.9 bits (151), Expect = 3e-12
Identities = 32/65 (49%), Positives = 39/65 (60%), Gaps = 1/65 (1%)
Query: 311 MARVTIEDGLKKINNRFKLTLCAVYRARQL-LKGHTKKIIGCDNDKVTVIALREISHGKI 369
MAR TIED L K+ NR++L + A RARQL + DK VIALREI+ GKI
Sbjct: 1 MARPTIEDLLDKVGNRYELVVVAAKRARQLAAGAPPLVDDEENKDKPVVIALREIAEGKI 60
Query: 370 GVEIR 374
+EI
Sbjct: 61 PIEIL 65
>gnl|CDD|188073 TIGR00690, rpoZ, DNA-directed RNA polymerase, omega subunit. This
small component of highly purified E. coli RNA
polymerase is not required for transcription, but acts
in assembly and is present in stochiometric amounts. The
trusted cutoff excludes archaeal homologs but captures
some organellar sequences [Transcription, DNA-dependent
RNA polymerase].
Length = 60
Score = 60.2 bits (146), Expect = 8e-12
Identities = 32/59 (54%), Positives = 39/59 (66%)
Query: 311 MARVTIEDGLKKINNRFKLTLCAVYRARQLLKGHTKKIIGCDNDKVTVIALREISHGKI 369
MAR TIED +KKI +R+ L L A RARQL I+ +NDK TVIALREI+ G +
Sbjct: 1 MARPTIEDAMKKIGSRYDLVLVAARRARQLQLEGGDPIVPEENDKPTVIALREIAAGLV 59
>gnl|CDD|202802 pfam03900, Porphobil_deamC, Porphobilinogen deaminase, C-terminal
domain.
Length = 72
Score = 59.2 bits (144), Expect = 3e-11
Identities = 22/74 (29%), Positives = 39/74 (52%), Gaps = 3/74 (4%)
Query: 586 QTVKAERAVSRNFNGSCKISLAAFAMVNNFNESEINLRAIITNPNGLKIITAEVNGPIDT 645
V AERA R G C++ + A+A++ + + L+ ++ +P+G ++ EV G I+
Sbjct: 2 LCVLAERAFLRELEGGCQVPIGAYAVLKD---GNLRLKGLVGSPDGTRVFEIEVRGDIED 58
Query: 646 PETVGLYAAELLKK 659
E +G AE L
Sbjct: 59 AEELGKKLAEELLA 72
>gnl|CDD|234050 TIGR02890, bacill_yteA, regulatory protein, yteA family. Members
of this predicted regulatory protein are found only in
endospore-forming members of the Firmicutes group of
bacteria, and in nearly every such species; Clostridium
perfringens seems to be an exception. The member from
Bacillus subtilis, the model system for the study of the
sporulation program, has been designated both yteA and
yzwB. Some (but not all) members of this family show a
strong sequence match to PFAM family pfam01258 the
C4-type zinc finger protein, DksA/TraR family, but only
one of the four key Cys residues is conserved. All
members of this protein family share an additional
C-terminal domain. Smaller proteins from the
proteobacteria with just the N-terminal domain,
including DksA and DksA2 are RNA polymerase-binding
regulatory proteins even if the Zn-binding site is not
conserved [Unknown function, General].
Length = 159
Score = 53.9 bits (130), Expect = 2e-08
Identities = 36/124 (29%), Positives = 56/124 (45%), Gaps = 14/124 (11%)
Query: 10 EQLAFFKFRLKKLENDLLKNIVKTTEYLRETILVPD----------PADRAT--IEEENT 57
+QLA K L + + +L + + + + PAD AT E E
Sbjct: 1 QQLAELKNMLLQEKKELEQRLKQMNKEDGIASQRESTGELSQYDNHPADLATELYEREKD 60
Query: 58 LELRARDRERKLLIKIQQSIINIDKKEYGWCKDTGEPIGILRLLAKPMATLSLEAQQRHE 117
+ LR + E + L +I+ ++ I+ YG C+ G+PI RL A P AT +E Q R E
Sbjct: 61 IALR--EHEERELREIEHALQKIENGTYGICEVCGKPIPYERLEAIPTATTCVECQNRKE 118
Query: 118 LKKK 121
+K
Sbjct: 119 VKND 122
>gnl|CDD|201690 pfam01258, zf-dskA_traR, Prokaryotic dksA/traR C4-type zinc finger.
Length = 36
Score = 44.7 bits (106), Expect = 1e-06
Identities = 17/33 (51%), Positives = 20/33 (60%)
Query: 85 YGWCKDTGEPIGILRLLAKPMATLSLEAQQRHE 117
YG C+D GE I RL A P ATL +E Q+ E
Sbjct: 3 YGICEDCGEEIPEARLEAVPGATLCIECQEERE 35
>gnl|CDD|201652 pfam01192, RNA_pol_Rpb6, RNA polymerase Rpb6. Rpb6 is an essential
subunit in the eukaryotic polymerases Pol I, II and III.
This family also contains the bacterial equivalent to
Rpb6, the omega subunit. Rpb6 and omega are structurally
conserved and both function in polymerase assembly.
Length = 57
Score = 40.7 bits (96), Expect = 6e-05
Identities = 22/57 (38%), Positives = 27/57 (47%)
Query: 317 EDGLKKINNRFKLTLCAVYRARQLLKGHTKKIIGCDNDKVTVIALREISHGKIGVEI 373
E K NR++L RA+QL G + K VIAL EI+ GKI EI
Sbjct: 1 ERLTSKYLNRYELARIIAKRAKQLSYGAPPLVDEESEIKPVVIALEEIADGKIPPEI 57
>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 = 38.9 bits (91), Expect = 0.003
Identities = 43/171 (25%), Positives = 77/171 (45%), Gaps = 16/171 (9%)
Query: 127 GNIFIISAPSGAGKSTLVN---ELLKKDHKIKLSISTTTRPMRPGEKNGREYYFTNIDNF 183
G + + PSGAGK TL++ L D ++ TRP G +N + + + F
Sbjct: 1 GRLIYVVGPSGAGKDTLLDYARARLAGDPRVHFVRRVITRPASAGGEN---HIALSTEEF 57
Query: 184 KKLQKSGKF-LEWAEVHGNFYGTSFFP--IVREIKSNVDILLEIDFQGAKQIKKKFPNAI 240
+ G F L W + HG YG P I + +++ +++ + ++++PN +
Sbjct: 58 DHREDGGAFALSW-QAHGLSYG---IPAEIDQWLEAGDVVVVNGSRAVLPEARQRYPNLL 113
Query: 241 GIFILPPSLDSLKERLYKRGQDKYDVISRRILSANKEISYANKFDYIIINN 291
+ I D L +RL RG++ + I R L+ + + A D I+N
Sbjct: 114 VVNITASP-DVLAQRLAARGRESREEIEER-LARSARFAAAP-ADVTTIDN 161
>gnl|CDD|226232 COG3709, COG3709, Uncharacterized component of phosphonate
metabolism [Inorganic ion transport and metabolism].
Length = 192
Score = 38.1 bits (89), Expect = 0.007
Identities = 37/156 (23%), Positives = 66/156 (42%), Gaps = 14/156 (8%)
Query: 125 SFGNIFIISAPSGAGKSTLVNEL---LKKDHKIKLSISTTTRPMRPGEKNGREYYFTNID 181
G + + PSGAGK TL++ L ++ TRP G ++ + +
Sbjct: 3 FMGRLIAVVGPSGAGKDTLLDAARARLAGRPRLHFVRRVITRPADAGGED---HDALSEA 59
Query: 182 NFKKLQKSGKF-LEWAEVHGNFYGTSFFP--IVREIKSNVDILLEIDFQGAKQIKKKFPN 238
F G F L W + HG YG P I + + +L+ Q ++++P
Sbjct: 60 EFNTRAGQGAFALSW-QAHGLSYG---IPAEIDLWLAAGDVVLVNGSRAVLPQARRRYPQ 115
Query: 239 AIGIFILPPSLDSLKERLYKRGQDKYDVISRRILSA 274
+ + + S + L +RL +RG++ + I R+ A
Sbjct: 116 -LLVVCITASPEVLAQRLAERGRESREEILARLARA 150
>gnl|CDD|233859 TIGR02419, C4_traR_proteo, phage/conjugal plasmid C-4 type zinc
finger protein, TraR family. Members of this family are
putative C4-type zinc finger proteins found almost
exclusively in prophage regions, actual phage, or
conjugal transfer regions of the Proteobactia. This
small protein (about 70 amino acids) appears homologous
to but is smaller than DksA (DnaK suppressor protein),
found to be critical for regulating transcription of
ribosomal RNA [Mobile and extrachromosomal element
functions, Prophage functions].
Length = 63
Score = 33.5 bits (77), Expect = 0.025
Identities = 20/70 (28%), Positives = 24/70 (34%), Gaps = 10/70 (14%)
Query: 45 DPADRATIEEENTLELRARDRERKLLIKIQQSIINIDKKEYGWCKDTGEPIGILRLLAKP 104
D DRA EL ER L + C+D GEPI R A P
Sbjct: 1 DEFDRAQ-------ELEEELLERALA---AARAKKVIGPSLRECEDCGEPIPEARREALP 50
Query: 105 MATLSLEAQQ 114
T + Q+
Sbjct: 51 GVTRCVSCQE 60
>gnl|CDD|206726 cd04163, Era, E. coli Ras-like protein (Era) is a multifunctional
GTPase. Era (E. coli Ras-like protein) is a
multifunctional GTPase found in all bacteria except some
eubacteria. It binds to the 16S ribosomal RNA (rRNA) of
the 30S subunit and appears to play a role in the
assembly of the 30S subunit, possibly by chaperoning the
16S rRNA. It also contacts several assembly elements of
the 30S subunit. Era couples cell growth with
cytokinesis and plays a role in cell division and energy
metabolism. Homologs have also been found in eukaryotes.
Era contains two domains: the N-terminal GTPase domain
and a C-terminal domain KH domain that is critical for
RNA binding. Both domains are important for Era
function. Era is functionally able to compensate for
deletion of RbfA, a cold-shock adaptation protein that
is required for efficient processing of the 16S rRNA.
Length = 168
Score = 34.7 bits (81), Expect = 0.065
Identities = 20/45 (44%), Positives = 27/45 (60%), Gaps = 10/45 (22%)
Query: 123 FKSFGNIFIISAPSGAGKSTLVNELLKKDHKIKLSIST----TTR 163
FKS G + II P+ GKSTL+N L+ + K+SI + TTR
Sbjct: 1 FKS-GFVAIIGRPN-VGKSTLLNALVGQ----KISIVSPKPQTTR 39
>gnl|CDD|234988 PRK01889, PRK01889, GTPase RsgA; Reviewed.
Length = 356
Score = 35.7 bits (83), Expect = 0.067
Identities = 11/17 (64%), Positives = 13/17 (76%)
Query: 135 PSGAGKSTLVNELLKKD 151
SG GKSTLVN LL ++
Sbjct: 203 SSGVGKSTLVNALLGEE 219
>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 = 34.2 bits (79), Expect = 0.082
Identities = 13/53 (24%), Positives = 22/53 (41%)
Query: 129 IFIISAPSGAGKSTLVNELLKKDHKIKLSISTTTRPMRPGEKNGREYYFTNID 181
+ ++ G+GKST LL++ + LS T + +R YY
Sbjct: 1 LILMVGLPGSGKSTFARRLLRELGAVVLSSDTLRKRLRGDGPPDISYYARASG 53
>gnl|CDD|206747 cd01854, YjeQ_EngC, Ribosomal interacting GTPase YjeQ/EngC, a
circularly permuted subfamily of the Ras GTPases. YjeQ
(YloQ in Bacillus subtilis) is a ribosomal small
subunit-dependent GTPase; hence also known as RsgA. YjeQ
is a late-stage ribosomal biogenesis factor involved in
the 30S subunit maturation, and it represents a protein
family whose members are broadly conserved in bacteria
and have been shown to be essential to the growth of E.
coli and B. subtilis. Proteins of the YjeQ family
contain all sequence motifs typical of the vast class of
P-loop-containing GTPases, but show a circular
permutation, with a G4-G1-G3 pattern of motifs as
opposed to the regular G1-G3-G4 pattern seen in most
GTPases. All YjeQ family proteins display a unique
domain architecture, which includes an N-terminal
OB-fold RNA-binding domain, the central permuted GTPase
domain, and a zinc knuckle-like C-terminal cysteine
domain.
Length = 211
Score = 34.7 bits (81), Expect = 0.087
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 127 GNIFIISAPSGAGKSTLVNELLKKDH 152
G ++ SG GKSTL+N LL +
Sbjct: 85 GKTSVLVGQSGVGKSTLLNALLPELV 110
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 34.9 bits (81), Expect = 0.15
Identities = 17/47 (36%), Positives = 26/47 (55%), Gaps = 4/47 (8%)
Query: 138 AGKSTLVNELLKKDHKIKLSISTTTRPM--RPGEKNGREYYFTNIDN 182
GKS+L+N +L ++ I I+ TTR E++GR+Y ID
Sbjct: 189 VGKSSLINAILGEERVIVSDIAGTTRDSIDIEFERDGRKYVL--IDT 233
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 34.3 bits (80), Expect = 0.23
Identities = 18/49 (36%), Positives = 27/49 (55%), Gaps = 10/49 (20%)
Query: 138 AGKSTLVNELLKKDHKIKLSISTTTR-----PMRPGEKNGREYYFTNID 181
GKS+L+N LL ++ I I+ TTR P E++G++Y ID
Sbjct: 184 VGKSSLINALLGEERVIVSDIAGTTRDSIDTPF---ERDGQKYTL--ID 227
>gnl|CDD|222775 PHA00080, PHA00080, DksA-like zinc finger domain containing
protein.
Length = 72
Score = 30.9 bits (70), Expect = 0.28
Identities = 21/82 (25%), Positives = 29/82 (35%), Gaps = 19/82 (23%)
Query: 44 PDPADRATIEEENTLELRARDRERKLLIKIQQSIINIDKKEYG----WCKDTGEPIGILR 99
D DRA E+ RER ++ N K C++ G+PI R
Sbjct: 1 ADIIDRAA-------EIEELQRER--------ALANRRNKYQAPSATHCEECGDPIPEAR 45
Query: 100 LLAKPMATLSLEAQQRHELKKK 121
A P + Q+ ELK
Sbjct: 46 REAVPGCRTCVSCQEILELKSY 67
>gnl|CDD|234631 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 33.6 bits (78), Expect = 0.29
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 127 GNIFIISAPSGAGKSTLVNELL 148
G + +++ SG GKSTL+N L
Sbjct: 164 GKVTVLAGQSGVGKSTLLNALA 185
>gnl|CDD|224084 COG1162, COG1162, Predicted GTPases [General function prediction
only].
Length = 301
Score = 33.4 bits (77), Expect = 0.33
Identities = 15/52 (28%), Positives = 23/52 (44%), Gaps = 2/52 (3%)
Query: 97 ILRLLAKPMATLSLEAQQRHELKKKSFKSFGNIFIISAPSGAGKSTLVNELL 148
+ P+ +S + E + G I ++ SG GKSTL+N LL
Sbjct: 136 EYEDIGYPVLFVSAKNGDGLEELAELLA--GKITVLLGQSGVGKSTLINALL 185
>gnl|CDD|217416 pfam03193, DUF258, Protein of unknown function, DUF258.
Length = 161
Score = 32.5 bits (75), Expect = 0.33
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 127 GNIFIISAPSGAGKSTLVNELL 148
G +++ SG GKSTL+N LL
Sbjct: 35 GKTSVLAGQSGVGKSTLLNALL 56
>gnl|CDD|236648 PRK10078, PRK10078, ribose 1,5-bisphosphokinase; Provisional.
Length = 186
Score = 32.8 bits (75), Expect = 0.34
Identities = 40/171 (23%), Positives = 71/171 (41%), Gaps = 35/171 (20%)
Query: 135 PSGAGKSTLVNELLKKDHKIKL-SISTTTRPMRPGEKN----GREYYFTNIDNFKKLQKS 189
PSG+GK +L+ L +++ L + TRP G +N + +FT
Sbjct: 10 PSGSGKDSLLAALRQREQTQLLVAHRYITRPASAGSENHIALSEQEFFTR-------AGQ 62
Query: 190 GKF-LEWAEVHGNFYGTSFFPIVREIKSNVDILLEIDF----QGAK----QIKKKFPNAI 240
F L W +G +YG + +D+ L F G++ Q + ++ +A+
Sbjct: 63 NLFALSW-HANGLYYG---------VGIEIDLWLHAGFDVLVNGSRAHLPQARARYQSAL 112
Query: 241 GIFILPPSLDSLKERLYKRGQDKYDVISRRILSANKEISYANKFDYIIINN 291
L S + L++RL RG++ I+ R+ A + D +NN
Sbjct: 113 LPVCLQVSPEILRQRLENRGRENASEINARLARAARY----QPQDCHTLNN 159
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 33.1 bits (77), Expect = 0.35
Identities = 19/47 (40%), Positives = 27/47 (57%), Gaps = 10/47 (21%)
Query: 121 KSFKSFGNIFIISAPSGAGKSTLVNELLKKDHKIKLSIST----TTR 163
FKS G + I+ P+ GKSTL+N L+ + K+SI + TTR
Sbjct: 1 MGFKS-GFVAIVGRPN-VGKSTLLNALVGQ----KISIVSPKPQTTR 41
>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 = 32.3 bits (73), Expect = 0.36
Identities = 13/77 (16%), Positives = 22/77 (28%), Gaps = 3/77 (3%)
Query: 127 GNIFIISAPSGAGKSTLVNEL---LKKDHKIKLSISTTTRPMRPGEKNGREYYFTNIDNF 183
G + +I P G+GK+TL L L + I ++ +
Sbjct: 2 GEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASG 61
Query: 184 KKLQKSGKFLEWAEVHG 200
+ L A
Sbjct: 62 SGELRLRLALALARKLK 78
>gnl|CDD|206648 cd00882, Ras_like_GTPase, Rat sarcoma (Ras)-like superfamily of
small guanosine triphosphatases (GTPases). Ras-like
GTPase superfamily. The Ras-like superfamily of small
GTPases consists of several families with an extremely
high degree of structural and functional similarity. The
Ras superfamily is divided into at least four families
in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families.
This superfamily also includes proteins like the GTP
translation factors, Era-like GTPases, and G-alpha chain
of the heterotrimeric G proteins. Members of the Ras
superfamily regulate a wide variety of cellular
functions: the Ras family regulates gene expression, the
Rho family regulates cytoskeletal reorganization and
gene expression, the Rab and Sar1/Arf families regulate
vesicle trafficking, and the Ran family regulates
nucleocytoplasmic transport and microtubule
organization. The GTP translation factor family
regulates initiation, elongation, termination, and
release in translation, and the Era-like GTPase family
regulates cell division, sporulation, and DNA
replication. Members of the Ras superfamily are
identified by the GTP binding site, which is made up of
five characteristic sequence motifs, and the switch I
and switch II regions.
Length = 161
Score = 32.4 bits (74), Expect = 0.40
Identities = 11/29 (37%), Positives = 15/29 (51%)
Query: 135 PSGAGKSTLVNELLKKDHKIKLSISTTTR 163
G GKS+L+N LL + + TTR
Sbjct: 5 RGGVGKSSLLNALLGGEVGEVSDVPGTTR 33
>gnl|CDD|237040 PRK12289, PRK12289, GTPase RsgA; Reviewed.
Length = 352
Score = 33.1 bits (76), Expect = 0.47
Identities = 13/40 (32%), Positives = 22/40 (55%), Gaps = 2/40 (5%)
Query: 108 LSLEAQQRHELKKKSFKSFGNIFIISAPSGAGKSTLVNEL 147
+S+E E + + I +++ PSG GKS+L+N L
Sbjct: 155 ISVETGIGLEALLEQLR--NKITVVAGPSGVGKSSLINRL 192
>gnl|CDD|234274 TIGR03594, GTPase_EngA, ribosome-associated GTPase EngA. EngA
(YfgK, Der) is a ribosome-associated essential GTPase
with a duplication of its GTP-binding domain. It is
broadly to universally distributed among bacteria. It
appears to function in ribosome biogenesis or stability
[Protein synthesis, Other].
Length = 429
Score = 33.2 bits (77), Expect = 0.49
Identities = 21/49 (42%), Positives = 27/49 (55%), Gaps = 10/49 (20%)
Query: 138 AGKSTLVNELLKKDHKIKLSISTTTR-----PMRPGEKNGREYYFTNID 181
GKSTLVN LL ++ I I+ TTR P E+NG++Y ID
Sbjct: 183 VGKSTLVNALLGEERVIVSDIAGTTRDSIDIPF---ERNGKKYTL--ID 226
>gnl|CDD|234033 TIGR02857, CydD, thiol reductant ABC exporter, CydD 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. Unfortunately, the gene symbol
nomenclature adopted based on this operon in B. subtilis
assigns cydC to the third gene in the operon where this
gene is actually homologous to the E. coli cydD gene. We
have chosen to name all homologs in this family in
accordance with the precedence of publication of the E.
coli name, CydD.
Length = 529
Score = 33.0 bits (76), Expect = 0.51
Identities = 13/22 (59%), Positives = 15/22 (68%)
Query: 127 GNIFIISAPSGAGKSTLVNELL 148
G + PSGAGKSTL+N LL
Sbjct: 348 GERVALVGPSGAGKSTLLNLLL 369
>gnl|CDD|238549 cd01129, PulE-GspE, PulE/GspE The type II secretory pathway is the
main terminal branch of the general secretory pathway
(GSP). It is responsible for the export the majority of
Gram-negative bacterial exoenzymes and toxins. PulE is a
cytoplasmic protein of the GSP, which contains an ATP
binding site and a tetracysteine motif. This subgroup
also includes PillB and HofB.
Length = 264
Score = 32.2 bits (74), Expect = 0.61
Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 5/77 (6%)
Query: 92 GEPIGILRLLAKPMATLSLEAQQRHELKKKSFKSFGN----IFIISAPSGAGKSTLVNEL 147
GE + +LR+L K L LE + F+ I +++ P+G+GK+T +
Sbjct: 42 GESV-VLRILDKKNQILDLEKLGLKPENLEIFRKLLEKPHGIILVTGPTGSGKTTTLYSA 100
Query: 148 LKKDHKIKLSISTTTRP 164
L + + + +I T P
Sbjct: 101 LSELNTPEKNIITVEDP 117
>gnl|CDD|234806 PRK00635, PRK00635, excinuclease ABC subunit A; Provisional.
Length = 1809
Score = 32.9 bits (75), Expect = 0.77
Identities = 15/48 (31%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 102 AKPMATLSLEAQQRHELKKKSFK-SFGNIFIISAPSGAGKSTLVNELL 148
+ TL+L +H LK + G + +++ SG+GKS+L+N+ L
Sbjct: 595 TNSLGTLTLSKATKHNLKDLTISLPLGRLTVVTGVSGSGKSSLINDTL 642
>gnl|CDD|234734 PRK00349, uvrA, excinuclease ABC subunit A; Reviewed.
Length = 943
Score = 32.7 bits (76), Expect = 0.77
Identities = 11/15 (73%), Positives = 13/15 (86%)
Query: 136 SGAGKSTLVNELLKK 150
SG+GKSTL+NE L K
Sbjct: 644 SGSGKSTLINETLYK 658
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 30.7 bits (70), Expect = 0.89
Identities = 8/27 (29%), Positives = 16/27 (59%)
Query: 128 NIFIISAPSGAGKSTLVNELLKKDHKI 154
I +++ SG+GK+TL+ L ++
Sbjct: 5 GIGVLTGESGSGKTTLLRRLARQLPNR 31
>gnl|CDD|226426 COG3911, COG3911, Predicted ATPase [General function prediction
only].
Length = 183
Score = 31.4 bits (71), Expect = 0.94
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 129 IFIISAPSGAGKSTLVNEL 147
FI++ GAGK+TL+ L
Sbjct: 11 RFILTGGPGAGKTTLLAAL 29
>gnl|CDD|206682 cd01895, EngA2, EngA2 GTPase contains the second domain of EngA.
This EngA2 subfamily CD represents the second GTPase
domain of EngA and its orthologs, which are composed of
two adjacent GTPase domains. Since the sequences of the
two domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family. Although the exact function of
these proteins has not been elucidated, studies have
revealed that the E. coli EngA homolog, Der, and
Neisseria gonorrhoeae EngA are essential for cell
viability. A recent report suggests that E. coli Der
functions in ribosome assembly and stability.
Length = 174
Score = 30.9 bits (71), Expect = 1.2
Identities = 18/49 (36%), Positives = 26/49 (53%), Gaps = 10/49 (20%)
Query: 138 AGKSTLVNELLKKDHKIKLSISTTTR-----PMRPGEKNGREYYFTNID 181
GKS+L+N LL ++ I I+ TTR P E +G++Y ID
Sbjct: 13 VGKSSLLNALLGEERVIVSDIAGTTRDSIDVPF---EYDGQKYTL--ID 56
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 31.8 bits (73), Expect = 1.3
Identities = 16/36 (44%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 128 NIFIISAPSGAGKSTLVNELLKKDHKIKLSISTTTR 163
+ II P+ GKS+L+N LL +D I I+ TTR
Sbjct: 219 KVVIIGRPN-VGKSSLLNALLGRDRAIVTDIAGTTR 253
>gnl|CDD|238899 cd01918, HprK_C, HprK/P, the bifunctional histidine-containing
protein kinase/phosphatase, controls the phosphorylation
state of the phosphocarrier protein HPr and regulates
the utilization of carbon sources by gram-positive
bacteria. It catalyzes both the ATP-dependent
phosphorylation of Ser-46 of HPr and its
dephosphorylation by phosphorolysis. The latter reaction
uses inorganic phosphate as substrate and produces
pyrophosphate. Phosphoenolpyruvate carboxykinase (PEPCK)
and the C-terminal catalytic domain of HprK/P are
structurally similar with conserved active site residues
suggesting these two phosphotransferases have related
functions. The HprK/P N-terminal domain is structurally
similar to the N-terminal domains of the MurE and MurF
amino acid ligases.
Length = 149
Score = 30.7 bits (70), Expect = 1.3
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 132 ISAPSGAGKSTLVNELLKKDH 152
I+ PSG GKS L EL+K+ H
Sbjct: 19 ITGPSGIGKSELALELIKRGH 39
>gnl|CDD|235825 PRK06547, PRK06547, hypothetical protein; Provisional.
Length = 172
Score = 30.9 bits (70), Expect = 1.4
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 129 IFIISAPSGAGKSTLVNEL 147
+I SG+GK+TL L
Sbjct: 17 TVLIDGRSGSGKTTLAGAL 35
>gnl|CDD|205733 pfam13555, AAA_29, P-loop containing region of AAA domain.
Length = 60
Score = 28.7 bits (65), Expect = 1.4
Identities = 8/18 (44%), Positives = 13/18 (72%)
Query: 127 GNIFIISAPSGAGKSTLV 144
+++ PSG+GKSTL+
Sbjct: 21 PKGTLLTGPSGSGKSTLI 38
>gnl|CDD|236870 PRK11174, PRK11174, cysteine/glutathione ABC transporter
membrane/ATP-binding component; Reviewed.
Length = 588
Score = 31.4 bits (72), Expect = 1.7
Identities = 18/48 (37%), Positives = 25/48 (52%), Gaps = 15/48 (31%)
Query: 101 LAKPMATLSLEAQQRHELKKKSFKSFGNIFIISAPSGAGKSTLVNELL 148
LA P+ +L A QR I ++ PSGAGK++L+N LL
Sbjct: 365 LAGPL-NFTLPAGQR-------------IALV-GPSGAGKTSLLNALL 397
>gnl|CDD|213205 cd03238, ABC_UvrA, ATP-binding cassette domain of the excision
repair protein UvrA. Nucleotide excision repair in
eubacteria is a process that repairs DNA damage by the
removal of a 12-13-mer oligonucleotide containing the
lesion. Recognition and cleavage of the damaged DNA is a
multistep ATP-dependent reaction that requires the UvrA,
UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases,
with UvrA having two ATP binding sites, which have the
characteristic signature of the family of ABC proteins,
and UvrB having one ATP binding site that is
structurally related to that of helicases.
Length = 176
Score = 30.4 bits (69), Expect = 1.7
Identities = 13/37 (35%), Positives = 19/37 (51%)
Query: 126 FGNIFIISAPSGAGKSTLVNELLKKDHKIKLSISTTT 162
+ +++ SG+GKSTLVNE L K +L
Sbjct: 20 LNVLVVVTGVSGSGKSTLVNEGLYASGKARLISFLPK 56
>gnl|CDD|224113 COG1192, Soj, ATPases involved in chromosome partitioning [Cell
division and chromosome partitioning].
Length = 259
Score = 31.0 bits (70), Expect = 1.8
Identities = 20/103 (19%), Positives = 47/103 (45%), Gaps = 6/103 (5%)
Query: 205 TSFFPIVREIKSNVDILLEIDFQGAKQIKKKFPNAIGIFILPPSLDSLKERLYKRGQDKY 264
TS+ + +++ ++ LL + I G+ ++P ++D L + + +
Sbjct: 47 TSWLGLRPDLEGDLYNLLS-GLKERPDILDYTVVIEGLDLIPSNID-----LAEGAEIEL 100
Query: 265 DVISRRILSANKEISYANKFDYIIINNKFSKALLQLKAIINAN 307
+ +++ +L + +DYIII+ S +L L A+ A+
Sbjct: 101 NAVAKELLLKRLLDPVKDDYDYIIIDTPPSLGVLTLNALAAAD 143
>gnl|CDD|129567 TIGR00475, selB, selenocysteine-specific elongation factor SelB.
In prokaryotes, the incorporation of selenocysteine as
the 21st amino acid, encoded by TGA, requires several
elements: SelC is the tRNA itself, SelD acts as a donor
of reduced selenium, SelA modifies a serine residue on
SelC into selenocysteine, and SelB is a
selenocysteine-specific translation elongation factor.
3-prime or 5-prime non-coding elements of mRNA have been
found as probable structures for directing
selenocysteine incorporation. This model describes the
elongation factor SelB, a close homolog rf EF-Tu. It may
function by replacing EF-Tu. A C-terminal domain not
found in EF-Tu is in all SelB sequences in the seed
alignment except that from Methanococcus jannaschii.
This model does not find an equivalent protein for
eukaryotes [Protein synthesis, Translation factors].
Length = 581
Score = 31.4 bits (71), Expect = 1.9
Identities = 23/91 (25%), Positives = 33/91 (36%), Gaps = 15/91 (16%)
Query: 73 IQQSIINIDKKEYGWCKDTGEPIGILRLLAKPMATLSL--------------EAQQRHEL 118
I +++ +D E G TGE + +L LL P + + E + L
Sbjct: 74 IDAALLVVDADE-GVMTQTGEHLAVLDLLGIPHTIVVITKADRVNEEEIKRTEMFMKQIL 132
Query: 119 KKKSFKSFGNIFIISAPSGAGKSTLVNELLK 149
F IF SA +G G L EL
Sbjct: 133 NSYIFLKNAKIFKTSAKTGQGIGELKKELKN 163
>gnl|CDD|232886 TIGR00231, small_GTP, small GTP-binding protein domain. Proteins
with a small GTP-binding domain recognized by this model
include Ras, RhoA, Rab11, translation elongation factor
G, translation initiation factor IF-2, tetratcycline
resistance protein TetM, CDC42, Era, ADP-ribosylation
factors, tdhF, and many others. In some proteins the
domain occurs more than once.This model recognizes a
large number of small GTP-binding proteins and related
domains in larger proteins. Note that the alpha chains
of heterotrimeric G proteins are larger proteins in
which the NKXD motif is separated from the GxxxxGK[ST]
motif (P-loop) by a long insert and are not easily
detected by this model [Unknown function, General].
Length = 162
Score = 30.4 bits (69), Expect = 1.9
Identities = 20/57 (35%), Positives = 26/57 (45%), Gaps = 3/57 (5%)
Query: 127 GNIFIISAPSGAGKSTLVNELLKKDHKIKLSISTTTRPMRPG--EKNGREYYFTNID 181
I I+ P GKSTL+N LL I TTR E++G+ Y F +D
Sbjct: 2 IKIVIVGDP-NVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLD 57
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 29.6 bits (66), Expect = 2.0
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 129 IFIISAPSGAGKSTLVNELLKK 150
I +I+ P G+GKSTL +L +K
Sbjct: 1 IILITGPPGSGKSTLAKKLAEK 22
>gnl|CDD|226360 COG3840, ThiQ, ABC-type thiamine transport system, ATPase component
[Coenzyme metabolism].
Length = 231
Score = 30.4 bits (69), Expect = 2.2
Identities = 13/19 (68%), Positives = 14/19 (73%)
Query: 127 GNIFIISAPSGAGKSTLVN 145
G I I PSGAGKSTL+N
Sbjct: 25 GEIVAILGPSGAGKSTLLN 43
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 30.6 bits (70), Expect = 2.6
Identities = 20/47 (42%), Positives = 27/47 (57%), Gaps = 10/47 (21%)
Query: 121 KSFKSFGNIFIISAPSGAGKSTLVNELLKKDHKIKLSIST----TTR 163
FKS G + II P+ GKSTL+N L+ + K+SI + TTR
Sbjct: 2 MKFKS-GFVAIIGRPN-VGKSTLLNALVGQ----KISIVSPKPQTTR 42
>gnl|CDD|234175 TIGR03348, VI_IcmF, type VI secretion protein IcmF. Members of
this protein family are IcmF homologs and tend to be
associated with type VI secretion systems [Cellular
processes, Pathogenesis].
Length = 1169
Score = 31.2 bits (71), Expect = 2.7
Identities = 8/36 (22%), Positives = 16/36 (44%), Gaps = 5/36 (13%)
Query: 116 HELKKKSFKSFGNI-----FIISAPSGAGKSTLVNE 146
LK+ + +++ P G+GK+TL+
Sbjct: 95 ALLKRSRLGGRRYLYDLPWYLVIGPPGSGKTTLLQN 130
>gnl|CDD|217066 pfam02492, cobW, CobW/HypB/UreG, nucleotide-binding domain. This
domain is found in HypB, a hydrogenase expression /
formation protein, and UreG a urease accessory protein.
Both these proteins contain a P-loop nucleotide binding
motif. HypB has GTPase activity and is a guanine
nucleotide binding protein. It is not known whether UreG
binds GTP or some other nucleotide. Both enzymes are
involved in nickel binding. HypB can store nickel and is
required for nickel dependent hydrogenase expression.
UreG is required for functional incorporation of the
urease nickel metallocenter. GTP hydrolysis may required
by these proteins for nickel incorporation into other
nickel proteins. This family of domains also contains
P47K, a Pseudomonas chlororaphis protein needed for
nitrile hydratase expression, and the cobW gene product,
which may be involved in cobalamin biosynthesis in
Pseudomonas denitrificans.
Length = 178
Score = 29.9 bits (68), Expect = 2.7
Identities = 8/23 (34%), Positives = 17/23 (73%)
Query: 129 IFIISAPSGAGKSTLVNELLKKD 151
+ +++ G+GK+TL+ LL+K+
Sbjct: 2 VTVLTGFLGSGKTTLLEHLLEKN 24
>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 = 29.9 bits (67), Expect = 2.7
Identities = 9/22 (40%), Positives = 16/22 (72%)
Query: 129 IFIISAPSGAGKSTLVNELLKK 150
+++ PSG GK++L+ ELL+
Sbjct: 26 SVLLTGPSGTGKTSLLRELLEG 47
>gnl|CDD|213238 cd03271, ABC_UvrA_II, ATP-binding cassette domain II of the
excision repair protein UvrA. Nucleotide excision
repair in eubacteria is a process that repairs DNA
damage by the removal of a 12-13-mer oligonucleotide
containing the lesion. Recognition and cleavage of the
damaged DNA is a multistep ATP-dependent reaction that
requires the UvrA, UvrB, and UvrC proteins. Both UvrA
and UvrB are ATPases, with UvrA having two ATP binding
sites, which have the characteristic signature of the
family of ABC proteins and UvrB having one ATP binding
site that is structurally related to that of helicases.
Length = 261
Score = 30.3 bits (69), Expect = 2.9
Identities = 8/17 (47%), Positives = 14/17 (82%)
Query: 132 ISAPSGAGKSTLVNELL 148
++ SG+GKS+L+N+ L
Sbjct: 26 VTGVSGSGKSSLINDTL 42
>gnl|CDD|206748 cd01855, YqeH, Circularly permuted YqeH GTPase. YqeH is an
essential GTP-binding protein. Depletion of YqeH induces
an excess initiation of DNA replication, suggesting that
it negatively controls initiation of chromosome
replication. The YqeH subfamily is common in eukaryotes
and sporadically present in bacteria with probable
acquisition by plants from chloroplasts. Proteins of the
YqeH family contain all sequence motifs typical of the
vast class of P-loop-containing GTPases, but show a
circular permutation, with a G4-G1-G3 pattern of motifs
as opposed to the regular G1-G3-G4 pattern seen in most
GTPases.
Length = 191
Score = 29.9 bits (68), Expect = 2.9
Identities = 15/45 (33%), Positives = 25/45 (55%), Gaps = 1/45 (2%)
Query: 120 KKSFKSFGNIFIISAPSGAGKSTLVNELLKKDHKIKLSISTTTRP 164
KK K G+++++ A + GKSTL+N LLK + + + R
Sbjct: 119 KKLAKYRGDVYVVGATN-VGKSTLINALLKSNGGKVQAQALVQRL 162
>gnl|CDD|232980 TIGR00450, mnmE_trmE_thdF, tRNA modification GTPase TrmE. TrmE,
also called MnmE and previously designated ThdF
(thiophene and furan oxidation protein), is a GTPase
involved in tRNA modification to create
5-methylaminomethyl-2-thiouridine in the wobble position
of some tRNAs. This protein and GidA form an
alpha2/beta2 heterotetramer [Protein synthesis, tRNA and
rRNA base modification].
Length = 442
Score = 30.5 bits (69), Expect = 3.1
Identities = 39/133 (29%), Positives = 59/133 (44%), Gaps = 15/133 (11%)
Query: 35 EYLRETILVPDP--ADRATIEEENTLELRARDRERKLLIKIQQSIINIDKKEYGWCKDTG 92
E + E IL P+ D A + L+ + + LL + Q +NID +E
Sbjct: 118 EAINELILAPNNKVKDIALNKLAGELDQKIEAIRKSLLQLLAQVEVNIDYEEDD------ 171
Query: 93 EPIGILR-LLAKPMATLS-LEAQQRHELKKKSFKSFGNIFIISAPSGAGKSTLVNELLKK 150
+ L LL +A L + + E FK + I+ +P+ GKS+L+N LLK+
Sbjct: 172 DEQDSLNQLLLSIIAELKDILNSYKLEKLDDGFK----LAIVGSPN-VGKSSLLNALLKQ 226
Query: 151 DHKIKLSISTTTR 163
D I I TTR
Sbjct: 227 DRAIVSDIKGTTR 239
>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 = 30.6 bits (69), Expect = 3.1
Identities = 18/73 (24%), Positives = 28/73 (38%), Gaps = 16/73 (21%)
Query: 126 FGNIFIISAPSGAGKSTLVNELLKKDHKIKLSISTTTRPMRPGEKNGREYYFTNIDNFKK 185
F I GKSTLVN+L +TT+ REY + +
Sbjct: 161 FVKTVAILGGESTGKSTLVNKLAAV-------FNTTSAWEY-----AREYVEEKLGGDEA 208
Query: 186 LQKSGKFLEWAEV 198
LQ + ++A++
Sbjct: 209 LQ----YSDYAQI 217
>gnl|CDD|223256 COG0178, UvrA, Excinuclease ATPase subunit [DNA replication,
recombination, and repair].
Length = 935
Score = 30.6 bits (70), Expect = 3.1
Identities = 15/46 (32%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 106 ATLSLEAQQRHELKKKSFKSFGNIFI-ISAPSGAGKSTLVNELLKK 150
L L+ +R+ LK + +F ++ SG+GKSTL+N+ L
Sbjct: 605 KWLELKGARRNNLKNIDVEIPLGVFTCVTGVSGSGKSTLINDTLVP 650
>gnl|CDD|224058 COG1135, AbcC, ABC-type metal ion transport system, ATPase
component [Inorganic ion transport and metabolism].
Length = 339
Score = 30.3 bits (69), Expect = 3.3
Identities = 12/18 (66%), Positives = 13/18 (72%)
Query: 127 GNIFIISAPSGAGKSTLV 144
G IF I SGAGKSTL+
Sbjct: 32 GEIFGIIGYSGAGKSTLL 49
>gnl|CDD|227614 COG5295, Hia, Autotransporter adhesin [Intracellular trafficking
and secretion / Extracellular structures].
Length = 715
Score = 30.6 bits (69), Expect = 3.3
Identities = 16/71 (22%), Positives = 32/71 (45%), Gaps = 8/71 (11%)
Query: 509 RGNIDTRLNKLDKGEYA--AIILAAAGLKRLNLQKRIRMLFSPNQILPAPGQGAIAIE-- 564
++ ++ K+D+ A A LAAA L + L + + G+ A+A+
Sbjct: 627 NTELNGKIGKVDRDARAGIASALAAASLPQAYLPGKSMVSIGGGTY---RGESALALGVS 683
Query: 565 -ILDNRKELME 574
I DN + +++
Sbjct: 684 RISDNGRWVIK 694
>gnl|CDD|222000 pfam13238, AAA_18, AAA domain.
Length = 128
Score = 28.9 bits (65), Expect = 3.4
Identities = 24/136 (17%), Positives = 51/136 (37%), Gaps = 19/136 (13%)
Query: 131 IISAPSGAGKSTLVNELLKKDHKIKLSISTTTRPMRPGEKNGREYYFTNIDNFKKLQKSG 190
+I+ G+GK+TL EL ++ + ++ +NG + +
Sbjct: 2 LITGTPGSGKTTLAKELAERLGDVLRDLAK---------ENGLVLELDEEITDESKRLDE 52
Query: 191 KFLEWAEVHGNFYGTSFFPIVREIKSNVDILLEIDFQGAKQIKKKFPNAIGIFILPPSLD 250
L I+ E+ +++ ID A+ ++F + + + + +
Sbjct: 53 DKLAKLL-------DKLEKIIEELAEGENVI--IDGHLAELELERFKDLVFVVLRAD-PE 102
Query: 251 SLKERLYKRGQDKYDV 266
L ERL KRG + +
Sbjct: 103 ELLERLKKRGYSEEKI 118
>gnl|CDD|182716 PRK10771, thiQ, thiamine transporter ATP-binding subunit;
Provisional.
Length = 232
Score = 29.9 bits (68), Expect = 3.7
Identities = 11/14 (78%), Positives = 12/14 (85%)
Query: 132 ISAPSGAGKSTLVN 145
I PSGAGKSTL+N
Sbjct: 30 ILGPSGAGKSTLLN 43
>gnl|CDD|224410 COG1493, HprK, Serine kinase of the HPr protein, regulates
carbohydrate metabolism [Signal transduction
mechanisms].
Length = 308
Score = 29.9 bits (68), Expect = 4.0
Identities = 13/22 (59%), Positives = 17/22 (77%)
Query: 131 IISAPSGAGKSTLVNELLKKDH 152
+I+ PSGAGKS L EL+K+ H
Sbjct: 149 LITGPSGAGKSELALELIKRGH 170
>gnl|CDD|181939 PRK09544, znuC, high-affinity zinc transporter ATPase; Reviewed.
Length = 251
Score = 29.7 bits (67), Expect = 4.2
Identities = 17/42 (40%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 108 LSLEAQQRHELKKKSFK-SFGNIFIISAPSGAGKSTLVNELL 148
+S+ QR L S + G I + P+GAGKSTLV +L
Sbjct: 10 VSVSFGQRRVLSDVSLELKPGKILTLLGPNGAGKSTLVRVVL 51
>gnl|CDD|213225 cd03258, ABC_MetN_methionine_transporter, ATP-binding cassette
domain of methionine transporter. MetN (also known as
YusC) is an ABC-type transporter encoded by metN of the
metNPQ operon in Bacillus subtilis that is involved in
methionine transport. Other members of this system
include the MetP permease and the MetQ substrate binding
protein. 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 = 233
Score = 29.5 bits (67), Expect = 4.3
Identities = 12/18 (66%), Positives = 13/18 (72%)
Query: 127 GNIFIISAPSGAGKSTLV 144
G IF I SGAGKSTL+
Sbjct: 31 GEIFGIIGRSGAGKSTLI 48
>gnl|CDD|213261 cd03294, ABC_Pro_Gly_Betaine, ATP-binding cassette domain of the
osmoprotectant proline/glycine betaine uptake system.
This family comprises 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 transporters is the
obligatory coupling of ATP hydrolysis to substrate
translocation. 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 = 269
Score = 29.5 bits (67), Expect = 4.7
Identities = 13/29 (44%), Positives = 18/29 (62%), Gaps = 3/29 (10%)
Query: 127 GNIFIISAPSGAGKSTLV---NELLKKDH 152
G IF+I SG+GKSTL+ N L++
Sbjct: 50 GEIFVIMGLSGSGKSTLLRCINRLIEPTS 78
>gnl|CDD|130344 TIGR01277, thiQ, thiamine ABC transporter, ATP-binding protein.
This model describes the energy-transducing ATPase
subunit ThiQ of the ThiBPQ thiamine (and thiamine
pyrophosphate) ABC transporter in several
Proteobacteria. This protein is found so far only in
Proteobacteria, and is found in complete genomes only if
the ThiB and ThiP subunits are also found [Transport and
binding proteins, Other].
Length = 213
Score = 29.4 bits (66), Expect = 4.8
Identities = 13/19 (68%), Positives = 14/19 (73%)
Query: 127 GNIFIISAPSGAGKSTLVN 145
G I I PSGAGKSTL+N
Sbjct: 24 GEIVAIMGPSGAGKSTLLN 42
>gnl|CDD|233062 TIGR00630, uvra, excinuclease ABC, A subunit. This family is a
member of the ABC transporter superfamily of proteins of
which all members for which functions are known except
the UvrA proteins are involved in the transport of
material through membranes. UvrA orthologs are involved
in the recognition of DNA damage as a step in nucleotide
excision repair. 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 = 925
Score = 30.0 bits (68), Expect = 4.8
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 127 GNIFIISAPSGAGKSTLVNELL 148
G I+ SG+GKSTL+N+ L
Sbjct: 634 GLFTCITGVSGSGKSTLINDTL 655
>gnl|CDD|237451 PRK13631, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 320
Score = 29.8 bits (67), Expect = 4.8
Identities = 22/71 (30%), Positives = 29/71 (40%), Gaps = 19/71 (26%)
Query: 129 IFIISAPSGAGKSTLV---NELLK--------KDHKIKLSISTTTRPMRPGEKNGREYYF 177
I+ I SG+GKSTLV N L+K D I + P K
Sbjct: 54 IYFIIGNSGSGKSTLVTHFNGLIKSKYGTIQVGDIYIGDKKNNHELITNPYSK------- 106
Query: 178 TNIDNFKKLQK 188
I NFK+L++
Sbjct: 107 -KIKNFKELRR 116
>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 = 29.1 bits (66), Expect = 4.9
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 127 GNIFIISAPSGAGKSTLVN 145
G I + P+G+GKSTL+
Sbjct: 25 GEIVALVGPNGSGKSTLLR 43
>gnl|CDD|225363 COG2804, PulE, Type II secretory pathway, ATPase PulE/Tfp pilus
assembly pathway, ATPase PilB [Cell motility and
secretion / Intracellular trafficking and secretion].
Length = 500
Score = 30.0 bits (68), Expect = 5.0
Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 7/74 (9%)
Query: 92 GEPIGILRLLAKPMATLSLE-----AQQRHELKKKSFKSFGNIFIISAPSGAGKSTLVNE 146
GE + +LR+L K L LE Q L + + G + +++ P+G+GK+T +
Sbjct: 220 GEKV-VLRILDKDQVILDLEKLGMSPFQLARLLRLLNRPQG-LILVTGPTGSGKTTTLYA 277
Query: 147 LLKKDHKIKLSIST 160
L + + + +I T
Sbjct: 278 ALSELNTPERNIIT 291
>gnl|CDD|238977 cd02019, NK, Nucleoside/nucleotide kinase (NK) is a protein
superfamily consisting of multiple families of enzymes
that share structural similarity and are functionally
related to the catalysis of the reversible phosphate
group transfer from nucleoside triphosphates to
nucleosides/nucleotides, nucleoside monophosphates, or
sugars. Members of this family play a wide variety of
essential roles in nucleotide metabolism, the
biosynthesis of coenzymes and aromatic compounds, as
well as the metabolism of sugar and sulfate.
Length = 69
Score = 27.3 bits (61), Expect = 5.1
Identities = 8/16 (50%), Positives = 12/16 (75%)
Query: 132 ISAPSGAGKSTLVNEL 147
I+ SG+GKST+ +L
Sbjct: 4 ITGGSGSGKSTVAKKL 19
>gnl|CDD|236442 PRK09270, PRK09270, nucleoside triphosphate hydrolase
domain-containing protein; Reviewed.
Length = 229
Score = 29.5 bits (67), Expect = 5.1
Identities = 10/17 (58%), Positives = 11/17 (64%)
Query: 132 ISAPSGAGKSTLVNELL 148
I+ P GAGKSTL L
Sbjct: 38 IAGPPGAGKSTLAEFLE 54
>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 = 29.7 bits (67), Expect = 5.2
Identities = 11/22 (50%), Positives = 15/22 (68%), Gaps = 1/22 (4%)
Query: 127 GNIFIISAPSGAGKSTLVNELL 148
N+ I+ PSG+GKSTL+ L
Sbjct: 2 PNMLIV-GPSGSGKSTLLKLLA 22
>gnl|CDD|233816 TIGR02302, aProt_lowcomp, TIGR02302 family protein. Members of
this family are long (~850 residue) bacterial proteins
from the alpha Proteobacteria. Each has 2-3 predicted
transmembrane helices near the N-terminus and a long
C-terminal region that includes stretches of
Gln/Gly-rich low complexity sequence, predicted by TMHMM
to be outside the membrane. In Bradyrhizobium japonicum,
two tandem reading frames are together homologous the
single members found in other species; the cutoffs
scores are set low enough that the longer scores above
the trusted cutoff and the shorter above the noise
cutoff for this model.
Length = 851
Score = 29.9 bits (67), Expect = 5.3
Identities = 27/126 (21%), Positives = 54/126 (42%), Gaps = 26/126 (20%)
Query: 19 LKKLENDLLKNIVKTTEYLRETI--LVPDPADRATIEEENTLELR--------------- 61
+K+L + L + Y+R+ L +P A + NT LR
Sbjct: 525 IKQLTDKLRAAM---QTYMRQLAQQLRNNPQQLARPLDPNTKVLRQQDLQNMMDQIENLA 581
Query: 62 ---ARDRERKLLIKIQQSIINIDKKEYGWCKDTGEPIGILRLLAKPMATLSLEAQQRHEL 118
RD+ ++LL ++QQ + N+ + G + G+ G + + M L +++ +L
Sbjct: 582 RSGDRDQAKQLLSQLQQMMNNLQMGQPGQGQQMGDQSGDME---QQMNKLGELMRKQQQL 638
Query: 119 KKKSFK 124
+ ++FK
Sbjct: 639 RDETFK 644
>gnl|CDD|206727 cd04164, trmE, trmE is a tRNA modification GTPase. TrmE (MnmE,
ThdF, MSS1) is a 3-domain protein found in bacteria and
eukaryotes. It controls modification of the uridine at
the wobble position (U34) of tRNAs that read codons
ending with A or G in the mixed codon family boxes. TrmE
contains a GTPase domain that forms a canonical Ras-like
fold. It functions a molecular switch GTPase, and
apparently uses a conformational change associated with
GTP hydrolysis to promote the tRNA modification
reaction, in which the conserved cysteine in the
C-terminal domain is thought to function as a catalytic
residue. In bacteria that are able to survive in
extremely low pH conditions, TrmE regulates
glutamate-dependent acid resistance.
Length = 159
Score = 29.0 bits (66), Expect = 5.4
Identities = 12/26 (46%), Positives = 16/26 (61%)
Query: 138 AGKSTLVNELLKKDHKIKLSISTTTR 163
GKS+L+N L +D I I+ TTR
Sbjct: 14 VGKSSLLNALAGRDRAIVSDIAGTTR 39
>gnl|CDD|233193 TIGR00929, VirB4_CagE, type IV secretion/conjugal transfer ATPase,
VirB4 family. Type IV secretion systems are found in
Gram-negative pathogens. They export proteins, DNA, or
complexes in different systems and are related to
plasmid conjugation systems. This model represents
related ATPases that include VirB4 in Agrobacterium
tumefaciens (DNA export) CagE in Helicobacter pylori
(protein export) and plasmid TraB (conjugation).
Length = 785
Score = 30.0 bits (68), Expect = 5.7
Identities = 12/25 (48%), Positives = 17/25 (68%), Gaps = 1/25 (4%)
Query: 124 KSFGNIFIISAPSGAGKSTLVNELL 148
K G+ I P+G+GK+TL+N LL
Sbjct: 432 KVLGHTLIF-GPTGSGKTTLLNFLL 455
>gnl|CDD|226969 COG4618, ArpD, ABC-type protease/lipase transport system, ATPase
and permease components [General function prediction
only].
Length = 580
Score = 29.9 bits (68), Expect = 5.7
Identities = 21/56 (37%), Positives = 26/56 (46%), Gaps = 8/56 (14%)
Query: 101 LAKPMATLSLEA-------QQRHELKKKSFK-SFGNIFIISAPSGAGKSTLVNELL 148
L P LS+E Q++ LK SF G I PSG+GKSTL L+
Sbjct: 328 LPAPQGALSVERLTAAPPGQKKPILKGISFALQAGEALGIIGPSGSGKSTLARLLV 383
>gnl|CDD|226643 COG4175, ProV, ABC-type proline/glycine betaine transport system,
ATPase component [Amino acid transport and metabolism].
Length = 386
Score = 29.7 bits (67), Expect = 5.7
Identities = 12/18 (66%), Positives = 14/18 (77%)
Query: 127 GNIFIISAPSGAGKSTLV 144
G IF+I SG+GKSTLV
Sbjct: 54 GEIFVIMGLSGSGKSTLV 71
>gnl|CDD|226359 COG3839, MalK, ABC-type sugar transport systems, ATPase components
[Carbohydrate transport and metabolism].
Length = 338
Score = 29.5 bits (67), Expect = 5.8
Identities = 18/53 (33%), Positives = 23/53 (43%), Gaps = 18/53 (33%)
Query: 105 MATLSLEAQQRHELKKKSFKSF------------GNIFIISAPSGAGKSTLVN 145
MA L L+ +KSF SF G ++ PSG GKSTL+
Sbjct: 1 MAELELKN------VRKSFGSFEVLKDVNLDIEDGEFVVLLGPSGCGKSTLLR 47
>gnl|CDD|237648 PRK14250, PRK14250, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 241
Score = 29.4 bits (66), Expect = 5.9
Identities = 18/39 (46%), Positives = 21/39 (53%), Gaps = 4/39 (10%)
Query: 118 LKKKSFKSFGN-IFIISAPSGAGKST---LVNELLKKDH 152
LK S K G I+ I PSGAGKST L+N L+
Sbjct: 19 LKDISVKFEGGAIYTIVGPSGAGKSTLIKLINRLIDPTE 57
>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 = 29.5 bits (67), Expect = 6.0
Identities = 12/28 (42%), Positives = 17/28 (60%), Gaps = 1/28 (3%)
Query: 122 SFKSFGNIFIISAPSGAGKSTLVNELLK 149
+ K+ ++ SGAGKSTL+N LL
Sbjct: 343 TIKAGQLTALV-GASGAGKSTLLNLLLG 369
>gnl|CDD|213265 cd03298, ABC_ThiQ_thiamine_transporter, ATP-binding cassette domain
of the thiamine transport system. Part of the
binding-protein-dependent transport system tbpA-thiPQ
for thiamine and TPP. Probably responsible for the
translocation of thiamine across the membrane. 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 = 29.0 bits (65), Expect = 6.2
Identities = 12/19 (63%), Positives = 14/19 (73%)
Query: 127 GNIFIISAPSGAGKSTLVN 145
G I I PSG+GKSTL+N
Sbjct: 24 GEITAIVGPSGSGKSTLLN 42
>gnl|CDD|188414 TIGR03899, TIGR03899, TIGR03899 family protein. Members of this
protein family are conserved hypothetical proteins with
a limited species distribution within the
Gammaproteobacteria. It is common in the genera Vibrio
and Shewanella, and in this resembles the C-terminal
domain and putative protein sorting motif TIGR03501.
This model, but design, does not extend to all
homologs,but rather represents a particular clade.
Length = 250
Score = 29.1 bits (66), Expect = 6.4
Identities = 12/37 (32%), Positives = 21/37 (56%)
Query: 55 ENTLELRARDRERKLLIKIQQSIINIDKKEYGWCKDT 91
+ T+ RA+ R+RKL + Q ++ +I K +C D
Sbjct: 16 DATVAERAQHRQRKLQEQQQSNLESILKLALSYCPDE 52
>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 = 29.2 bits (66), Expect = 6.4
Identities = 10/42 (23%), Positives = 14/42 (33%), Gaps = 6/42 (14%)
Query: 113 QQRHELKKKSFKSF------GNIFIISAPSGAGKSTLVNELL 148
+ + + G I SG+GKSTL L
Sbjct: 13 YGGGKFAFHALNNVSLEIERGETLGIVGESGSGKSTLARLLA 54
>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 = 29.1 bits (66), Expect = 6.7
Identities = 13/41 (31%), Positives = 26/41 (63%), Gaps = 1/41 (2%)
Query: 120 KKSFKSFGNIFIISAPSGAGKSTLVNELLKKDHKIKLSIST 160
+++ ++ GNI ++S +G+GK+TL+ LL + + I T
Sbjct: 123 RQAVQARGNI-LVSGGTGSGKTTLLYALLNEINTDDERIVT 162
>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 = 28.5 bits (65), Expect = 6.9
Identities = 10/15 (66%), Positives = 13/15 (86%)
Query: 135 PSGAGKSTLVNELLK 149
PSG+GKSTL+ LL+
Sbjct: 36 PSGSGKSTLLKLLLR 50
>gnl|CDD|222194 pfam13521, AAA_28, AAA domain.
Length = 162
Score = 28.7 bits (65), Expect = 7.0
Identities = 6/18 (33%), Positives = 10/18 (55%)
Query: 130 FIISAPSGAGKSTLVNEL 147
+I+ GK+TL+ L
Sbjct: 2 IVITGGPSTGKTTLLEAL 19
>gnl|CDD|200134 TIGR01842, type_I_sec_PrtD, type I secretion system ABC
transporter, PrtD family. Type I protein secretion is a
system in some Gram-negative bacteria to export proteins
(often proteases) across both inner and outer membranes
to the extracellular medium. This is one of three
proteins of the type I secretion apparatus. Targeted
proteins are not cleaved at the N-terminus, but rather
carry signals located toward the extreme C-terminus to
direct type I secretion [Protein fate, Protein and
peptide secretion and trafficking].
Length = 544
Score = 29.6 bits (67), Expect = 7.0
Identities = 18/56 (32%), Positives = 26/56 (46%), Gaps = 8/56 (14%)
Query: 101 LAKPMATLSLEA-------QQRHELKKKSFK-SFGNIFIISAPSGAGKSTLVNELL 148
L +P LS+E ++ L+ SF G I PSG+GKSTL ++
Sbjct: 310 LPEPEGHLSVENVTIVPPGGKKPTLRGISFSLQAGEALAIIGPSGSGKSTLARLIV 365
>gnl|CDD|213180 cd03213, ABCG_EPDR, Eye pigment and drug resistance transporter
subfamily G of the ATP-binding cassette superfamily.
ABCG transporters are involved in eye pigment (EP)
precursor transport, regulation of lipid-trafficking
mechanisms, and pleiotropic drug resistance (DR). DR is
a well-described phenomenon occurring in fungi and
shares several similarities with processes in bacteria
and higher eukaryotes. Compared to other members of the
ABC transporter subfamilies, the ABCG transporter family
is composed of proteins that have an ATP-binding
cassette domain at the N-terminus and a TM
(transmembrane) domain at the C-terminus.
Length = 194
Score = 28.7 bits (65), Expect = 7.3
Identities = 11/13 (84%), Positives = 12/13 (92%)
Query: 135 PSGAGKSTLVNEL 147
PSGAGKSTL+N L
Sbjct: 43 PSGAGKSTLLNAL 55
>gnl|CDD|204088 pfam08888, HopJ, HopJ type III effector protein. Pathovars of
Pseudomonas syringae interact with their plant hosts via
the action of Hrp outer protein (Hop) effector proteins,
injected into plant cells by the type III secretion
system. The proteins in this family are called HopJ
after the original member HopPmaJ.
Length = 110
Score = 27.9 bits (63), Expect = 7.5
Identities = 11/21 (52%), Positives = 13/21 (61%), Gaps = 2/21 (9%)
Query: 599 NGSCKISLAAFAMVNNFNESE 619
GSCKI AFA +N +E E
Sbjct: 49 EGSCKI--FAFAQLNGLSEEE 67
>gnl|CDD|129528 TIGR00436, era, GTP-binding protein Era. Era is an essential
GTPase in Escherichia coli and many other bacteria. It
plays a role in ribosome biogenesis. Few bacteria lack
this protein [Protein synthesis, Other].
Length = 270
Score = 28.9 bits (65), Expect = 7.6
Identities = 17/55 (30%), Positives = 24/55 (43%), Gaps = 1/55 (1%)
Query: 127 GNIFIISAPSGAGKSTLVNELLKKDHKIKLSISTTTRPMRPGEKNGREYYFTNID 181
G + I+ P+ GKSTL+N+L + I + TTR G ID
Sbjct: 1 GFVAILGRPN-VGKSTLLNQLHGQKISITSPKAQTTRNRISGIHTTGASQIIFID 54
>gnl|CDD|223597 COG0523, COG0523, Putative GTPases (G3E family) [General function
prediction only].
Length = 323
Score = 29.2 bits (66), Expect = 7.7
Identities = 11/26 (42%), Positives = 18/26 (69%), Gaps = 1/26 (3%)
Query: 129 IFIISAPSGAGKSTLVNELLK-KDHK 153
+ +I+ G+GK+TL+N LL +D K
Sbjct: 3 VTVITGFLGSGKTTLLNHLLANRDGK 28
>gnl|CDD|215634 PLN03211, PLN03211, ABC transporter G-25; Provisional.
Length = 659
Score = 29.5 bits (66), Expect = 7.7
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 127 GNIFIISAPSGAGKSTLVNEL 147
G I + PSG+GKSTL+N L
Sbjct: 94 GEILAVLGPSGSGKSTLLNAL 114
>gnl|CDD|213196 cd03229, ABC_Class3, ATP-binding cassette domain of the binding
protein-dependent transport systems. This class is
comprised of all BPD (Binding Protein Dependent) systems
that are largely represented in archaea and eubacteria
and are primarily involved in scavenging solutes from
the environment. ABC transporters are a large family of
proteins involved in the transport of a wide variety of
different compounds, like sugars, ions, peptides, and
more complex organic molecules. The nucleotide binding
domain shows the highest similarity between all members
of the family. ABC transporters are a subset of
nucleotide hydrolases that contain a signature motif,
Q-loop, and H-loop/switch region, in addition to, the
Walker A motif/P-loop and Walker B motif commonly found
in a number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 178
Score = 28.7 bits (65), Expect = 7.7
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 127 GNIFIISAPSGAGKSTLVN 145
G I + PSG+GKSTL+
Sbjct: 26 GEIVALLGPSGSGKSTLLR 44
>gnl|CDD|224059 COG1136, SalX, ABC-type antimicrobial peptide transport system,
ATPase component [Defense mechanisms].
Length = 226
Score = 28.6 bits (65), Expect = 7.7
Identities = 11/19 (57%), Positives = 13/19 (68%)
Query: 127 GNIFIISAPSGAGKSTLVN 145
G I PSG+GKSTL+N
Sbjct: 31 GEFVAIVGPSGSGKSTLLN 49
>gnl|CDD|239386 cd03112, CobW_like, The function of this protein family is unkown.
The amino acid sequence of YjiA protein in E. coli
contains several conserved motifs that characterizes it
as a P-loop GTPase. YijA gene is among the genes
significantly induced in response to DNA-damage caused
by mitomycin. YijA gene is a homologue of the CobW gene
which encodes the cobalamin synthesis protein/P47K.
Length = 158
Score = 28.4 bits (64), Expect = 7.9
Identities = 10/22 (45%), Positives = 17/22 (77%)
Query: 137 GAGKSTLVNELLKKDHKIKLSI 158
GAGK+TL+N +L + H K+++
Sbjct: 10 GAGKTTLLNHILTEQHGRKIAV 31
>gnl|CDD|234957 PRK01526, PRK01526, Maf-like protein; Reviewed.
Length = 205
Score = 28.7 bits (64), Expect = 8.1
Identities = 13/29 (44%), Positives = 21/29 (72%), Gaps = 2/29 (6%)
Query: 527 IILAAAGLKRLNLQKRIRMLFSPNQILPA 555
IILA++ R+ L RI+++ P+QI+PA
Sbjct: 10 IILASSSPARIELLNRIKII--PSQIIPA 36
>gnl|CDD|236863 PRK11153, metN, DL-methionine transporter ATP-binding subunit;
Provisional.
Length = 343
Score = 29.0 bits (66), Expect = 8.3
Identities = 13/19 (68%), Positives = 15/19 (78%), Gaps = 2/19 (10%)
Query: 127 GNIF-IISAPSGAGKSTLV 144
G IF +I A SGAGKSTL+
Sbjct: 31 GEIFGVIGA-SGAGKSTLI 48
>gnl|CDD|223603 COG0529, CysC, Adenylylsulfate kinase and related kinases
[Inorganic ion transport and metabolism].
Length = 197
Score = 28.4 bits (64), Expect = 8.4
Identities = 10/38 (26%), Positives = 18/38 (47%)
Query: 116 HELKKKSFKSFGNIFIISAPSGAGKSTLVNELLKKDHK 153
+ ++ G + + SG+GKST+ N L +K
Sbjct: 12 KQEREALKGQKGAVIWFTGLSGSGKSTIANALEEKLFA 49
>gnl|CDD|233207 TIGR00955, 3a01204, The Eye Pigment Precursor Transporter (EPP)
Family protein. [Transport and binding proteins,
Other].
Length = 617
Score = 29.2 bits (66), Expect = 8.6
Identities = 17/56 (30%), Positives = 27/56 (48%), Gaps = 3/56 (5%)
Query: 94 PIGILRLLAKPMATLSLEAQQRHELKKKS--FKSFGNIFIISAPSGAGKSTLVNEL 147
+L+++ E ++H LK S K G + + SGAGK+TL+N L
Sbjct: 17 DGSWKQLVSRLRGCFCRERPRKHLLKNVSGVAKP-GELLAVMGSSGAGKTTLMNAL 71
>gnl|CDD|213222 cd03255, ABC_MJ0796_LolCDE_FtsE, ATP-binding cassette domain of the
transporters involved in export of lipoprotein and
macrolide, and cell division protein. This family is
comprised of MJ0796 ATP-binding cassette,
macrolide-specific ABC-type efflux carrier (MacAB), and
proteins involved in cell division (FtsE), and release
of lipoproteins from the cytoplasmic membrane (LolCDE).
They are clustered together phylogenetically. MacAB is
an exporter that confers resistance to macrolides, while
the LolCDE system is not a transporter at all. An FtsE
null mutants showed filamentous growth and appeared
viable on high salt medium only, indicating a role for
FtsE in cell division and/or salt transport. The LolCDE
complex catalyzes the release of lipoproteins from the
cytoplasmic membrane prior to their targeting to the
outer membrane.
Length = 218
Score = 28.6 bits (65), Expect = 8.8
Identities = 11/19 (57%), Positives = 13/19 (68%)
Query: 127 GNIFIISAPSGAGKSTLVN 145
G I PSG+GKSTL+N
Sbjct: 30 GEFVAIVGPSGSGKSTLLN 48
>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 = 9.0
Identities = 7/18 (38%), Positives = 11/18 (61%)
Query: 127 GNIFIISAPSGAGKSTLV 144
G + +++ G GKSTL
Sbjct: 33 GGLTLLAGAPGTGKSTLA 50
>gnl|CDD|215451 PLN02840, PLN02840, tRNA dimethylallyltransferase.
Length = 421
Score = 29.0 bits (65), Expect = 9.2
Identities = 12/22 (54%), Positives = 16/22 (72%)
Query: 129 IFIISAPSGAGKSTLVNELLKK 150
+ +IS P+GAGKS L EL K+
Sbjct: 23 VIVISGPTGAGKSRLALELAKR 44
>gnl|CDD|220925 pfam10987, DUF2806, Protein of unknown function (DUF2806). This
bacterial family of proteins has no known function.
Length = 223
Score = 28.4 bits (64), Expect = 9.6
Identities = 10/39 (25%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 59 ELRARDRERKLLIKIQQSIINIDKKEYGWCKD--TGEPI 95
RA R++ ++ QQ++ +I +C +GEP+
Sbjct: 1 AERAAKRQQIQELRKQQNLESIVALALNYCPSEVSGEPL 39
>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 = 28.3 bits (64), Expect = 9.8
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 132 ISAPSGAGKSTLVNELL 148
I PSG+GKSTL +L
Sbjct: 33 IIGPSGSGKSTLARLIL 49
>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 = 9.9
Identities = 11/28 (39%), Positives = 15/28 (53%), Gaps = 1/28 (3%)
Query: 128 NIFIISAPSGAGKSTLVNELLKKDHKIK 155
NI ++ SG+GK+TL LL I
Sbjct: 1 NIALV-GHSGSGKTTLAEALLYATGAID 27
>gnl|CDD|213246 cd03279, ABC_sbcCD, ATP-binding cassette domain of sbcCD. SbcCD
and other Mre11/Rad50 (MR) complexes are implicated in
the metabolism of DNA ends. They cleave ends sealed by
hairpin structures and are thought to play a role in
removing protein bound to DNA termini.
Length = 213
Score = 28.4 bits (64), Expect = 10.0
Identities = 9/16 (56%), Positives = 13/16 (81%)
Query: 128 NIFIISAPSGAGKSTL 143
+F+I P+GAGKST+
Sbjct: 29 GLFLICGPTGAGKSTI 44
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
0.320 0.138 0.387
Gapped
Lambda K H
0.267 0.0534 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 35,341,091
Number of extensions: 3684626
Number of successful extensions: 4312
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4284
Number of HSP's successfully gapped: 210
Length of query: 672
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 569
Effective length of database: 6,369,140
Effective search space: 3624040660
Effective search space used: 3624040660
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 62 (28.1 bits)