RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780826|ref|YP_003065239.1| phosphoenolpyruvate
carboxykinase [Candidatus Liberibacter asiaticus str. psy62]
(509 letters)
>gnl|CDD|181788 PRK09344, PRK09344, phosphoenolpyruvate carboxykinase; Provisional.
Length = 526
Score = 792 bits (2047), Expect = 0.0
Identities = 267/505 (52%), Positives = 345/505 (68%), Gaps = 3/505 (0%)
Query: 1 MEKFDLEGSSRVYRNLSTSRLYEESIRREKTILTCDGALRALTGQHTGRSAFDKFIVRDS 60
+E + + S V+ NLS + LYEE++RR + +LT GAL TG+ TGRS DKFIVRD
Sbjct: 8 LEAYGITNLSNVHYNLSYAELYEEALRRGEGVLTDTGALAVDTGKFTGRSPKDKFIVRDP 67
Query: 61 HTENDVFWEN-NKYISPADFDTLKADMLDYIKDKDLFLQDLVACPHTKNAISVCVVTQYA 119
TE+ ++W + NK ISP FD LK +L Y+ KDLF+ D A + + V V+T+ A
Sbjct: 68 STEDTIWWGDDNKPISPEKFDALKQKVLAYLSGKDLFVVDGFAGADPEYRLPVRVITELA 127
Query: 120 WHSLFIRNLLKHKEDLGAVPNMMSLQVVVLPDFSADPNRHGCCSETIIAVDLTAGLILIG 179
WH+LF+RNL + ++ P F ADP R G SET IA++ T ++LIG
Sbjct: 128 WHALFVRNLFIRPSEEELASFEPDFTIINAPKFKADPERDGTNSETFIAINFTERIVLIG 187
Query: 180 GTSYAGEIKKSVFTYLNHIFPERGIMPMHCSINMDKEKEDVALFFGLSGTGKTTLSASVD 239
GT YAGE+KKS+F+ +N++ P +G++PMHCS N+ +E DVALFFGLSGTGKTTLSA +
Sbjct: 188 GTDYAGEMKKSIFSVMNYLLPLKGVLPMHCSANVGEE-GDVALFFGLSGTGKTTLSADPN 246
Query: 240 RFLIGDDEHGWSKEGVFNFEGGCYAKSINLSKETEPEIFSASCRFGTVLENVVVDECGIP 299
R LIGDDEHGW GVFNFEGGCYAK+INLS+E EPEI+ A RFG VLENVVVDE G
Sbjct: 247 RKLIGDDEHGWDDGGVFNFEGGCYAKTINLSEEAEPEIYDA-IRFGAVLENVVVDEDGTV 305
Query: 300 NFKDSSVTENTRAAYPLNFIHNHAPQSIGKHPKHVIMLAADAFGVLPPVAYLNPEKAVYY 359
+F D S+TENTRAAYP+ I N S HPK++I L ADAFGVLPPV+ L PE+A+Y+
Sbjct: 306 DFDDGSLTENTRAAYPIEHIPNAVKPSRAGHPKNIIFLTADAFGVLPPVSKLTPEQAMYH 365
Query: 360 FLSGYTAKVAGTEKGVLKPEATFSACFGAPFMPRDPVQYGNILKDYIVKYCVDCWLVNTG 419
FLSGYTAKVAGTE+GV +P+ TFS CFGAPF+P P Y +L + I + +LVNTG
Sbjct: 366 FLSGYTAKVAGTERGVTEPQPTFSTCFGAPFLPLHPTVYAELLGERIKAHGAKVYLVNTG 425
Query: 420 WTAGSYGEGYRMPLSVTRALLKAIFDNSIKSVPYRVDENFGFSVPLEVKGVDRKLLNPRD 479
WT G YG G R+ + TRA++ AI D S+ + D FG +VP V GVD ++L+PR+
Sbjct: 426 WTGGPYGTGKRISIKYTRAIINAILDGSLDNAETTTDPIFGLAVPTSVPGVDSEILDPRN 485
Query: 480 SWNDVEAYDQKMRELLLMFENNAEK 504
+W D AYD+K ++L +F N EK
Sbjct: 486 TWADKAAYDEKAKKLARLFRENFEK 510
>gnl|CDD|185549 PTZ00311, PTZ00311, phosphoenolpyruvate carboxykinase; Provisional.
Length = 561
Score = 575 bits (1484), Expect = e-165
Identities = 237/511 (46%), Positives = 325/511 (63%), Gaps = 11/511 (2%)
Query: 7 EGSSRVYRNLSTSRLYEESIRREK-TILTCDGALRALTGQHTGRSAFDKFIVRDSHTEND 65
++ ++RNL+ LYE +++ EK T +T GAL +G TGRS DK IV++ +E+D
Sbjct: 39 LHNTTIHRNLTVPELYEHALKYEKNTSITSTGALCVYSGAKTGRSPKDKRIVKEDSSEDD 98
Query: 66 VFWEN-NKYISPADFDTLKADMLDYIKDKD-LFLQDLVACPHTKNAISVCVVTQYAWHSL 123
++W N +S F+ K +DY+ ++ LF+ D A K + V V+T A+H+L
Sbjct: 99 IWWGKVNIPLSEESFEINKKRAIDYLNTRERLFVVDGYAGWDPKYRLKVRVITTRAYHAL 158
Query: 124 FIRNLL--KHKEDLGAVPNMMSLQVVVL--PDFSADPNRHGCCSETIIAVDLTAGLILIG 179
F+RN+L E+L + +F A+ G SET +A++ ++I
Sbjct: 159 FMRNMLIRPTNEELKKFGEDFVPDFTIYNAGEFKANRLIEGVTSETSVALNFKRREMVIL 218
Query: 180 GTSYAGEIKKSVFTYLNHIFPERGIMPMHCSINMDKEKEDVALFFGLSGTGKTTLSASVD 239
GT YAGE+KK + T + ++ P++G++P+H S N+ K K DV LFFGLSGTGKTTLSA +
Sbjct: 219 GTQYAGEMKKGILTVMMYLMPKQGVLPLHSSANVGK-KGDVTLFFGLSGTGKTTLSADPN 277
Query: 240 RFLIGDDEHGWSKEGVFNFEGGCYAKSINLSKETEPEIFSASCRFGTVLENVVVD-ECGI 298
R LIGDDEH W+ +GVFN EGGCYAK I+LSKETEPEI++A RFG VLENVV+D
Sbjct: 278 RKLIGDDEHVWTDDGVFNIEGGCYAKCIDLSKETEPEIYNA-IRFGAVLENVVLDKVTRE 336
Query: 299 PNFKDSSVTENTRAAYPLNFIHNHAPQSIGKHPKHVIMLAADAFGVLPPVAYLNPEKAVY 358
+F D S+TENTR AYPL I N ++G HPK++I L DAFGVLPPV+ L PE+A+Y
Sbjct: 337 VDFNDISITENTRCAYPLEHIPNAKIPAVGGHPKNIIFLTCDAFGVLPPVSKLTPEQAMY 396
Query: 359 YFLSGYTAKVAGTEKGVLKPEATFSACFGAPFMPRDPVQYGNILKDYIVKYCVDCWLVNT 418
+F+SGYTAKVAGTE GV +P ATFSACFG PF+ P Y +L + I K+ WL+NT
Sbjct: 397 HFISGYTAKVAGTEVGVKEPTATFSACFGEPFLVLHPTVYAEMLAEKIKKHNTRVWLLNT 456
Query: 419 GWTAGSYGE-GYRMPLSVTRALLKAIFDNSIKSVPYRVDENFGFSVPLEVKGVDRKLLNP 477
GW GSYG G RMPL TRA++ AI D +K Y FG +P GV +LL+P
Sbjct: 457 GWIGGSYGSGGKRMPLKYTRAIIDAIHDGELKKAEYEKFPIFGLQIPKSCAGVPSELLDP 516
Query: 478 RDSWNDVEAYDQKMRELLLMFENNAEKKQIK 508
R++W D A+D++++EL F+ N +K K
Sbjct: 517 RNAWKDKAAFDKQLKELAAKFQKNFKKYADK 547
>gnl|CDD|161774 TIGR00224, pckA, phosphoenolpyruvate carboxykinase (ATP). Involved
in the gluconeogenesis pathway. It converts oxaloacetic
acid to phosphoenolpyruvate using ATP. Enzyme is a
monomer. The reaction is also catalysed by
phosphoenolpyruvate carboxykinase (GTP) (EC 4.1.1.32)
using GTP instead of ATP, described in
PROSITE:PDOC00421.
Length = 532
Score = 519 bits (1337), Expect = e-147
Identities = 222/505 (43%), Positives = 306/505 (60%), Gaps = 18/505 (3%)
Query: 12 VYRNLSTSRLYEESIRR-----EKTILTCDGALRALTGQHTGRSAFDKFIVRDSHTENDV 66
+ N S ++LYEE ++ EK +LT GA+ TG TGRS DK+IV D T++ +
Sbjct: 21 IVYNPSYAQLYEEELKPSLTGYEKGVLTSTGAVAVDTGIFTGRSPKDKYIVEDETTKDTI 80
Query: 67 FW-ENNKYISPADFDTLKADMLDYIKDKDLFLQDLVACPHTKNAISVCVVTQYAWHSLFI 125
+W NK +S + LK + + K LF+ D K +SV VVT+ AW + F+
Sbjct: 81 WWGPVNKPLSEETWQHLKGLVTRQLSRKRLFVVDAFCGADPKYRLSVRVVTEVAWQAHFV 140
Query: 126 RNLL--KHKEDLGAV-PNMMSLQVVVLPDFSADPNRHGCCSETIIAVDLTAGLILIGGTS 182
+N+ +E+L P+ + + + G SE +A +LT + LIGGT
Sbjct: 141 KNMFIRPTEEELAGFEPDFTVMNGAKFTN--PNWKEQGLNSENFVAFNLTERMQLIGGTW 198
Query: 183 YAGEIKKSVFTYLNHIFPERGIMPMHCSINMDKEKEDVALFFGLSGTGKTTLSASVDRFL 242
Y GE+KK +F+ +N++ P +GI+ MHCS N+ EK DVALFFGLSGTGKTTLS R L
Sbjct: 199 YGGEMKKGMFSMMNYLLPLKGILSMHCSANVG-EKGDVALFFGLSGTGKTTLSTDPKRRL 257
Query: 243 IGDDEHGWSKEGVFNFEGGCYAKSINLSKETEPEIFSASCRFGTVLENVVVDECGIPNFK 302
IGDDEHGW +GVFNFEGGCYAK+I+LS+E EPEI++A R +LENVVV E G +F
Sbjct: 258 IGDDEHGWDDDGVFNFEGGCYAKTIHLSEEKEPEIYNA-IRRDALLENVVVREDGTVDFD 316
Query: 303 DSSVTENTRAAYPLNFIHN-HAPQSIGKHPKHVIMLAADAFGVLPPVAYLNPEKAVYYFL 361
D S TENTR +YP+ I N P S H VI L ADAFGVLPPV+ L PE+ +Y+FL
Sbjct: 317 DGSKTENTRVSYPIYHIDNIVKPVSAAGHATKVIFLTADAFGVLPPVSKLTPEQTMYHFL 376
Query: 362 SGYTAKVAGTEKGVLKPEATFSACFGAPFMPRDPVQYGNILKDYIVKYCVDCWLVNTGWT 421
SG+TAK+AGTE+G+ +P TFSACFGA F+ P QY +L + +LVNTGW
Sbjct: 377 SGFTAKLAGTERGITEPTPTFSACFGAAFLSLHPTQYAEVLVKRMQAAGAQAYLVNTGWN 436
Query: 422 AGSYGEGYRMPLSVTRALLKAIFDNSIKSVPYRVDENFGFSVPLEVKGVDRKLLNPRDSW 481
G G R+ + TRA++ AI D S+++ F ++P E+ GVD K+L+PR+++
Sbjct: 437 ----GTGKRISIKDTRAIIDAILDGSLENAEMFTLPIFNLAIPTELPGVDTKILDPRNTY 492
Query: 482 NDVEAYDQKMRELLLMFENNAEKKQ 506
E + +K L +F +N +K
Sbjct: 493 ASKEQWQEKAETLANLFVDNFKKYA 517
>gnl|CDD|178207 PLN02597, PLN02597, phosphoenolpyruvate carboxykinase [ATP].
Length = 555
Score = 508 bits (1309), Expect = e-144
Identities = 228/508 (44%), Positives = 318/508 (62%), Gaps = 25/508 (4%)
Query: 12 VYRNLSTSRLYEESIRREK-TILTCDGALRALTGQHTGRSAFDKFIVRDSHTENDVFWEN 70
V NLS + LYE++I+ EK + +T GAL L+G TGRS DK +VRD TE++++W
Sbjct: 35 VLYNLSPAELYEQAIKYEKGSFITSTGALATLSGAKTGRSPKDKRVVRDETTEDELWWGK 94
Query: 71 ---NKYISPADFDTLKADMLDYIKDKD-LFLQDLVACPHTKNAISVCVVTQYAWHSLFIR 126
N + F + +DY+ D +F+ D +N I V +V+ A+HSLF+
Sbjct: 95 GSPNIEMDEETFLVNRERAVDYLNSLDKVFVNDQFLNWDPENRIKVRIVSARAYHSLFMH 154
Query: 127 NLLKHKEDLGAVPNMMSLQVVVLPDFS--------ADPNRHGCCSETIIAVDLTAGLILI 178
N+ P L+ PDF+ + H S T I ++L ++I
Sbjct: 155 NMCIR-------PTPEELEDFGTPDFTIYNAGQFPCNRYTHYMTSSTSIDLNLKRKEMVI 207
Query: 179 GGTSYAGEIKKSVFTYLNHIFPERGIMPMHCSINMDKEKEDVALFFGLSGTGKTTLSASV 238
GT YAGE+KK +F+ ++++ P RGI+ +H NM K+ DVALFFGLSGTGKTTLS
Sbjct: 208 LGTQYAGEMKKGLFSLMHYLMPMRGILSLHSGCNMGKD-GDVALFFGLSGTGKTTLSTDP 266
Query: 239 DRFLIGDDEHGWSKEGVFNFEGGCYAKSINLSKETEPEIFSASCRFGTVLENVVVDECGI 298
+R+LIGDDEH WS GV N EGGCYAK I+LS+E EP+I++A +FGTVLENVV DE
Sbjct: 267 NRYLIGDDEHCWSDNGVSNIEGGCYAKCIDLSEEKEPDIWNA-IKFGTVLENVVFDEHTR 325
Query: 299 P-NFKDSSVTENTRAAYPLNFIHN-HAPQSIGKHPKHVIMLAADAFGVLPPVAYLNPEKA 356
++ D SVTENTRA+YP+ +I N P +G HPK+VI+LA DAFGVLPPV+ L +
Sbjct: 326 EVDYSDKSVTENTRASYPIEYIPNAKIPC-VGPHPKNVILLACDAFGVLPPVSKLTLAQT 384
Query: 357 VYYFLSGYTAKVAGTEKGVLKPEATFSACFGAPFMPRDPVQYGNILKDYIVKYCVDCWLV 416
+Y+F+SGYTA VAGTE G+ +P ATFSACFGA F+ P +Y +L + + K+ WLV
Sbjct: 385 MYHFISGYTALVAGTEDGIKEPTATFSACFGAAFIMLHPTKYAAMLAEKMQKHGATAWLV 444
Query: 417 NTGWTAGSYGEGYRMPLSVTRALLKAIFDNSIKSVPYRVDENFGFSVPLEVKGVDRKLLN 476
NTGW+ GSYG G RM L+ TR ++ AI S+ + Y FG VP E++GV ++L+
Sbjct: 445 NTGWSGGSYGVGKRMSLAYTRKIIDAIHSGSLLNAEYVKTPIFGLEVPTEIEGVPSEILD 504
Query: 477 PRDSWNDVEAYDQKMRELLLMFENNAEK 504
P ++W+D +AYD+ + +L +F+ N E
Sbjct: 505 PENTWSDKKAYDETLNKLAGLFKKNFEV 532
>gnl|CDD|183331 PRK11831, PRK11831, putative ABC transporter ATP-binding protein
YrbF; Provisional.
Length = 269
Score = 39.7 bits (93), Expect = 0.002
Identities = 50/203 (24%), Positives = 84/203 (41%), Gaps = 36/203 (17%)
Query: 202 RGIMPMHCSINMDKEKEDVALFFGLSGTGKTTLSASVDRFLIGDDEHGWSKEGVFNFEGG 261
RG + +I++ + + G SG GKTTL LIG E +F+ E
Sbjct: 17 RGNRCIFDNISLTVPRGKITAIMGPSGIGKTTLLR-----LIGGQIAPDHGEILFDGE-- 69
Query: 262 CYAKSINLSKETEPEIFSASCRFGTVLENVVVDECGIPNFKDSSVTENTRAAYPLNFIHN 321
N+ + +++ R + ++ + F D +V +N AYPL H
Sbjct: 70 ------NIPAMSRSRLYTVRKRMSMLFQSGAL-------FTDMNVFDNV--AYPLRE-HT 113
Query: 322 HAPQSIGKHPKHVIMLAADAFGVLPPVAYLNPEKAVYYFLSGYTAKVAGTEKGV-LKPEA 380
P + +M+ +A G L A L P + LSG A+ A + + L+P+
Sbjct: 114 QLPAPL---LHSTVMMKLEAVG-LRGAAKLMPSE-----LSGGMARRAALARAIALEPDL 164
Query: 381 TFSACFGAPFMPRDPVQYGNILK 403
F PF+ +DP+ G ++K
Sbjct: 165 IM---FDEPFVGQDPITMGVLVK 184
>gnl|CDD|172963 PRK14490, PRK14490, putative bifunctional molybdopterin-guanine
dinucleotide biosynthesis protein MobB/MobA;
Provisional.
Length = 369
Score = 33.5 bits (77), Expect = 0.14
Identities = 15/37 (40%), Positives = 20/37 (54%)
Query: 223 FFGLSGTGKTTLSASVDRFLIGDDEHGWSKEGVFNFE 259
F G SG+GKTTL ++ R L G+ K G F+
Sbjct: 10 FCGYSGSGKTTLITALVRRLSERFSVGYYKHGCHRFD 46
>gnl|CDD|184595 PRK14266, PRK14266, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 250
Score = 33.0 bits (75), Expect = 0.18
Identities = 20/66 (30%), Positives = 32/66 (48%), Gaps = 5/66 (7%)
Query: 195 LNHIFPERGIMPMHCSINMDKEKEDVALFFGLSGTGKTTLSASVDRFLIGDDEHGWSKEG 254
LN F + I+ ++N+D K V G SG GK+T +++R + D G+ EG
Sbjct: 9 LNTYFDDAHILK---NVNLDIPKNSVTALIGPSGCGKSTFIRTLNR--MNDLIPGFRHEG 63
Query: 255 VFNFEG 260
+G
Sbjct: 64 HIYLDG 69
>gnl|CDD|163523 TIGR03811, tyr_de_CO2_Ent, tyrosine decarboxylase, Enterococcus
type. This model represents tyrosine decarboxylases in
the family of the Enterococcus faecalis enzyme Tdc.
These enzymes often are encoded next to
tyrosine/tyramine antiporter, together comprising a
system in which tyrosine decarboxylation can protect
against exposure to acid conditions. This clade differs
from the archaeal tyrosine decarboxylases associated
with methanofuran biosynthesis.
Length = 608
Score = 32.1 bits (73), Expect = 0.33
Identities = 16/45 (35%), Positives = 23/45 (51%), Gaps = 8/45 (17%)
Query: 48 GRSAF----DKFI----VRDSHTENDVFWENNKYISPADFDTLKA 84
GR+ F D FI +++ H E VF E +YIS ++ KA
Sbjct: 326 GRAIFLDEDDNFIPYDDLQEVHAEYGVFTEKKEYISREVYNAYKA 370
>gnl|CDD|172750 PRK14262, PRK14262, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 250
Score = 32.2 bits (73), Expect = 0.36
Identities = 18/51 (35%), Positives = 26/51 (50%), Gaps = 2/51 (3%)
Query: 210 SINMDKEKEDVALFFGLSGTGKTTLSASVDRFLIGDDEHGWSKEGVFNFEG 260
++ M K + G SG GKTTL S++R + D G+ EG F+G
Sbjct: 21 NVTMKIFKNQITAIIGPSGCGKTTLLRSINR--MNDHIPGFRVEGKIYFKG 69
>gnl|CDD|131258 TIGR02203, MsbA_lipidA, lipid A export permease/ATP-binding protein
MsbA. This family consists of a single polypeptide
chain transporter in the ATP-binding cassette (ABC)
transporter family, MsbA, which exports lipid A. It may
also act in multidrug resistance. Lipid A, a part of
lipopolysaccharide, is found in the outer leaflet of the
outer membrane of most Gram-negative bacteria. Members
of this family are restricted to the Proteobacteria
(although lipid A is more broadly distributed) and often
are clustered with lipid A biosynthesis genes.
Length = 571
Score = 31.6 bits (72), Expect = 0.55
Identities = 16/50 (32%), Positives = 24/50 (48%), Gaps = 1/50 (2%)
Query: 192 FTYLNHIFPERGIMPMHCSINMDKEKEDVALFFGLSGTGKTTLSASVDRF 241
F + +P R P SI++ E + G SG+GK+TL + RF
Sbjct: 333 FRNVTFRYPGRDR-PALDSISLVIEPGETVALVGRSGSGKSTLVNLIPRF 381
>gnl|CDD|184589 PRK14248, PRK14248, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 268
Score = 31.1 bits (70), Expect = 0.62
Identities = 19/50 (38%), Positives = 25/50 (50%), Gaps = 2/50 (4%)
Query: 211 INMDKEKEDVALFFGLSGTGKTTLSASVDRFLIGDDEHGWSKEGVFNFEG 260
I+MD EK V G SG GK+T S++R + D EG +EG
Sbjct: 40 ISMDIEKHAVTALIGPSGCGKSTFLRSINR--MNDLIPSARSEGEILYEG 87
>gnl|CDD|162133 TIGR00959, ffh, signal recognition particle protein. This model
represents Ffh (Fifty-Four Homolog), the protein
component that forms the bacterial (and organellar)
signal recognition particle together with a 4.5S RNA.
Ffh is a GTPase homologous to eukaryotic SRP54 and also
to the GTPase FtsY (TIGR00064) that is the receptor for
the signal recognition particle.
Length = 428
Score = 31.1 bits (71), Expect = 0.66
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 210 SINMDKEKEDVALFFGLSGTGKTTLSA 236
S+N+ K+ V L GL G+GKTT
Sbjct: 91 SLNLAKKPPTVILMVGLQGSGKTTTCG 117
>gnl|CDD|130261 TIGR01193, bacteriocin_ABC, ABC-type bacteriocin transporter. This
model describes ABC-type bacteriocin transporter. The
amino terminal domain (pfam03412) processes the
N-terminal leader peptide from the bacteriocin while
C-terminal domains resemble ABC transporter membrane
protein and ATP-binding cassette domain. In general,
bacteriocins are agents which are responsible for
killing or inhibiting the closely related species or
even different strains of the same species. Bacteriocins
are usually encoded by bacterial plasmids. Bacteriocins
are named after the species and hence in literature one
encounters various names e.g., leucocin from Leuconostic
geldium; pedicocin from Pedicoccus acidilactici; sakacin
from Lactobacillus sake etc.
Length = 708
Score = 30.9 bits (70), Expect = 0.73
Identities = 23/88 (26%), Positives = 41/88 (46%), Gaps = 15/88 (17%)
Query: 211 INMDKEKEDVALFFGLSGTGKTTLSASVDRFLIG--DDEHGWSKEGVF---NFEGGCYAK 265
I++ + G+SG+GK+TL+ + L+G G F + + +
Sbjct: 493 ISLTIKMNSKTTIVGMSGSGKSTLA----KLLVGFFQARSGEILLNGFSLKDIDRHTLRQ 548
Query: 266 SINLSKETEPEIFSASCRFGTVLENVVV 293
IN + EP IFS G++LEN+++
Sbjct: 549 FINYLPQ-EPYIFS-----GSILENLLL 570
>gnl|CDD|130492 TIGR01425, SRP54_euk, signal recognition particle protein SRP54.
This model represents examples from the eukaryotic
cytosol of the signal recognition particle protein
component, SRP54. This GTP-binding protein is a
component of the eukaryotic signal recognition particle,
along with several other protein subunits and a 7S RNA.
Some species, including Arabidopsis, have several
closely related forms. The extreme C-terminal region is
glycine-rich and lower in complexity, poorly conserved
between species, and excluded from this model.
Length = 429
Score = 30.6 bits (69), Expect = 0.91
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 5/47 (10%)
Query: 187 IKKSVFTYLNHIFPERGIMPMHCSINMDKEKEDVALFFGLSGTGKTT 233
I+ +VF L ++ + P + K K++V +F GL G+GKTT
Sbjct: 74 IQHAVFKELCNL-----VDPGVEAFTPKKGKQNVIMFVGLQGSGKTT 115
>gnl|CDD|182182 PRK09984, PRK09984, phosphonate/organophosphate ester transporter
subunit; Provisional.
Length = 262
Score = 30.8 bits (69), Expect = 0.99
Identities = 40/170 (23%), Positives = 66/170 (38%), Gaps = 26/170 (15%)
Query: 210 SINMDKEKEDVALFFGLSGTGKTTLSASVDRFLIGDDEHGWSKEGVFNF--EGGCYAKSI 267
+++++ ++ G SG+GK+TL + + GD G E + G A+ I
Sbjct: 22 AVDLNIHHGEMVALLGPSGSGKSTLLRHLSGLITGDKSAGSHIELLGRTVQREGRLARDI 81
Query: 268 NLSKETEPEIFSASCRFG-----TVLENVVVDECGIPNFKDSSVT-----ENTRAAYPL- 316
S+ IF +F +VLENV++ G F + + + RA L
Sbjct: 82 RKSRANTGYIFQ---QFNLVNRLSVLENVLIGALGSTPFWRTCFSWFTREQKQRALQALT 138
Query: 317 -----NFIHNHAPQSIGKHPKHV-----IMLAADAFGVLPPVAYLNPEKA 356
+F H G + V +M A P+A L+PE A
Sbjct: 139 RVGMVHFAHQRVSTLSGGQQQRVAIARALMQQAKVILADEPIASLDPESA 188
>gnl|CDD|161686 TIGR00064, ftsY, signal recognition particle-docking protein FtsY.
There is a weak division between FtsY and SRP54; both
are GTPases. In E.coli, ftsY is an essential gene
located in an operon with cell division genes ftsE and
ftsX, but its apparent function is as the signal
recognition particle docking protein.
Length = 272
Score = 30.3 bits (69), Expect = 1.1
Identities = 15/57 (26%), Positives = 25/57 (43%), Gaps = 9/57 (15%)
Query: 187 IKKSVFTYLNHIFPERGIMPMHCSINMDKEKEDVALFFGLSGTGKTTLSASVDRFLI 243
+K+ + L E +++ K +V LF G++G GKTT A + L
Sbjct: 50 LKEYLKEILKETDLEL---------IVEENKPNVILFVGVNGVGKTTTIAKLANKLK 97
>gnl|CDD|172745 PRK14257, PRK14257, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 329
Score = 30.5 bits (68), Expect = 1.1
Identities = 24/75 (32%), Positives = 37/75 (49%), Gaps = 8/75 (10%)
Query: 186 EIKKSVFTYLNHIFPERGIMPMHCSINMDKEKEDVALFFGLSGTGKTTLSASVDRFLIGD 245
EI+ F Y+N R +H +N+D ++ V F G SG GK+T ++++ + D
Sbjct: 82 EIRNFNFWYMN-----RTKHVLH-DLNLDIKRNKVTAFIGPSGCGKSTFLRNLNQ--LND 133
Query: 246 DEHGWSKEGVFNFEG 260
G S EG F G
Sbjct: 134 LIEGTSHEGEIYFLG 148
>gnl|CDD|184586 PRK14240, PRK14240, phosphate transporter ATP-binding protein;
Provisional.
Length = 250
Score = 30.4 bits (69), Expect = 1.2
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 210 SINMDKEKEDVALFFGLSGTGKTTLSASVDR 240
IN+D E+ V G SG GK+T +++R
Sbjct: 21 KINLDIEENQVTALIGPSGCGKSTFLRTLNR 51
>gnl|CDD|172751 PRK14263, PRK14263, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 261
Score = 30.0 bits (67), Expect = 1.5
Identities = 18/76 (23%), Positives = 31/76 (40%), Gaps = 16/76 (21%)
Query: 199 FPERGIMPMHCSI--------------NMDKEKEDVALFFGLSGTGKTTLSASVDRFLIG 244
+ M C + ++ K ++ F G SG GK+T+ S++R +
Sbjct: 1 MVSEAPIVMDCKLDKIFYGNFMAVRDSHVPIRKNEITGFIGPSGCGKSTVLRSLNR--MN 58
Query: 245 DDEHGWSKEGVFNFEG 260
D G+ EG +F G
Sbjct: 59 DLVKGFRFEGHVHFLG 74
>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.
Length = 363
Score = 29.8 bits (67), Expect = 1.5
Identities = 9/33 (27%), Positives = 19/33 (57%)
Query: 210 SINMDKEKEDVALFFGLSGTGKTTLSASVDRFL 242
++ K ++ + GLSG+GK+T ++R +
Sbjct: 11 DADLAIAKGEIFVIMGLSGSGKSTTVRMLNRLI 43
>gnl|CDD|184937 PRK14974, PRK14974, cell division protein FtsY; Provisional.
Length = 336
Score = 29.9 bits (68), Expect = 1.5
Identities = 17/63 (26%), Positives = 28/63 (44%), Gaps = 1/63 (1%)
Query: 180 GTSYAGEIKKSVFTYLNHIFPERGIMPMHCSINMDKEKEDVALFFGLSGTGKTTLSASVD 239
G +K ++ L + + + I K K V +F G++GTGKTT A +
Sbjct: 103 GEDVEEIVKNALKEALLEVLSVGDLFDLIEEIK-SKGKPVVIVFVGVNGTGKTTTIAKLA 161
Query: 240 RFL 242
+L
Sbjct: 162 YYL 164
>gnl|CDD|131368 TIGR02315, ABC_phnC, phosphonate ABC transporter, ATP-binding
protein. Phosphonates are a class of
phosphorus-containing organic compound with a stable
direct C-P bond rather than a C-O-P linkage. A number of
bacterial species have operons, typically about 14 genes
in size, with genes for ATP-dependent transport of
phosphonates, degradation, and regulation of the
expression of the system. Members of this protein family
are the ATP-binding cassette component of tripartite ABC
transporters of phosphonates.
Length = 243
Score = 30.0 bits (68), Expect = 1.6
Identities = 24/103 (23%), Positives = 37/103 (35%), Gaps = 25/103 (24%)
Query: 211 INMDKEKEDVALFFGLSGTGKTTLSASVDRFLIGDDEHGWSKEGVFNFEGGCYAKSINLS 270
IN++ + G SG GK+TL ++R L+ G EG +++
Sbjct: 21 INLNINPGEFVAIIGPSGAGKSTLLRCINR-LVEPS------SGSILLEGT------DIT 67
Query: 271 KETEPEIFSASCRFG------------TVLENVVVDECGIPNF 301
K ++ R G TVLENV+ G
Sbjct: 68 KLRGKKLRKLRRRIGMIFQHYNLIERLTVLENVLHGRLGYKPT 110
>gnl|CDD|184919 PRK14955, PRK14955, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 397
Score = 29.9 bits (67), Expect = 1.8
Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 9/74 (12%)
Query: 84 ADMLDYIKDKDLF-LQDLVACPHTKNAISVCVVTQYAWHS-----LFIRNLLKHKEDLGA 137
A++L+YI D+ F + D VA +A+++ V Q+ + F+ L++H +
Sbjct: 251 AELLNYIDDEHFFAVTDAVA---DGDAVAMLDVAQFVIRNGYDEQDFLEKLIEHLRNFLV 307
Query: 138 VPNMMSLQVVVLPD 151
V N+ S ++V PD
Sbjct: 308 VHNLRSTRLVERPD 321
>gnl|CDD|178847 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed.
Length = 328
Score = 29.7 bits (68), Expect = 2.0
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 222 LFFGLSGTGKTTLS 235
L +G G GKTTL+
Sbjct: 55 LLYGPPGLGKTTLA 68
>gnl|CDD|128665 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 = 29.3 bits (65), Expect = 2.4
Identities = 8/13 (61%), Positives = 9/13 (69%)
Query: 222 LFFGLSGTGKTTL 234
L G G+GKTTL
Sbjct: 6 LIVGPPGSGKTTL 18
>gnl|CDD|130045 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.
Length = 247
Score = 29.2 bits (66), Expect = 2.8
Identities = 23/60 (38%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 211 INMDKEKEDVALFFGLSGTGKTTLSASVDRFLIGDDEHGWSKEGVFNFEG-GCYAKSINL 269
IN+D K V G SG GK+TL S++R + D G EG F+G Y K I++
Sbjct: 20 INLDIPKNQVTALIGPSGCGKSTLLRSLNR--MNDLVPGVRIEGKVLFDGQDIYDKKIDV 77
>gnl|CDD|180719 PRK06835, PRK06835, DNA replication protein DnaC; Validated.
Length = 329
Score = 29.1 bits (66), Expect = 2.9
Identities = 14/24 (58%), Positives = 18/24 (75%), Gaps = 1/24 (4%)
Query: 212 NMDKEKEDVALFFGLSGTGKTTLS 235
N DK E++ LF+G +GTGKT LS
Sbjct: 178 NFDKNNENL-LFYGNTGTGKTFLS 200
>gnl|CDD|177953 PLN02319, PLN02319, aminomethyltransferase.
Length = 404
Score = 28.9 bits (65), Expect = 3.1
Identities = 14/41 (34%), Positives = 19/41 (46%), Gaps = 1/41 (2%)
Query: 411 VDCWLVNTGWTAGSYGEGYRMPLSVTRALLKAIFDNSIKSV 451
DC+L TG+T G G +P L KA+ + S V
Sbjct: 215 ADCFLTRTGYT-GEDGFEISVPSEHAVDLAKALLEKSEGKV 254
>gnl|CDD|182692 PRK10744, pstB, phosphate transporter ATP-binding protein;
Provisional.
Length = 260
Score = 28.8 bits (65), Expect = 3.4
Identities = 13/25 (52%), Positives = 16/25 (64%)
Query: 210 SINMDKEKEDVALFFGLSGTGKTTL 234
+IN+D K V F G SG GK+TL
Sbjct: 31 NINLDIAKNQVTAFIGPSGCGKSTL 55
>gnl|CDD|180120 PRK05506, PRK05506, bifunctional sulfate adenylyltransferase
subunit 1/adenylylsulfate kinase protein; Provisional.
Length = 632
Score = 28.7 bits (65), Expect = 3.7
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 220 VALFFGLSGTGKTTLSASVDRFL 242
F GLSG+GK+T++ V+R L
Sbjct: 462 TVWFTGLSGSGKSTIANLVERRL 484
>gnl|CDD|172760 PRK14272, PRK14272, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 252
Score = 28.8 bits (64), Expect = 3.8
Identities = 11/32 (34%), Positives = 19/32 (59%)
Query: 209 CSINMDKEKEDVALFFGLSGTGKTTLSASVDR 240
++N+D ++ V G SG GKTT +++R
Sbjct: 21 KNVNLDVQRGTVNALIGPSGCGKTTFLRAINR 52
>gnl|CDD|179157 PRK00889, PRK00889, adenylylsulfate kinase; Provisional.
Length = 175
Score = 28.4 bits (64), Expect = 3.8
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 223 FFGLSGTGKTTLSASVDRFLI 243
F GLSG GKTT++ ++ L
Sbjct: 9 FTGLSGAGKTTIARALAEKLR 29
>gnl|CDD|179026 PRK00440, rfc, replication factor C small subunit; Reviewed.
Length = 319
Score = 28.7 bits (65), Expect = 3.8
Identities = 13/25 (52%), Positives = 17/25 (68%)
Query: 222 LFFGLSGTGKTTLSASVDRFLIGDD 246
LF G GTGKTT + ++ R L G+D
Sbjct: 42 LFAGPPGTGKTTAALALARELYGED 66
>gnl|CDD|179661 PRK03846, PRK03846, adenylylsulfate kinase; Provisional.
Length = 198
Score = 28.4 bits (64), Expect = 4.0
Identities = 9/20 (45%), Positives = 16/20 (80%)
Query: 223 FFGLSGTGKTTLSASVDRFL 242
F GLSG+GK+T++ +++ L
Sbjct: 29 FTGLSGSGKSTVAGALEEAL 48
>gnl|CDD|184585 PRK14239, PRK14239, phosphate transporter ATP-binding protein;
Provisional.
Length = 252
Score = 28.6 bits (64), Expect = 4.1
Identities = 11/31 (35%), Positives = 20/31 (64%)
Query: 210 SINMDKEKEDVALFFGLSGTGKTTLSASVDR 240
S+++D ++ G SG+GK+TL S++R
Sbjct: 23 SVSLDFYPNEITALIGPSGSGKSTLLRSINR 53
>gnl|CDD|162209 TIGR01116, ATPase-IIA1_Ca, sarco/endoplasmic reticulum
calcium-translocating P-type ATPase. The calcium P-type
ATPases have been characterized as Type IIA based on a
phylogenetic analysis which distinguishes this group
from the Type IIB PMCA calcium pump modelled by
TIGR01517. A separate analysis divides Type IIA into
sub-types, SERCA and PMR1, the latter of which is
modelled by TIGR01522.
Length = 917
Score = 27.8 bits (62), Expect = 6.0
Identities = 11/46 (23%), Positives = 20/46 (43%), Gaps = 6/46 (13%)
Query: 393 RDPVQ-----YGNILKDYIVKYCVDCWLVNTG-WTAGSYGEGYRMP 432
P+Q +G +L I C+ W++N G + + G G+
Sbjct: 190 DTPLQKKLDEFGELLSKVIGLICILVWVINIGHFNDPALGGGWIQG 235
>gnl|CDD|184582 PRK14236, PRK14236, phosphate transporter ATP-binding protein;
Provisional.
Length = 272
Score = 27.7 bits (62), Expect = 6.6
Identities = 12/26 (46%), Positives = 14/26 (53%)
Query: 209 CSINMDKEKEDVALFFGLSGTGKTTL 234
I+M K V F G SG GK+TL
Sbjct: 42 FDISMRIPKNRVTAFIGPSGCGKSTL 67
>gnl|CDD|179118 PRK00771, PRK00771, signal recognition particle protein Srp54;
Provisional.
Length = 437
Score = 27.9 bits (63), Expect = 6.9
Identities = 10/32 (31%), Positives = 16/32 (50%)
Query: 211 INMDKEKEDVALFFGLSGTGKTTLSASVDRFL 242
+ K + GL G+GKTT +A + R+
Sbjct: 88 PLVLPLKPQTIMLVGLQGSGKTTTAAKLARYF 119
>gnl|CDD|183056 PRK11248, tauB, taurine transporter ATP-binding subunit;
Provisional.
Length = 255
Score = 27.7 bits (62), Expect = 7.1
Identities = 14/40 (35%), Positives = 23/40 (57%)
Query: 195 LNHIFPERGIMPMHCSINMDKEKEDVALFFGLSGTGKTTL 234
++H++ + G P IN+ E ++ + G SG GKTTL
Sbjct: 4 ISHLYADYGGKPALEDINLTLESGELLVVLGPSGCGKTTL 43
>gnl|CDD|183986 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 27.7 bits (63), Expect = 7.1
Identities = 8/13 (61%), Positives = 10/13 (76%)
Query: 222 LFFGLSGTGKTTL 234
+ +G GTGKTTL
Sbjct: 40 ILWGPPGTGKTTL 52
>gnl|CDD|184587 PRK14241, PRK14241, phosphate transporter ATP-binding protein;
Provisional.
Length = 258
Score = 27.8 bits (62), Expect = 7.4
Identities = 11/30 (36%), Positives = 19/30 (63%)
Query: 211 INMDKEKEDVALFFGLSGTGKTTLSASVDR 240
+N++ E V F G SG GK+T+ +++R
Sbjct: 23 VNLNIEPRSVTAFIGPSGCGKSTVLRTLNR 52
>gnl|CDD|163223 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.
Length = 852
Score = 27.6 bits (62), Expect = 7.6
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 222 LFFGLSGTGKTTLSASVDRFLIGDDEH 248
LF G +G GKT L+ ++ FL D++
Sbjct: 599 LFLGPTGVGKTELAKALAEFLFDDEDA 625
>gnl|CDD|132456 TIGR03415, ABC_choXWV_ATP, choline ABC transporter, ATP-binding
protein. Members of this protein family are the
ATP-binding subunit of a three-protein transporter. This
family belongs, more broadly, to the family of proline
and glycine-betaine transporters, but members have been
identified by direct characterization and by
bioinformatic means as choline transporters. Many
species have several closely-related members of this
family, probably with variable abilities to act
additionally on related quaternary amines.
Length = 382
Score = 27.8 bits (62), Expect = 7.6
Identities = 10/29 (34%), Positives = 21/29 (72%)
Query: 212 NMDKEKEDVALFFGLSGTGKTTLSASVDR 240
++D E+ ++ + GLSG+GK++L +V+
Sbjct: 44 SLDIEEGEICVLMGLSGSGKSSLLRAVNG 72
>gnl|CDD|182793 PRK10867, PRK10867, signal recognition particle protein;
Provisional.
Length = 433
Score = 27.7 bits (63), Expect = 7.9
Identities = 10/33 (30%), Positives = 18/33 (54%)
Query: 210 SINMDKEKEDVALFFGLSGTGKTTLSASVDRFL 242
+N+ + V + GL G GKTT + + ++L
Sbjct: 92 ELNLAAKPPTVIMMVGLQGAGKTTTAGKLAKYL 124
>gnl|CDD|181233 PRK08116, PRK08116, hypothetical protein; Validated.
Length = 268
Score = 27.7 bits (62), Expect = 8.1
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 222 LFFGLSGTGKTTLSASVDRFLI 243
L +G GTGKT L+A + LI
Sbjct: 118 LLWGSVGTGKTYLAACIANELI 139
>gnl|CDD|162839 TIGR02397, dnaX_nterm, DNA polymerase III, subunit gamma and tau.
This model represents the well-conserved first ~ 365
amino acids of the translation of the dnaX gene. The
full-length product of the dnaX gene in the model
bacterium E. coli is the DNA polymerase III tau subunit.
A translational frameshift leads to early termination
and a truncated protein subunit gamma, about 1/3 shorter
than tau and present in roughly equal amounts. This
frameshift mechanism is not necessarily universal for
species with DNA polymerase III but appears conserved in
the exterme thermophile Thermus thermophilis.
Length = 355
Score = 27.5 bits (62), Expect = 8.5
Identities = 8/14 (57%), Positives = 11/14 (78%)
Query: 222 LFFGLSGTGKTTLS 235
LF G GTGKT+++
Sbjct: 40 LFSGPRGTGKTSIA 53
>gnl|CDD|132027 TIGR02982, heterocyst_DevA, ABC exporter ATP-binding subunit, DevA
family. Members of this protein family are found mostly
in the Cyanobacteria, but also in the Planctomycetes.
Cyanobacterial examples are involved in heterocyst
formation, by which some fraction of members of the
colony undergo a developmental change and become capable
of nitrogen fixation. The DevBCA proteins are thought
export of either heterocyst-specific glycolipids or an
enzyme essential for formation of the laminated layer
found in heterocysts.
Length = 220
Score = 27.3 bits (61), Expect = 8.7
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 210 SINMDKEKEDVALFFGLSGTGKTTL 234
IN++ ++ + G SG+GKTTL
Sbjct: 23 DINLEINPGEIVILTGPSGSGKTTL 47
>gnl|CDD|177823 PLN02165, PLN02165, adenylate isopentenyltransferase.
Length = 334
Score = 27.5 bits (61), Expect = 9.0
Identities = 11/36 (30%), Positives = 18/36 (50%)
Query: 200 PERGIMPMHCSINMDKEKEDVALFFGLSGTGKTTLS 235
P R ++ M K+ V + G +G+GK+ LS
Sbjct: 25 PPRSVVTMTSVAMEQNCKDKVVVIMGATGSGKSRLS 60
>gnl|CDD|129547 TIGR00455, apsK, adenylylsulfate kinase (apsK). Important residue
(active site in E.coli) is residue 100 of the seed
alignment.
Length = 184
Score = 27.4 bits (61), Expect = 9.3
Identities = 9/28 (32%), Positives = 18/28 (64%)
Query: 215 KEKEDVALFFGLSGTGKTTLSASVDRFL 242
+ V GLSG+GK+T++ ++++ L
Sbjct: 15 GHRGVVIWLTGLSGSGKSTIANALEKKL 42
>gnl|CDD|164809 PHA00442, PHA00442, host recBCD nuclease inhibitor.
Length = 59
Score = 27.3 bits (60), Expect = 9.4
Identities = 6/15 (40%), Positives = 10/15 (66%)
Query: 477 PRDSWNDVEAYDQKM 491
RD+WND++ Y +
Sbjct: 11 TRDAWNDMQGYIDSL 25
>gnl|CDD|172748 PRK14260, PRK14260, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 259
Score = 27.3 bits (60), Expect = 9.4
Identities = 21/62 (33%), Positives = 32/62 (51%), Gaps = 3/62 (4%)
Query: 211 INMDKEKEDVALFFGLSGTGKTTLSASVDRFLIGDDEHGWSKEGVFNFEG-GCYAKSINL 269
I+MD + V G SG GK+T +++R I + E EGV +F G Y IN+
Sbjct: 26 ISMDIYRNKVTAIIGPSGCGKSTFIKTLNR--ISELEGPVKVEGVVDFFGQNIYDPRINI 83
Query: 270 SK 271
++
Sbjct: 84 NR 85
>gnl|CDD|162642 TIGR01988, Ubi-OHases, Ubiquinone biosynthesis hydroxylase,
UbiH/UbiF/VisC/COQ6 family. This model represents a
family of FAD-dependent hydroxylases (monooxygenases)
which are all believed to act in the aerobic ubiquinone
biosynthesis pathway. A separate set of hydroxylases, as
yet undiscovered, are believed to be active under
anaerobic conditions. In E. coli three enzyme activities
have been described, UbiB (which acts first at position
6, see TIGR01982), UbiH (which acts at position 4, ) and
UbiF (which acts at position 5). UbiH and UbiF are
similar to one another and form the basis of this
subfamily. Interestingly, E. coli contains another
hydroxylase gene, called visC, that is highly similar to
UbiF, adjacent to UbiH and, when mutated, results in a
phenotype similar to that of UbiH (which has also been
named visB). Several other species appear to have three
homologs in this family, although they assort themselves
differently on phylogenetic trees (e.g. Xylella and
Mesorhizobium) making it difficult to ascribe a specific
activity to each one. Eukaryotes appear to have only a
single homolog in this subfamily (COQ6) which
complements UbiH, but also possess a non-orthologous
gene, COQ7 which complements UbiF.
Length = 385
Score = 27.2 bits (61), Expect = 9.8
Identities = 11/39 (28%), Positives = 18/39 (46%), Gaps = 6/39 (15%)
Query: 311 RAAYPLNFIHNHAPQSIGKHPKHVIMLAADAFGVLPPVA 349
R A+PL+ HA + + + L DA + P+A
Sbjct: 260 RHAFPLSLT--HAKRYVAPR----LALIGDAAHTIHPLA 292
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.320 0.137 0.416
Gapped
Lambda K H
0.267 0.0622 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 8,395,915
Number of extensions: 543158
Number of successful extensions: 1260
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1235
Number of HSP's successfully gapped: 62
Length of query: 509
Length of database: 5,994,473
Length adjustment: 98
Effective length of query: 411
Effective length of database: 3,876,889
Effective search space: 1593401379
Effective search space used: 1593401379
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: 59 (26.7 bits)