Align glycine dehydrogenase [decarboxylating]; EC 1.4.4.2 (characterized)
to candidate AO353_08720 AO353_08720 glycine dehydrogenase
Query= CharProtDB::CH_003480
(957 letters)
>FitnessBrowser__pseudo3_N2E3:AO353_08720
Length = 957
Score = 1258 bits (3255), Expect = 0.0
Identities = 633/957 (66%), Positives = 753/957 (78%), Gaps = 8/957 (0%)
Query: 4 TLSQLENSGAFIERHIGPDAAQQQEMLNAVGAQSLNALTGQIVPKDIQLATPPQVGAPAT 63
+LSQL + AF+ RH+GPD A+QQ ML+++G S L Q VP I+L +
Sbjct: 6 SLSQLRDPNAFLRRHLGPDTAEQQAMLDSLGLGSRVELIEQTVPPGIRLNRVLDLPPALD 65
Query: 64 EYAALAELKAIASRNKRFTSYIGMGYTAVQLPPVILRNMLENPGWYTAYTPYQPEVSQGR 123
E AALA+L+ A +N+ +TS IGMGY P VILRN+LENPGWYTAYTPYQPE++QGR
Sbjct: 66 EEAALAKLRGYAEQNQVWTSLIGMGYHGTLTPAVILRNVLENPGWYTAYTPYQPEIAQGR 125
Query: 124 LEALLNFQQVTLDLTGLDMASASLLDEATAAAEAMAMAKRVSKLKNANRFFVASDVHPQT 183
LEALLNFQQ+T+DLTGL++A+ASLLDEATAAAEAMA+AKRV+K K+ N FFV + HPQT
Sbjct: 126 LEALLNFQQLTIDLTGLELANASLLDEATAAAEAMALAKRVAKSKS-NLFFVDENCHPQT 184
Query: 184 LDVVRTRAETFGFEVIVDDAQKVLDHQDVFGVLLQQVGTTGEIHDYTALISELKSRKIVV 243
+ VV+TRAE FGFE+IVD + HQ VFG LLQ T G+I D LI L +++ +
Sbjct: 185 ISVVKTRAEGFGFELIVDTVDNLKQHQ-VFGALLQYPDTHGDIRDLRPLIDHLHAQQALA 243
Query: 244 SVAADIMALVLLTAPGKQGADIVFGSAQRFGVPMGYGGPHAAFFAAKDEYKRSMPGRIIG 303
VAAD+++L+LLT PG+ GAD+VFGS+QRFGVPMGYGGPHAAFFA++DE+KR++PGRIIG
Sbjct: 244 CVAADLLSLLLLTPPGEMGADVVFGSSQRFGVPMGYGGPHAAFFASRDEFKRAIPGRIIG 303
Query: 304 VSKDAAGNTALRMAMQTREQHIRREKANSNICTSQVLLANIASLYAVYHGPVGLKRIANR 363
VSKDA GN ALRMA+QTREQHIRREKANSNICT+QVLLANIAS YAVYHGP GLKRIA R
Sbjct: 304 VSKDARGNVALRMALQTREQHIRREKANSNICTAQVLLANIASFYAVYHGPQGLKRIAQR 363
Query: 364 IHRLTDILAAGLQQKGLKLRHAHYFDTLCVEVA-DKAGVLTRAEAAEINLRSDILNAVGI 422
+HRLT ILAAGL++ G+ + H+FDTL +EV + ++ A+AA+INLR VG+
Sbjct: 364 VHRLTCILAAGLERNGITRLNQHFFDTLTLEVGGSQTAIIDSAKAAQINLRILGRGQVGL 423
Query: 423 TLDETTTRENVMQLFNVLLGDNHGLDIDTLDKDVAHDSRSIQPAMLRDDEILTHPVFNRY 482
+LDE+ V +LF+V LG +HGLD+ LD + I ++LR L HPVFN +
Sbjct: 424 SLDESCDERTVAKLFDVFLGADHGLDVAELDGEPLVSG--IPESLLRTTSYLRHPVFNAH 481
Query: 483 HSETEMMRYMHSLERKDLALNQAMIPLGSCTMKLNAAAEMIPITWPEFAELHPFCPPEQA 542
HSETEM+RY+ LE KDLALNQ+MIPLGSCTMKLNA++EMIPITWP FA LHPF P EQA
Sbjct: 482 HSETEMLRYLKQLENKDLALNQSMIPLGSCTMKLNASSEMIPITWPAFANLHPFAPKEQA 541
Query: 543 EGYQQMIAQLADWLVKLTGYDAVCMQPNSGAQGEYAGLLAIRHYHESRNEGHRDICLIPA 602
GY MI++L WL +TG+DA+CMQPNSGAQGEYAGLLAIR YHESR +G RDICLIPA
Sbjct: 542 VGYSLMISELESWLCAITGFDAICMQPNSGAQGEYAGLLAIRKYHESRQQGARDICLIPA 601
Query: 603 SAHGTNPASAHMAGMQVVVVACDKNGNIDLTDLRAKAEQAGDNLSCIMVTYPSTHGVYEE 662
SAHGTNPASA MAGM+V++V CD GN+DL DL+AKA AGD LSC+M TYPSTHGVYEE
Sbjct: 602 SAHGTNPASAQMAGMRVMIVDCDDAGNVDLDDLKAKATAAGDKLSCLMATYPSTHGVYEE 661
Query: 663 TIREVCEVVHQFGGQVYLDGANMNAQVGITSPGFIGADVSHLNLHKTFCIPHGGGGPGMG 722
I E+CEV+H GGQVY+DGAN+NAQVG+ P IGADVSH+NLHKTFCIPHGGGGPGMG
Sbjct: 662 GISEICEVIHSHGGQVYMDGANLNAQVGLARPADIGADVSHMNLHKTFCIPHGGGGPGMG 721
Query: 723 PIGVKAHLAPFVPGHSVVQIEGMLTRQGAVSAAPFGSASILPISWMYIRMMGAEGLKKAS 782
PIGV+AHLAPFV H VV IEG + GAVSAAP+GSASILPISWMYI MMG + L AS
Sbjct: 722 PIGVRAHLAPFVANHPVVPIEGPHPQNGAVSAAPWGSASILPISWMYIAMMGPQ-LADAS 780
Query: 783 QVAILNANYIASRLQDAFPVLYTGRDGRVAHECILDIRPLKEETGISELDIAKRLIDYGF 842
+VAIL+ANY+A L AFPVLYTGR+ RVAHECILD+RPLK +TGISE D+AKRL+DYGF
Sbjct: 781 EVAILSANYLAKHLSGAFPVLYTGRNERVAHECILDLRPLKAQTGISEEDVAKRLMDYGF 840
Query: 843 HAPTMSFPVAGTLMVEPTESESKVELDRFIDAMLAIRAEIDQVKAGVWPLEDNPLVNAPH 902
HAPTMSFPV GTLMVEPTESESK ELDRFI AML+IRAEI +V+ G W EDNPL +PH
Sbjct: 841 HAPTMSFPVPGTLMVEPTESESKAELDRFISAMLSIRAEIAEVQNGNWSAEDNPLKRSPH 900
Query: 903 IQSELVAEWAHPYSREVAVFPAGVA--DKYWPTVKRLDDVYGDRNLFCSCVPISEYQ 957
+++ W PYS E AV P KYWPTV R+D+VYGDRNLFC+CVP+ EY+
Sbjct: 901 TLADITGVWDRPYSIEQAVTPDAHTRLHKYWPTVNRVDNVYGDRNLFCACVPVDEYR 957
Lambda K H
0.319 0.134 0.395
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 2315
Number of extensions: 83
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 957
Length of database: 957
Length adjustment: 44
Effective length of query: 913
Effective length of database: 913
Effective search space: 833569
Effective search space used: 833569
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: 57 (26.6 bits)
Align candidate AO353_08720 AO353_08720 (glycine dehydrogenase)
to HMM TIGR00461 (gcvP: glycine dehydrogenase (EC 1.4.4.2))
# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file: ../tmp/path.carbon/TIGR00461.hmm
# target sequence database: /tmp/gapView.5085.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR00461 [M=939]
Accession: TIGR00461
Description: gcvP: glycine dehydrogenase
Scores for complete sequences (score includes all domains):
--- full sequence --- --- best 1 domain --- -#dom-
E-value score bias E-value score bias exp N Sequence Description
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
0 1536.8 0.0 0 1536.6 0.0 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_08720 AO353_08720 glycine dehydrogenas
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_08720 AO353_08720 glycine dehydrogenase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1536.6 0.0 0 0 1 939 [] 19 950 .. 19 950 .. 0.99
Alignments for each domain:
== domain 1 score: 1536.6 bits; conditional E-value: 0
TIGR00461 1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknkkv 65
rhlGpd+aeq+ ml++lG + +lieq vp+ irl+r l l+ + e +ala+l+ a++n++
lcl|FitnessBrowser__pseudo3_N2E3:AO353_08720 19 RHLGPDTAEQQAMLDSLGLGSRVELIEQTVPPGIRLNRVLDLPPALDEEAALAKLRGYAEQNQVW 83
9**************************************************************** PP
TIGR00461 66 ksyiGkGyyatilppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevanas 130
+s iG+Gy +t++p vi+rn+lenpgwytaytpyqpei+qGrleallnfq++++dltGle+anas
lcl|FitnessBrowser__pseudo3_N2E3:AO353_08720 84 TSLIGMGYHGTLTPAVILRNVLENPGWYTAYTPYQPEIAQGRLEALLNFQQLTIDLTGLELANAS 148
***************************************************************** PP
TIGR00461 131 lldegtaaaeamalsfrvskkkankfvvakdvhpqtlevvktraeplgievivddaskvkkavdv 195
llde+taaaeamal++rv+k+k+n f+v++++hpqt++vvktrae +g+e+ivd ++++k++ +v
lcl|FitnessBrowser__pseudo3_N2E3:AO353_08720 149 LLDEATAAAEAMALAKRVAKSKSNLFFVDENCHPQTISVVKTRAEGFGFELIVDTVDNLKQH-QV 212
*****************************************************999888876.6* PP
TIGR00461 196 lGvllqypatdGeildykalidelksrkalvsvaadllaltlltppgklGadivlGsaqrfGvpl 260
+G+llqyp t+G+i d++ lid+l+ ++al +vaadll+l lltppg++Gad+v+Gs+qrfGvp+
lcl|FitnessBrowser__pseudo3_N2E3:AO353_08720 213 FGALLQYPDTHGDIRDLRPLIDHLHAQQALACVAADLLSLLLLTPPGEMGADVVFGSSQRFGVPM 277
***************************************************************** PP
TIGR00461 261 GyGGphaaffavkdeykrklpGrivGvskdalGntalrlalqtreqhirrdkatsnictaqvlla 325
GyGGphaaffa++de+kr +pGri+Gvskda Gn alr+alqtreqhirr+ka+snictaqvlla
lcl|FitnessBrowser__pseudo3_N2E3:AO353_08720 278 GYGGPHAAFFASRDEFKRAIPGRIIGVSKDARGNVALRMALQTREQHIRREKANSNICTAQVLLA 342
***************************************************************** PP
TIGR00461 326 nvaslyavyhGpkGlkniarrifrltsilaaglkrknyelrnktyfdtltvevgekaasevlkaa 390
n+as yavyhGp+Glk+ia+r++rlt ilaagl+r++ n+++fdtlt+evg + ++ +a
lcl|FitnessBrowser__pseudo3_N2E3:AO353_08720 343 NIASFYAVYHGPQGLKRIAQRVHRLTCILAAGLERNGITRLNQHFFDTLTLEVGGSQT-AIIDSA 406
*****************************************************98777.788999 PP
TIGR00461 391 eeaeinlravvltevgialdetttkedvldllkvlagkdnlglsseelsed.vansfpaellrdd 454
++a+inlr + ++vg++lde+ ++ v +l++v++g d +gl++ el+ + + + +p+ llr+
lcl|FitnessBrowser__pseudo3_N2E3:AO353_08720 407 KAAQINLRILGRGQVGLSLDESCDERTVAKLFDVFLGAD-HGLDVAELDGEpLVSGIPESLLRTT 470
*************************************87.********98725568********* PP
TIGR00461 455 eilrdevfnryhsetellrylhrleskdlalnqsmiplGsctmklnataemlpitwpefaeihpf 519
+lr++vfn +hsete+lryl++le+kdlalnqsmiplGsctmklna+ em+pitwp fa++hpf
lcl|FitnessBrowser__pseudo3_N2E3:AO353_08720 471 SYLRHPVFNAHHSETEMLRYLKQLENKDLALNQSMIPLGSCTMKLNASSEMIPITWPAFANLHPF 535
***************************************************************** PP
TIGR00461 520 apaeqveGykeliaqlekwlveitGfdaislqpnsGaqGeyaGlrvirsyhesrgeehrniclip 584
ap eq+ Gy +i++le+wl+ itGfdai++qpnsGaqGeyaGl +ir+yhesr+++ r+iclip
lcl|FitnessBrowser__pseudo3_N2E3:AO353_08720 536 APKEQAVGYSLMISELESWLCAITGFDAICMQPNSGAQGEYAGLLAIRKYHESRQQGARDICLIP 600
***************************************************************** PP
TIGR00461 585 asahGtnpasaamaGlkvvpvkcdkeGnidlvdlkakaekagdelaavmvtypstyGvfeetire 649
asahGtnpasa+maG++v+ v+cd+ Gn+dl dlkaka agd+l+++m typst+Gv+ee+i e
lcl|FitnessBrowser__pseudo3_N2E3:AO353_08720 601 ASAHGTNPASAQMAGMRVMIVDCDDAGNVDLDDLKAKATAAGDKLSCLMATYPSTHGVYEEGISE 665
***************************************************************** PP
TIGR00461 650 vidivhrfGGqvyldGanmnaqvGltspgdlGadvchlnlhktfsiphGGGGpgmgpigvkshla 714
+++++h+ GGqvy+dGan+naqvGl++p+d+Gadv+h+nlhktf+iphGGGGpgmgpigv++hla
lcl|FitnessBrowser__pseudo3_N2E3:AO353_08720 666 ICEVIHSHGGQVYMDGANLNAQVGLARPADIGADVSHMNLHKTFCIPHGGGGPGMGPIGVRAHLA 730
***************************************************************** PP
TIGR00461 715 pflpktdlvsvvelegesksigavsaapyGsasilpisymyikmmGaeGlkkasevailnanyla 779
pf+ + + vv +eg + + gavsaap+Gsasilpis+myi+mmG++ l asevail+anyla
lcl|FitnessBrowser__pseudo3_N2E3:AO353_08720 731 PFVAN---HPVVPIEGPHPQNGAVSAAPWGSASILPISWMYIAMMGPQ-LADASEVAILSANYLA 791
*****...88999**********************************8.99************** PP
TIGR00461 780 krlkdaykilfvgrdervahecildlrelkekagiealdvakrlldyGfhaptlsfpvaGtlmve 844
k l a+++l++gr+ervahecildlr+lk+++gi+++dvakrl+dyGfhapt+sfpv+Gtlmve
lcl|FitnessBrowser__pseudo3_N2E3:AO353_08720 792 KHLSGAFPVLYTGRNERVAHECILDLRPLKAQTGISEEDVAKRLMDYGFHAPTMSFPVPGTLMVE 856
***************************************************************** PP
TIGR00461 845 ptesesleeldrfidamiaikeeidavkaGeiklednilknaphslqslivaewadpysreeaay 909
pteses+ eldrfi am++i++ei +v++G++++edn+lk +ph+l + i++ w pys e+a+
lcl|FitnessBrowser__pseudo3_N2E3:AO353_08720 857 PTESESKAELDRFISAMLSIRAEIAEVQNGNWSAEDNPLKRSPHTLAD-ITGVWDRPYSIEQAVT 920
********************************************8875.9*************** PP
TIGR00461 910 papvlkyfkfwptvarlddtyGdrnlvcsc 939
p + ++ +k+wptv+r+d++yGdrnl+c+c
lcl|FitnessBrowser__pseudo3_N2E3:AO353_08720 921 PDAHTRLHKYWPTVNRVDNVYGDRNLFCAC 950
*****************************9 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (939 nodes)
Target sequences: 1 (957 residues searched)
Passed MSV filter: 1 (1); expected 0.0 (0.02)
Passed bias filter: 1 (1); expected 0.0 (0.02)
Passed Vit filter: 1 (1); expected 0.0 (0.001)
Passed Fwd filter: 1 (1); expected 0.0 (1e-05)
Initial search space (Z): 1 [actual number of targets]
Domain search space (domZ): 1 [number of targets reported over threshold]
# CPU time: 0.07u 0.03s 00:00:00.10 Elapsed: 00:00:00.09
# Mc/sec: 9.13
//
[ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory