Alignments for a candidate for serA in Thauera aminoaromatica S2

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Thauera aminoaromatica S2

Align Putative phosphoglycerate dehydrogenase (EC:1.1.1.95) (characterized)
to candidate WP_004324577.1 C665_RS17450 FAD-linked oxidase

Query= reanno::HerbieS:HSERO_RS19500
         (1333 letters)



>NCBI__GCF_000310185.1:WP_004324577.1
          Length = 1292

 Score = 1726 bits (4471), Expect = 0.0
 Identities = 878/1326 (66%), Positives = 1026/1326 (77%), Gaps = 51/1326 (3%)

Query: 22   RLREIPYNYTSFSDREIVIRLLGEESWSLLDELRGKRQTGRSARMLYEVLGDIWVVRRNP 81
            RLREIPYNYTSFSDREIVIRLLG E+W++LD+LR +R TGRSARMLYEVLGDIWVVRRNP
Sbjct: 4    RLREIPYNYTSFSDREIVIRLLGAEAWAVLDQLRTERVTGRSARMLYEVLGDIWVVRRNP 63

Query: 82   YLQDDLLDNPKRRAALIEALNHRLGEVDKRRLATDQAEAGDAEAQRRSASVEALLKAAKK 141
            YL+DDLL + +RR ALI AL+HRL E+DKRR   D               V  L+  A++
Sbjct: 64   YLEDDLLTSRERRDALIGALDHRLNEIDKRRQGNDH--------------VTLLVARARE 109

Query: 142  AIADFAEEFRQTYDLRKRATKVLGRFTAKDNIKFDGLSRVSHVTDATDWRVEYPFVVLTP 201
            A+++F   F  T   RK   K L R T +DNI FDG +RVSHVTDATDWRVEYPFVVL P
Sbjct: 110  AVSNFERWFDDTARRRKAVLKALARHTRRDNICFDGHARVSHVTDATDWRVEYPFVVLYP 169

Query: 202  DTEDEMAGLVKACIELGLTIIPRGGGTGYTGGAIPLTPMSAVINTEKLEQLGAVEMEILP 261
            DTE+EMA LV+ CI LGLTIIPRGGGTGYTGGA+PL   S VINTEKL  + AVE  +LP
Sbjct: 170  DTEEEMAPLVRECIALGLTIIPRGGGTGYTGGAVPLDASSVVINTEKLLAMSAVEPTVLP 229

Query: 262  GLD----KPYATIYSGAGVVTKRVSDAAEKAGFVFAVDPTSAEASCIGGNVAMNAGGKKA 317
            G+D    +PY TI +GAGVVT+RVS+AA  AG VFAVDPTSA ASCIGGN+AMNAGGKKA
Sbjct: 230  GIDGAMAEPYPTIRTGAGVVTERVSEAAALAGRVFAVDPTSASASCIGGNIAMNAGGKKA 289

Query: 318  VLWGTALDNLASWRMVDPQGDWLEVTRLDHNLGKIHDVEVARFKLEWSHPGEKGQKTEVF 377
            VLWGTALDNLA W+MV P G+WLEV RLDHN GKIH+ E  RF+L        G      
Sbjct: 290  VLWGTALDNLAWWKMVTPDGNWLEVERLDHNFGKIHEQETVRFRLRRFD----GLTNAAL 345

Query: 378  KTEILEISGKKFRKEGLGKDVTDKFLSGLPGVQKEGCDGLITSARWILHKMPKQTRTVCL 437
              EIL + G   RK GLGKDVTDKFL G+PGVQKEG DGLI +ARW+LHKMP  TRTVCL
Sbjct: 346  GEEILAMPGAACRKVGLGKDVTDKFLGGVPGVQKEGTDGLIVAARWVLHKMPPVTRTVCL 405

Query: 438  EFFGQARDAIPSIVEIKDYLDAETKKGGA------ILAGLEHLDERYLRAVGYATKSKRG 491
            EFFGQ R+A+P+IVEI D+     K GGA       LAGLEHLDERY++AVGYATK++R 
Sbjct: 406  EFFGQVREAVPAIVEITDFF----KPGGAGHAAGVQLAGLEHLDERYVKAVGYATKARRH 461

Query: 492  VLPKMVLIGDIVGDDENAVAAAASEVIRMANNRVGEGFVAVSPEARKKFWLDRSRTAAIA 551
              PKMVLIGDIVG DE+AV  AASEV+RM N R  EGF+AVSPE RK+FWL+RSRTAAI+
Sbjct: 462  GRPKMVLIGDIVGHDEDAVMKAASEVVRMTNARGSEGFIAVSPEQRKRFWLERSRTAAIS 521

Query: 552  KHTNAFKINEDVVIPLNRMGEYTDGIERINIELSIKNKLQLLAELDSFFVKGNLPLGKSD 611
            +HTNAFKINEDVVIPL RMGEY DGIERINIELS++NK+ L   L  F ++G LPL   D
Sbjct: 522  RHTNAFKINEDVVIPLPRMGEYCDGIERINIELSLQNKIALCDRLAEF-LQGELPLEIKD 580

Query: 612  DAEGDDIPAAEMLEDRVHQAESLLEQTHARWSYLLANLDKPLGEAKGELAALGLEKMLPV 671
              EG D  A  ++ D   QA   +     RW +LL  LD  L EA+ + AA G++     
Sbjct: 581  --EGLDREA--LVSDHRAQALEQVAGVRRRWQWLLDKLDLALAEAEPQFAAYGVQA---- 632

Query: 672  FEQRLVDQPEA-AVFHVVQDRTVRISWKQEVRAQLRQIFSGAAFKLILEECQAIHKRVLR 730
                L ++  +  +FH +QD ++R+SWK+E+R  L Q F GA F  IL     IH+ VLR
Sbjct: 633  --GELSNRAASPTLFHRLQDYSIRVSWKEELRPLLEQTFDGALFAPILARIAEIHREVLR 690

Query: 731  GRVFVALHMHAGDGNVHTNIPVNSDHYEMLQDAHVAVARIMKLARSLNGVISGEHGIGIT 790
            GRVFVALHMHAGDGNVHTN+PVNSDHYEMLQ A+ AV RIM LARSL+GVISGEHGIGIT
Sbjct: 691  GRVFVALHMHAGDGNVHTNLPVNSDHYEMLQTANRAVDRIMALARSLDGVISGEHGIGIT 750

Query: 791  KLEFLTEDEIGEFREYKKRVDPEGRFNKGKLLNLPGMEADLSNAYTPSFGLMGHESLIMQ 850
            KL++LT+DE+  F  YK++VDPEGRFN+GKL+    +  +L NAYTPSF LMGHESLIM+
Sbjct: 751  KLDYLTDDEMANFWSYKEKVDPEGRFNRGKLMRKGPIRGNLDNAYTPSFNLMGHESLIME 810

Query: 851  QSDIGAIASSVKDCLRCGKCKPVCSTHVPRANLLYSPRNKILATSLLVEAFLYEEQTRRG 910
            Q+D+G IA  +KDCLRCGKCKPVCSTHVPRANLLYSPRNKIL+TSLL+EAFLYEEQTRRG
Sbjct: 811  QTDVGEIAHDIKDCLRCGKCKPVCSTHVPRANLLYSPRNKILSTSLLIEAFLYEEQTRRG 870

Query: 911  VSIKHWEEFEDVADHCTVCHKCVTPCPVDIDFGDVSMNMRNLLRKMGKKSFNAGTNAAMF 970
            VS+ HW EFEDVADHCT+CHKC  PCPVDIDFGDVS+ MRNLLRK GKKSFN G  AAM 
Sbjct: 871  VSLAHWAEFEDVADHCTICHKCEKPCPVDIDFGDVSIKMRNLLRKQGKKSFNPGKAAAMA 930

Query: 971  FLNATDPATINATRKVMTQWGFKAQRLGNDLMKKF--AKKQTQKPPATVGKPPVKEQVIH 1028
            FL   DP TI A R  M  WG+KAQR  ++L KKF   + Q + PPAT+GK P+K QVIH
Sbjct: 931  FLTIKDPTTIKAIRTGMIDWGYKAQRFAHELGKKFGLVQPQVKAPPATLGKAPIKAQVIH 990

Query: 1029 FINKKMPGNLPKKTARALLDIEDDKIVPIIRNPKTTTADTEAVFYFPGCGSERLFSQVGL 1088
            FINK MPGNLPK+T+RALLDIEDDK++P+IR+P     ++EAVFYFPGCGSERLFSQVGL
Sbjct: 991  FINKPMPGNLPKRTSRALLDIEDDKVIPVIRDPHKANGESEAVFYFPGCGSERLFSQVGL 1050

Query: 1089 ATQAMLWNVGVQTVLPPGYLCCGYPQRGTGDFEKGEKIITDNRVLFHRMANTLNYLDIKT 1148
            ATQAML++VG  TVLPPGYLCCGYPQ   G+ EKG+KI TDNRVLFHR+ANTLNYLDIKT
Sbjct: 1051 ATQAMLYHVGAHTVLPPGYLCCGYPQTAAGEEEKGQKITTDNRVLFHRVANTLNYLDIKT 1110

Query: 1149 VVVSCGTCYDQLQGYEFEKIFPGCRIIDIHEYLLEKGVKLEGVTGTRYMYHDPCHSPMKQ 1208
            V+VSCGTC DQLQ YEFEKIFPGCR++DIHEYL+EKGVKLEGV G +YMYH+PCH+PMKQ
Sbjct: 1111 VIVSCGTCMDQLQKYEFEKIFPGCRLLDIHEYLMEKGVKLEGVGGVKYMYHEPCHTPMKQ 1170

Query: 1209 QDPLKTVNSLITTIDAQKIEKNDRCCGESGTFGVSRPDVSTQVRFRKEEEMRKGSDKVRA 1268
               +K  N L+ T    +++ +DRCCGESGT  V+RPD+STQVRFRK+EE+ KG+ K+R 
Sbjct: 1171 YQGIKVANELMGT----RVDLSDRCCGESGTLAVARPDISTQVRFRKQEEIEKGAAKLRE 1226

Query: 1269 DGFTGDVKILTSCPSCFQGLSRYNEDA-GTTADYIVVEMARHLLGENWMPEYVERANNGG 1327
                  +K+LTSCPSC QG+ RY +DA G   DYIVVE+ARHLLGENW+P+YV +AN+GG
Sbjct: 1227 GDPNAKIKMLTSCPSCLQGMHRYADDAGGIEPDYIVVELARHLLGENWLPDYVAKANSGG 1286

Query: 1328 IERILV 1333
            IER+L+
Sbjct: 1287 IERVLL 1292


Lambda     K      H
   0.319    0.136    0.402 

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: 4152
Number of extensions: 152
Number of successful extensions: 9
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: 1333
Length of database: 1292
Length adjustment: 48
Effective length of query: 1285
Effective length of database: 1244
Effective search space:  1598540
Effective search space used:  1598540
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 (21.7 bits)
S2: 59 (27.3 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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About GapMind

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis