Alignments for a candidate for serA in Sulfuritalea hydrogenivorans DSM 22779

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Sulfuritalea hydrogenivorans DSM 22779

Align Putative phosphoglycerate dehydrogenase (EC:1.1.1.95) (characterized)
to candidate WP_041101219.1 SUTH_RS17940 FAD/FMN-binding oxidoreductase

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



>NCBI__GCF_000828635.1:WP_041101219.1
          Length = 1261

 Score = 1718 bits (4449), Expect = 0.0
 Identities = 877/1322 (66%), Positives = 1025/1322 (77%), Gaps = 74/1322 (5%)

Query: 22   RLREIPYNYTSFSDREIVIRLLGEESWSLLDELRGKRQTGRSARMLYEVLGDIWVVRRNP 81
            RLREIPYNYTSFSDREIVIRLLG E+W+ L+ELR +R TGRSARMLYEVLGDIWVVRRNP
Sbjct: 4    RLREIPYNYTSFSDREIVIRLLGAEAWATLNELRAERVTGRSARMLYEVLGDIWVVRRNP 63

Query: 82   YLQDDLLDNPKRRAALIEALNHRLGEVDKRRLATDQAEAGDAEAQRRSASVEALLKAAKK 141
            YL+DDLL N +RR AL+EAL HRL E+DKRR      E G    +R    V  LL AA+ 
Sbjct: 64   YLEDDLLGNRERREALVEALRHRLREIDKRR------EVGTPRNER----VALLLTAAQA 113

Query: 142  AIADFAEEFRQTYDLRKRATKVLGRFTAKDNIKFDGLSRVSHVTDATDWRVEYPFVVLTP 201
            A+  F   F +T  LRK+A K L R T +DNI FDGL+RVSHVTDATDWRVEYPFVVL P
Sbjct: 114  AVQSFERWFEETRSLRKKALKALARHTRRDNICFDGLARVSHVTDATDWRVEYPFVVLAP 173

Query: 202  DTEDEMAGLVKACIELGLTIIPRGGGTGYTGGAIPLTPMSAVINTEKLEQLGAVEMEILP 261
            DTEDEMA LV+ACIELGLTIIPRGGGTGYTGGA+PL  +S VINTEKL  LGAVEM+ LP
Sbjct: 174  DTEDEMAPLVRACIELGLTIIPRGGGTGYTGGAVPLDALSVVINTEKLIDLGAVEMKRLP 233

Query: 262  GLDKPYATIYSGAGVVTKRVSDAAEKAGFVFAVDPTSAEASCIGGNVAMNAGGKKAVLWG 321
            G D+ YAT+ +GAG+VT+RV +AAEKA  VFA DPTSA+ASCIGGN+AMNAGGKKAVLWG
Sbjct: 234  GTDRDYATVRTGAGLVTRRVMEAAEKAELVFACDPTSADASCIGGNIAMNAGGKKAVLWG 293

Query: 322  TALDNLASWRMVDPQGDWLEVTRLDHNLGKIHDVEVARFKL-EWSHPGEKGQKTEVFKTE 380
            TALDNLASWRMV P G+WL+V RL+HN GKIH+ E   F+L  W   G+K         E
Sbjct: 294  TALDNLASWRMVTPDGNWLDVERLNHNFGKIHEQETVSFRLVRWDATGKK-----KLGEE 348

Query: 381  ILEISGKKFRKEGLGKDVTDKFLSGLPGVQKEGCDGLITSARWILHKMPKQTRTVCLEFF 440
             L++ G+ FRKEGLGKDVTDKFL+G+PGVQKEG DGLITSA W+LHKMP  TRTVCLEFF
Sbjct: 349  QLDVPGRLFRKEGLGKDVTDKFLAGIPGVQKEGTDGLITSAVWVLHKMPPVTRTVCLEFF 408

Query: 441  GQARDAIPSIVEIKDYLDAETKKGGA------ILAGLEHLDERYLRAVGYATKSKRGVLP 494
            G+  DA+PSIVEI DY     K GGA       LAGLEHLDERY+RAVGYATK+KR   P
Sbjct: 409  GRVTDAVPSIVEITDYF----KPGGAGLAAGVQLAGLEHLDERYVRAVGYATKAKRHGRP 464

Query: 495  KMVLIGDIVGDDENAVAAAASEVIRMANNRVGEGFVAVSPEARKKFWLDRSRTAAIAKHT 554
            KMVLIGDIVG D+ AV AAASEV+RMAN R  EGF+AVSPEARKKFWLDR+RTAAI+KHT
Sbjct: 465  KMVLIGDIVGADDTAVMAAASEVVRMANARGAEGFIAVSPEARKKFWLDRARTAAISKHT 524

Query: 555  NAFKINEDVVIPLNRMGEYTDGIERINIELSIKNKLQLLAELDSFFVKGNLPLGKSDDAE 614
            NAFK+NEDVVIPL RMG+Y DGIERINIELSI NK++ LA+  S F+KG LPL   D   
Sbjct: 525  NAFKVNEDVVIPLPRMGDYCDGIERINIELSIANKIE-LADALSEFLKGELPLHAGD--- 580

Query: 615  GDDIPAAEMLEDRVHQAESLLEQTHARWSYLLANLDKPLGEAKGELAALGLEKMLPVFEQ 674
              ++    +L D+  QA  L+ +  A W  LL NLD+   E                   
Sbjct: 581  -ANLDPELLLGDKREQALELIAEVRAGWQGLLDNLDRHFAE------------------- 620

Query: 675  RLVDQPEAAVFHVVQDRTVRISWKQEVRAQLRQIFSGAAFKLILEECQAIHKRVLRGRVF 734
                         +QD  +R+SWK E++A L  +F G AF+ +LE   AIH+ VLRGRVF
Sbjct: 621  -------------LQDYRLRVSWKTELKAPLEALFDGNAFRPVLERITAIHQEVLRGRVF 667

Query: 735  VALHMHAGDGNVHTNIPVNSDHYEMLQDAHVAVARIMKLARSLNGVISGEHGIGITKLEF 794
            VALHMHAGDGNVHTNIPVNSDHY MLQ A+ AV RIM LA+SL GVISGEHGIGITKLEF
Sbjct: 668  VALHMHAGDGNVHTNIPVNSDHYAMLQTAYKAVERIMALAKSLGGVISGEHGIGITKLEF 727

Query: 795  LTEDEIGEFREYKKRVDPEGRFNKGKLLNLPGMEADLSNAYTPSFGLMGHESLIMQQSDI 854
            L +DEI  FR+YK++VDP+G FN+GKL+       DL+NAYTPSF L+G ESLIM+QSD+
Sbjct: 728  LGDDEIRPFRDYKQKVDPDGCFNRGKLM----AGGDLANAYTPSFALLGVESLIMEQSDV 783

Query: 855  GAIASSVKDCLRCGKCKPVCSTHVPRANLLYSPRNKILATSLLVEAFLYEEQTRRGVSIK 914
            G I+ S+K+CLRCGKCKPVCSTHVPRANLLYSPRNKIL TSLL+EAFLYEEQTRRG+S++
Sbjct: 784  GRISESIKNCLRCGKCKPVCSTHVPRANLLYSPRNKILGTSLLIEAFLYEEQTRRGISLQ 843

Query: 915  HWEEFEDVADHCTVCHKCVTPCPVDIDFGDVSMNMRNLLRKMGKKSFNAGTNAAMFFLNA 974
            H++EF DVADHCTVCHKCVTPCPVDIDFGDVS+ MRN LR+ GKK FN GT AAM FL+A
Sbjct: 844  HFDEFSDVADHCTVCHKCVTPCPVDIDFGDVSVAMRNFLRRQGKKKFNPGTAAAMGFLSA 903

Query: 975  TDPATINATRKVMTQWGFKAQRLGNDLMKKFA--KKQTQKPPATVGKPPVKEQVIHFINK 1032
            TDPATI   R  M Q G+KAQRLG+ L K F   +   + PPAT+G+P +K QVIHF+NK
Sbjct: 904  TDPATIKLVRAGMIQLGYKAQRLGHALAKSFGLIQDSVKHPPATLGRPELKAQVIHFLNK 963

Query: 1033 KMPGNLPKKTARALLDIEDDKIVPIIRNPKTTTADTEAVFYFPGCGSERLFSQVGLATQA 1092
             MP ++P +T+RALLD+EDD ++P+IR+P+ T  D+EAVFYFPGCGSERLFSQVGLATQA
Sbjct: 964  PMPKDVPNRTSRALLDVEDDSLIPVIRDPQRTAEDSEAVFYFPGCGSERLFSQVGLATQA 1023

Query: 1093 MLWNVGVQTVLPPGYLCCGYPQRGTGDFEKGEKIITDNRVLFHRMANTLNYLDIKTVVVS 1152
            MLW+ G  TVLPPGYLCCGYPQ  +GD +KG+ I T NRVLFHR+ANTLNYLDIKTVVVS
Sbjct: 1024 MLWHAGATTVLPPGYLCCGYPQTASGDEDKGQAITTANRVLFHRVANTLNYLDIKTVVVS 1083

Query: 1153 CGTCYDQLQGYEFEKIFPGCRIIDIHEYLLEKGVKLEGVTGTRYMYHDPCHSPMKQQDPL 1212
            CGTC DQL  YEF KIFPGCR++DIHE+L EKG+KL+GV G +YMYH+PCH+PMK    +
Sbjct: 1084 CGTCMDQLLKYEFGKIFPGCRLVDIHEWLFEKGIKLDGVKGMQYMYHEPCHTPMKHYSGV 1143

Query: 1213 KTVNSLITTIDAQKIEKNDRCCGESGTFGVSRPDVSTQVRFRKEEEMRKGSDKVRADGFT 1272
            K  N+L+     Q+++ +DRCCGESG+  VSRPDVSTQ+RFRK++E+  G+ ++R  G  
Sbjct: 1144 KVANALM----GQRVDLSDRCCGESGSLAVSRPDVSTQIRFRKQQEIEAGAAELRRVGAG 1199

Query: 1273 GD-VKILTSCPSCFQGLSRYNEDAGTTADYIVVEMARHLLGENWMPEYVERANNGGIERI 1331
            G  VKILTSCPSC QGLSRY  DA  +ADYIVVEMAR +LG +WM  Y+  AN+GGIERI
Sbjct: 1200 GTAVKILTSCPSCLQGLSRYENDADISADYIVVEMARAILGPDWMQNYLRAANSGGIERI 1259

Query: 1332 LV 1333
            L+
Sbjct: 1260 LL 1261


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: 4067
Number of extensions: 146
Number of successful extensions: 11
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: 1261
Length adjustment: 48
Effective length of query: 1285
Effective length of database: 1213
Effective search space:  1558705
Effective search space used:  1558705
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 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

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

Related tools

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