Alignments for a candidate for serA in Dechlorosoma suillum PS

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Dechlorosoma suillum PS

Align Putative phosphoglycerate dehydrogenase (EC:1.1.1.95) (characterized)
to candidate Dsui_0736 Dsui_0736 FAD/FMN-dependent dehydrogenase

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



>FitnessBrowser__PS:Dsui_0736
          Length = 1292

 Score = 1766 bits (4573), Expect = 0.0
 Identities = 891/1317 (67%), Positives = 1035/1317 (78%), Gaps = 33/1317 (2%)

Query: 22   RLREIPYNYTSFSDREIVIRLLGEESWSLLDELRGKRQTGRSARMLYEVLGDIWVVRRNP 81
            RLREIPYNYTSFSDREIVIRLLGE+ W +LDELR +R TGRSARMLYEVLGDIWVV+RNP
Sbjct: 4    RLREIPYNYTSFSDREIVIRLLGEDMWRVLDELRAERVTGRSARMLYEVLGDIWVVQRNP 63

Query: 82   YLQDDLLDNPKRRAALIEALNHRLGEVDKRRLATDQAEAGDAEAQRRSASVEALLKAAKK 141
            YL+DDLL  P RR AL++AL HRL EV+KRR       AG  E   RS  V  L++AA K
Sbjct: 64   YLEDDLLATPSRREALVQALRHRLAEVEKRR----SESAG--EDPERSRKVAQLVEAAHK 117

Query: 142  AIADFAEEFRQTYDLRKRATKVLGRFTAKDNIKFDGLSRVSHVTDATDWRVEYPFVVLTP 201
            A+  F + F  T  LR++  K L R T KDN+ FDGL+RVSHVTDATDWRVEYPFVVL P
Sbjct: 118  AVDRFEQRFIDTLMLRRKVLKTLTRHTRKDNVAFDGLARVSHVTDATDWRVEYPFVVLYP 177

Query: 202  DTEDEMAGLVKACIELGLTIIPRGGGTGYTGGAIPLTPMSAVINTEKLEQLGAVEMEILP 261
            DTE+E+  LV+ CIELGLTIIPRGGGTGYTGGA+PL+P+S VINTEKL  +G VE  ILP
Sbjct: 178  DTEEEIGPLVRGCIELGLTIIPRGGGTGYTGGAVPLSPLSVVINTEKLIDIGPVEEIILP 237

Query: 262  GLDKPYATIYSGAGVVTKRVSDAAEKAGFVFAVDPTSAEASCIGGNVAMNAGGKKAVLWG 321
            G DKPYATI +  GVVT RVS+AA  AG VFAVDPTSA ASCIGGN+AMNAGGKKAVLWG
Sbjct: 238  GHDKPYATIRTSVGVVTDRVSEAASAAGRVFAVDPTSASASCIGGNIAMNAGGKKAVLWG 297

Query: 322  TALDNLASWRMVDPQGDWLEVTRLDHNLGKIHDVEVARFKLEWSHPGEKGQKTEVFKTEI 381
            TALDNLA W+MV P G+WLEV RL+HN GKIH+ E   F+L+        +  ++   E+
Sbjct: 298  TALDNLAWWKMVTPDGNWLEVERLNHNFGKIHEQEKVEFRLKRFD----ARSYKLLSEEV 353

Query: 382  LEISGKKFRKEGLGKDVTDKFLSGLPGVQKEGCDGLITSARWILHKMPKQTRTVCLEFFG 441
            L + G   RK GLGKDVTDKFL G+PGVQKEG DG+I +ARW+LHKMP  TRTVCLEFFG
Sbjct: 354  LTLPGAACRKTGLGKDVTDKFLGGVPGVQKEGTDGIIVAARWVLHKMPPVTRTVCLEFFG 413

Query: 442  QARDAIPSIVEIKDYLD--AETKKGGAILAGLEHLDERYLRAVGYATKSKRGVLPKMVLI 499
            Q R+A+PSIVEI DY     E  K G  LAGLEHLDERY++AVGYATK+KR   PKMVLI
Sbjct: 414  QVREAVPSIVEITDYFKPGGEGHKAGVQLAGLEHLDERYVKAVGYATKAKRHGRPKMVLI 473

Query: 500  GDIVGDDENAVAAAASEVIRMANNRVGEGFVAVSPEARKKFWLDRSRTAAIAKHTNAFKI 559
            GDIVG DENAV  AAS+V++M N R  EGF+A++PE RKKFWLDRSRTAAI+KHTNAFK+
Sbjct: 474  GDIVGHDENAVMQAASDVVKMTNVRGAEGFIAITPETRKKFWLDRSRTAAISKHTNAFKV 533

Query: 560  NEDVVIPLNRMGEYTDGIERINIELSIKNKLQLLAELDSFFVKGNLPLGKSDDAEGDDIP 619
            NEDVVIPL RMG+Y DGIERINIELS++NKL L   L  FF KG+LP+  +D     D+ 
Sbjct: 534  NEDVVIPLPRMGDYCDGIERINIELSLQNKLDLCDALTEFF-KGDLPVNSADTKLDKDV- 591

Query: 620  AAEMLEDRVHQAESLLEQTHARWSYLLANLDKPLGEAKGELAALGLEKMLPVFEQRLVDQ 679
               ++EDR  +A   +    ARW +LL NLD PL EA+   A  G+     V  +     
Sbjct: 592  ---LIEDRRERALEHISDVRARWQWLLDNLDLPLAEAEQRFAEFGV-----VAGELTNRA 643

Query: 680  PEAAVFHVVQDRTVRISWKQEVRAQLRQIFSGAAFKLILEECQAIHKRVLRGRVFVALHM 739
                +FH +QD +VR SWK+E++  L  IF+GA ++ + E+  A+ K VLRGRVFVALHM
Sbjct: 644  ANPTLFHRLQDYSVRASWKKELKEPLDNIFNGATYRPLSEKMAAVQKEVLRGRVFVALHM 703

Query: 740  HAGDGNVHTNIPVNSDHYEMLQDAHVAVARIMKLARSLNGVISGEHGIGITKLEFLTEDE 799
            HAGDGNVHTNIPVNSDHYEMLQ A+ AV RIM LARSL+GVISGEHGIGITKLEFLT++E
Sbjct: 704  HAGDGNVHTNIPVNSDHYEMLQTANRAVERIMHLARSLDGVISGEHGIGITKLEFLTDEE 763

Query: 800  IGEFREYKKRVDPEGRFNKGKLLNLPGMEADLSNAYTPSFGLMGHESLIMQQSDIGAIAS 859
            IG FR YK++VDPEGRFNKGKL+  PG   DL NAYTPSF L+G ESLIM+QS+IG IA 
Sbjct: 764  IGPFRAYKEKVDPEGRFNKGKLM--PG--GDLHNAYTPSFSLLGAESLIMEQSEIGKIAD 819

Query: 860  SVKDCLRCGKCKPVCSTHVPRANLLYSPRNKILATSLLVEAFLYEEQTRRGVSIKHWEEF 919
            S+KDCLRCGKCKPVCSTHVPRANLLYSPRNKIL TSLL+EAFLYEEQTRRG+S++H++EF
Sbjct: 820  SIKDCLRCGKCKPVCSTHVPRANLLYSPRNKILGTSLLIEAFLYEEQTRRGISLQHFDEF 879

Query: 920  EDVADHCTVCHKCVTPCPVDIDFGDVSMNMRNLLRKMGKKSFNAGTNAAMFFLNATDPAT 979
             DVADHCTVCH+CV PCPVDIDFGDVS+ MRN LRK GKK  + G  A M+FL   DPAT
Sbjct: 880  NDVADHCTVCHRCVKPCPVDIDFGDVSVAMRNFLRKQGKKKLDPGKAATMWFLTMKDPAT 939

Query: 980  INATRKVMTQWGFKAQRLGNDLMKKFAKKQ--TQKPPATVGKPPVKEQVIHFINKKMPGN 1037
            I   R +M  WG+K QRLG  L K F   Q   Q PPAT+G+P VK QVIHFINK MPGN
Sbjct: 940  IKLARTMMIGWGYKLQRLGVKLAKTFGLTQGIVQHPPATLGRPSVKAQVIHFINKPMPGN 999

Query: 1038 LPKKTARALLDIEDDKIVPIIRNPKTTTADTEAVFYFPGCGSERLFSQVGLATQAMLWNV 1097
            LPK+T+RALLDIEDD +VP+IR+P+  T D++AVFYFPGCGSERLFSQVGLATQAML+  
Sbjct: 1000 LPKRTSRALLDIEDDHVVPVIRDPQKATEDSDAVFYFPGCGSERLFSQVGLATQAMLYET 1059

Query: 1098 GVQTVLPPGYLCCGYPQRGTGDFEKGEKIITDNRVLFHRMANTLNYLDIKTVVVSCGTCY 1157
            G  TVLPPGYLCCGYPQ   G+ +KG+KIITDNRVLFHR+A TLNYLDIKTV+VSCGTC 
Sbjct: 1060 GAVTVLPPGYLCCGYPQNAAGEEDKGQKIITDNRVLFHRVATTLNYLDIKTVIVSCGTCM 1119

Query: 1158 DQLQGYEFEKIFPGCRIIDIHEYLLEKGVKLEGVTGTRYMYHDPCHSPMKQQDPLKTVNS 1217
            DQLQ YEFEKIFPGCR++DIHEYLLEKGVKLEGV GT+YMYH+PCH+PMK    +K VN 
Sbjct: 1120 DQLQKYEFEKIFPGCRLLDIHEYLLEKGVKLEGVKGTQYMYHEPCHTPMKTYSGIKVVND 1179

Query: 1218 LITTIDAQKIEKNDRCCGESGTFGVSRPDVSTQVRFRKEEEMRKGSDKVRAD-GFTGDVK 1276
            L+     Q+++ NDRCCGESG+F +SRPD+STQVRFRK+EE+ KG+ K+R D G    VK
Sbjct: 1180 LM----GQRVDLNDRCCGESGSFALSRPDISTQVRFRKQEEIEKGATKLRQDFGVQDQVK 1235

Query: 1277 ILTSCPSCFQGLSRYNEDAGTTADYIVVEMARHLLGENWMPEYVERANNGGIERILV 1333
            ILTSCPSC QGLSRY  DA   ADYIVVEMA+ LLGENWM +YV++AN+GGIER+L+
Sbjct: 1236 ILTSCPSCLQGLSRYEPDADIQADYIVVEMAKTLLGENWMAQYVQKANSGGIERVLL 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: 4191
Number of extensions: 175
Number of successful extensions: 10
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 09 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