Alignments for a candidate for serA in Methylococcus capsulatus Bath

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Methylococcus capsulatus Bath

Align Putative phosphoglycerate dehydrogenase (EC:1.1.1.95) (characterized)
to candidate WP_010961011.1 MCA_RS08655 FAD-linked oxidase

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



>NCBI__GCF_000008325.1:WP_010961011.1
          Length = 1308

 Score = 1819 bits (4712), Expect = 0.0
 Identities = 912/1326 (68%), Positives = 1073/1326 (80%), Gaps = 33/1326 (2%)

Query: 15   PHGATP-PRLREIPYNYTSFSDREIVIRLLGEESWSLLDELRGKRQTGRSARMLYEVLGD 73
            PH   P PRLREIPYNYTSFSDREIVIRLLGE+ W +L++LR +R TGRSARMLYEVLGD
Sbjct: 9    PHNTGPGPRLREIPYNYTSFSDREIVIRLLGEDMWQVLEDLRTERVTGRSARMLYEVLGD 68

Query: 74   IWVVRRNPYLQDDLLDNPKRRAALIEALNHRLGEVDKRRLATDQAEAGDAEAQRRSASVE 133
            IW V+RNPYL+DDLLDN  RR AL+EAL HRL ++++RR      E G +E   R+A V 
Sbjct: 69   IWAVQRNPYLEDDLLDNEGRRRALLEALRHRLRQMEQRRAGI---EVGRSE---RAAKVA 122

Query: 134  ALLKAAKKAIADFAEEFRQTYDLRKRATKVLGRFTAKDNIKFDGLSRVSHVTDATDWRVE 193
             LL+AA +A+  F   F  T +LR+RA  +L R T KDNI FDG +RV+HVTDATDWRVE
Sbjct: 123  LLLQAAHQAVDAFEACFEHTRELRRRALTLLSRHTRKDNICFDGYARVTHVTDATDWRVE 182

Query: 194  YPFVVLTPDTEDEMAGLVKACIELGLTIIPRGGGTGYTGGAIPLTPMSAVINTEKLEQLG 253
            YPFVVL P +E E+  LV+ CIELGLTIIPRGGGTGYTGGA+PLTP+SAVINTEKL +L 
Sbjct: 183  YPFVVLYPCSEQEVGHLVRDCIELGLTIIPRGGGTGYTGGAVPLTPLSAVINTEKLLELS 242

Query: 254  AVEME-ILPGLDKPYATIYSGAGVVTKRVSDAAEKAGFVFAVDPTSAEASCIGGNVAMNA 312
            AVE E +LPG+D+P AT+++GAGVVT+RV DAAE+AG VFA DPTSA+ASCIGGN+AMNA
Sbjct: 243  AVERETLLPGVDRPCATVFTGAGVVTRRVMDAAEQAGLVFACDPTSADASCIGGNIAMNA 302

Query: 313  GGKKAVLWGTALDNLASWRMVDPQGDWLEVTRLDHNLGKIHDVEVARFKLE-WSHPGEKG 371
            GGKKAVLWGTALDNLASWRMV P G+WLEV RL+HNLG+IHD +  +F+L  +   G + 
Sbjct: 303  GGKKAVLWGTALDNLASWRMVTPDGNWLEVERLNHNLGRIHDQDEVKFRLRRYDADGHR- 361

Query: 372  QKTEVFKTEILEISGKKFRKEGLGKDVTDKFLSGLPGVQKEGCDGLITSARWILHKMPKQ 431
                + + EIL + G +FRK GLGKDVTDKFL GLPG+QKEGCDG+ITSARWILH+MP  
Sbjct: 362  ----LLEEEILTLPGHRFRKTGLGKDVTDKFLGGLPGIQKEGCDGIITSARWILHEMPPY 417

Query: 432  TRTVCLEFFGQARDAIPSIVEIKDYLDAETKKGGA--ILAGLEHLDERYLRAVGYATKSK 489
            TRT CLEFFGQ R+A+P+IVEI+DYL + +K GGA  +LAGLEHLDERY++AVGYATK++
Sbjct: 418  TRTFCLEFFGQVREAVPAIVEIQDYLGSLSKSGGARVMLAGLEHLDERYVKAVGYATKAR 477

Query: 490  RGVLPKMVLIGDIVGDDENAVAAAASEVIRMANNRVGEGFVAVSPEARKKFWLDRSRTAA 549
            R   PKMVL+GDIVGDD++AVA AAS+V+R+ N R  EGF+AVSPEAR+KFWLDR+RTAA
Sbjct: 478  RHGRPKMVLLGDIVGDDDDAVARAASQVVRLCNARSAEGFIAVSPEARRKFWLDRARTAA 537

Query: 550  IAKHTNAFKINEDVVIPLNRMGEYTDGIERINIELSIKNKLQLLAELDSFFVKGNLPLGK 609
            IAKHTNAFKINEDVVIPL RMG+Y DGIERINIELS++NKL+L   L    + G LPL  
Sbjct: 538  IAKHTNAFKINEDVVIPLARMGDYCDGIERINIELSLRNKLKLCDALAEC-LGGELPLRA 596

Query: 610  SDDAEGDDIPAAEMLEDRVHQAESLLEQTHARWSYLLANLDKPLGEAKGELAALGLEKML 669
             +D     I   E++ DR   A   +     RW +LL +LD PL +A+   A LG+E   
Sbjct: 597  YEDG----INKTELIGDRRALALDAVAAVRERWQWLLDHLDLPLEQAEARFAELGIEA-- 650

Query: 670  PVFEQRLVDQPEA-AVFHVVQDRTVRISWKQEVRAQLRQIFSGAAFKLILEECQAIHKRV 728
                  L ++ E   +FH +QD +VR+SWK+E+  +L+ IF G +F+ I+E  +A+HK V
Sbjct: 651  ----GALTNRTERPTLFHRLQDHSVRVSWKKELLPRLKSIFEGDSFRPIVERIEAVHKAV 706

Query: 729  LRGRVFVALHMHAGDGNVHTNIPVNSDHYEMLQDAHVAVARIMKLARSLNGVISGEHGIG 788
            LRGRVFVALHMHAGDGNVHTN+PVNSDHYEMLQ+A+ AV RIM LARSL GVISGEHGIG
Sbjct: 707  LRGRVFVALHMHAGDGNVHTNLPVNSDHYEMLQEANAAVVRIMALARSLGGVISGEHGIG 766

Query: 789  ITKLEFLTEDEIGEFREYKKRVDPEGRFNKGKLLNLPGMEADLSNAYTPSFGLMGHESLI 848
            ITK EFLTE+E+  F  YK +VDPEGRFN+GKL+  PG  A L  AYTPSF LMG ESLI
Sbjct: 767  ITKYEFLTEEEVAPFHAYKAQVDPEGRFNQGKLM--PG--AGLRAAYTPSFSLMGFESLI 822

Query: 849  MQQSDIGAIASSVKDCLRCGKCKPVCSTHVPRANLLYSPRNKILATSLLVEAFLYEEQTR 908
            MQQSDIGAIA SVKDCLRCGKCKPVCSTHVP+ANL YSPRNKILATSLL+EAFLYEEQTR
Sbjct: 823  MQQSDIGAIADSVKDCLRCGKCKPVCSTHVPQANLPYSPRNKILATSLLIEAFLYEEQTR 882

Query: 909  RGVSIKHWEEFEDVADHCTVCHKCVTPCPVDIDFGDVSMNMRNLLRKMGKKSFNAGTNAA 968
            RGVSI HW+EFEDVADHCTVCHKC  PCPVDIDFG VSMNMRNLLRKMGK+SFN    AA
Sbjct: 883  RGVSITHWKEFEDVADHCTVCHKCYNPCPVDIDFGQVSMNMRNLLRKMGKQSFNPAKTAA 942

Query: 969  MFFLNATDPATINATRKVMTQWGFKAQRLGNDLMKKFAKKQTQKPPATVGKPPVKEQVIH 1028
            + FLN T P  I A R  + +WG++ QRLG+ L++ + + QT++PPA++GKP V EQVIH
Sbjct: 943  LAFLNVTRPNAIKALRTTLIEWGYRGQRLGHLLLRPWGQTQTRRPPASLGKPKVTEQVIH 1002

Query: 1029 FINKKMPGNLPKKTARALLDIEDDKIVPIIRNPKTTTADTEAVFYFPGCGSERLFSQVGL 1088
            FINKKMPG LP KTARALLDIED+++VP+IR+P+ T  D+EAVFYFPGCGSERLFSQVGL
Sbjct: 1003 FINKKMPGQLPGKTARALLDIEDNQVVPVIRDPRKTAVDSEAVFYFPGCGSERLFSQVGL 1062

Query: 1089 ATQAMLWNVGVQTVLPPGYLCCGYPQRGTGDFEKGEKIITDNRVLFHRMANTLNYLDIKT 1148
            ATQAML+ +GVQTVLPPGYLCCG+PQR  G F+K EKI TDNRVLFHR+ANTLNYLDIKT
Sbjct: 1063 ATQAMLYEIGVQTVLPPGYLCCGFPQRAAGQFDKAEKITTDNRVLFHRVANTLNYLDIKT 1122

Query: 1149 VVVSCGTCYDQLQGYEFEKIFPGCRIIDIHEYLLEKGVKLEGVTGTRYMYHDPCHSPMKQ 1208
            VVVSCGTC DQL  YEF++IFPG R++DIHEYLLEKGVKLEGV G RY+YHDPCHSPMKQ
Sbjct: 1123 VVVSCGTCLDQLASYEFDRIFPGSRVLDIHEYLLEKGVKLEGVNGVRYLYHDPCHSPMKQ 1182

Query: 1209 QDPLKTVNSLITTIDAQKIEKNDRCCGESGTFGVSRPDVSTQVRFRKEEEMRKGSDKVRA 1268
            QDPLKTVN+LI T D  +I K++RCCGESGT  ++RPD++TQVRFRKE E++  +  VRA
Sbjct: 1183 QDPLKTVNALIATADGSRIAKSERCCGESGTLAIARPDIATQVRFRKEAELKSDAASVRA 1242

Query: 1269 DGFTGDVKILTSCPSCFQGLSRYNEDAG-TTADYIVVEMARHLLGENWMPEYVERANNGG 1327
            DGF G VK+LTSCPSC QGL RY ED     ADYIVVE+ARH+LGENWM +YVERA NGG
Sbjct: 1243 DGFDGPVKVLTSCPSCLQGLQRYREDVDRLDADYIVVEIARHVLGENWMKDYVERAVNGG 1302

Query: 1328 IERILV 1333
            +ERILV
Sbjct: 1303 VERILV 1308


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: 4189
Number of extensions: 151
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: 1308
Length adjustment: 49
Effective length of query: 1284
Effective length of database: 1259
Effective search space:  1616556
Effective search space used:  1616556
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