Alignments for a candidate for serA in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Herbaspirillum seropedicae SmR1

Align Putative phosphoglycerate dehydrogenase (EC:1.1.1.95) (characterized)
to candidate HSERO_RS19500 HSERO_RS19500 FAD-linked oxidase

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



>FitnessBrowser__HerbieS:HSERO_RS19500
          Length = 1333

 Score = 2677 bits (6938), Expect = 0.0
 Identities = 1333/1333 (100%), Positives = 1333/1333 (100%)

Query: 1    MNAPAQIQALLTDAPHGATPPRLREIPYNYTSFSDREIVIRLLGEESWSLLDELRGKRQT 60
            MNAPAQIQALLTDAPHGATPPRLREIPYNYTSFSDREIVIRLLGEESWSLLDELRGKRQT
Sbjct: 1    MNAPAQIQALLTDAPHGATPPRLREIPYNYTSFSDREIVIRLLGEESWSLLDELRGKRQT 60

Query: 61   GRSARMLYEVLGDIWVVRRNPYLQDDLLDNPKRRAALIEALNHRLGEVDKRRLATDQAEA 120
            GRSARMLYEVLGDIWVVRRNPYLQDDLLDNPKRRAALIEALNHRLGEVDKRRLATDQAEA
Sbjct: 61   GRSARMLYEVLGDIWVVRRNPYLQDDLLDNPKRRAALIEALNHRLGEVDKRRLATDQAEA 120

Query: 121  GDAEAQRRSASVEALLKAAKKAIADFAEEFRQTYDLRKRATKVLGRFTAKDNIKFDGLSR 180
            GDAEAQRRSASVEALLKAAKKAIADFAEEFRQTYDLRKRATKVLGRFTAKDNIKFDGLSR
Sbjct: 121  GDAEAQRRSASVEALLKAAKKAIADFAEEFRQTYDLRKRATKVLGRFTAKDNIKFDGLSR 180

Query: 181  VSHVTDATDWRVEYPFVVLTPDTEDEMAGLVKACIELGLTIIPRGGGTGYTGGAIPLTPM 240
            VSHVTDATDWRVEYPFVVLTPDTEDEMAGLVKACIELGLTIIPRGGGTGYTGGAIPLTPM
Sbjct: 181  VSHVTDATDWRVEYPFVVLTPDTEDEMAGLVKACIELGLTIIPRGGGTGYTGGAIPLTPM 240

Query: 241  SAVINTEKLEQLGAVEMEILPGLDKPYATIYSGAGVVTKRVSDAAEKAGFVFAVDPTSAE 300
            SAVINTEKLEQLGAVEMEILPGLDKPYATIYSGAGVVTKRVSDAAEKAGFVFAVDPTSAE
Sbjct: 241  SAVINTEKLEQLGAVEMEILPGLDKPYATIYSGAGVVTKRVSDAAEKAGFVFAVDPTSAE 300

Query: 301  ASCIGGNVAMNAGGKKAVLWGTALDNLASWRMVDPQGDWLEVTRLDHNLGKIHDVEVARF 360
            ASCIGGNVAMNAGGKKAVLWGTALDNLASWRMVDPQGDWLEVTRLDHNLGKIHDVEVARF
Sbjct: 301  ASCIGGNVAMNAGGKKAVLWGTALDNLASWRMVDPQGDWLEVTRLDHNLGKIHDVEVARF 360

Query: 361  KLEWSHPGEKGQKTEVFKTEILEISGKKFRKEGLGKDVTDKFLSGLPGVQKEGCDGLITS 420
            KLEWSHPGEKGQKTEVFKTEILEISGKKFRKEGLGKDVTDKFLSGLPGVQKEGCDGLITS
Sbjct: 361  KLEWSHPGEKGQKTEVFKTEILEISGKKFRKEGLGKDVTDKFLSGLPGVQKEGCDGLITS 420

Query: 421  ARWILHKMPKQTRTVCLEFFGQARDAIPSIVEIKDYLDAETKKGGAILAGLEHLDERYLR 480
            ARWILHKMPKQTRTVCLEFFGQARDAIPSIVEIKDYLDAETKKGGAILAGLEHLDERYLR
Sbjct: 421  ARWILHKMPKQTRTVCLEFFGQARDAIPSIVEIKDYLDAETKKGGAILAGLEHLDERYLR 480

Query: 481  AVGYATKSKRGVLPKMVLIGDIVGDDENAVAAAASEVIRMANNRVGEGFVAVSPEARKKF 540
            AVGYATKSKRGVLPKMVLIGDIVGDDENAVAAAASEVIRMANNRVGEGFVAVSPEARKKF
Sbjct: 481  AVGYATKSKRGVLPKMVLIGDIVGDDENAVAAAASEVIRMANNRVGEGFVAVSPEARKKF 540

Query: 541  WLDRSRTAAIAKHTNAFKINEDVVIPLNRMGEYTDGIERINIELSIKNKLQLLAELDSFF 600
            WLDRSRTAAIAKHTNAFKINEDVVIPLNRMGEYTDGIERINIELSIKNKLQLLAELDSFF
Sbjct: 541  WLDRSRTAAIAKHTNAFKINEDVVIPLNRMGEYTDGIERINIELSIKNKLQLLAELDSFF 600

Query: 601  VKGNLPLGKSDDAEGDDIPAAEMLEDRVHQAESLLEQTHARWSYLLANLDKPLGEAKGEL 660
            VKGNLPLGKSDDAEGDDIPAAEMLEDRVHQAESLLEQTHARWSYLLANLDKPLGEAKGEL
Sbjct: 601  VKGNLPLGKSDDAEGDDIPAAEMLEDRVHQAESLLEQTHARWSYLLANLDKPLGEAKGEL 660

Query: 661  AALGLEKMLPVFEQRLVDQPEAAVFHVVQDRTVRISWKQEVRAQLRQIFSGAAFKLILEE 720
            AALGLEKMLPVFEQRLVDQPEAAVFHVVQDRTVRISWKQEVRAQLRQIFSGAAFKLILEE
Sbjct: 661  AALGLEKMLPVFEQRLVDQPEAAVFHVVQDRTVRISWKQEVRAQLRQIFSGAAFKLILEE 720

Query: 721  CQAIHKRVLRGRVFVALHMHAGDGNVHTNIPVNSDHYEMLQDAHVAVARIMKLARSLNGV 780
            CQAIHKRVLRGRVFVALHMHAGDGNVHTNIPVNSDHYEMLQDAHVAVARIMKLARSLNGV
Sbjct: 721  CQAIHKRVLRGRVFVALHMHAGDGNVHTNIPVNSDHYEMLQDAHVAVARIMKLARSLNGV 780

Query: 781  ISGEHGIGITKLEFLTEDEIGEFREYKKRVDPEGRFNKGKLLNLPGMEADLSNAYTPSFG 840
            ISGEHGIGITKLEFLTEDEIGEFREYKKRVDPEGRFNKGKLLNLPGMEADLSNAYTPSFG
Sbjct: 781  ISGEHGIGITKLEFLTEDEIGEFREYKKRVDPEGRFNKGKLLNLPGMEADLSNAYTPSFG 840

Query: 841  LMGHESLIMQQSDIGAIASSVKDCLRCGKCKPVCSTHVPRANLLYSPRNKILATSLLVEA 900
            LMGHESLIMQQSDIGAIASSVKDCLRCGKCKPVCSTHVPRANLLYSPRNKILATSLLVEA
Sbjct: 841  LMGHESLIMQQSDIGAIASSVKDCLRCGKCKPVCSTHVPRANLLYSPRNKILATSLLVEA 900

Query: 901  FLYEEQTRRGVSIKHWEEFEDVADHCTVCHKCVTPCPVDIDFGDVSMNMRNLLRKMGKKS 960
            FLYEEQTRRGVSIKHWEEFEDVADHCTVCHKCVTPCPVDIDFGDVSMNMRNLLRKMGKKS
Sbjct: 901  FLYEEQTRRGVSIKHWEEFEDVADHCTVCHKCVTPCPVDIDFGDVSMNMRNLLRKMGKKS 960

Query: 961  FNAGTNAAMFFLNATDPATINATRKVMTQWGFKAQRLGNDLMKKFAKKQTQKPPATVGKP 1020
            FNAGTNAAMFFLNATDPATINATRKVMTQWGFKAQRLGNDLMKKFAKKQTQKPPATVGKP
Sbjct: 961  FNAGTNAAMFFLNATDPATINATRKVMTQWGFKAQRLGNDLMKKFAKKQTQKPPATVGKP 1020

Query: 1021 PVKEQVIHFINKKMPGNLPKKTARALLDIEDDKIVPIIRNPKTTTADTEAVFYFPGCGSE 1080
            PVKEQVIHFINKKMPGNLPKKTARALLDIEDDKIVPIIRNPKTTTADTEAVFYFPGCGSE
Sbjct: 1021 PVKEQVIHFINKKMPGNLPKKTARALLDIEDDKIVPIIRNPKTTTADTEAVFYFPGCGSE 1080

Query: 1081 RLFSQVGLATQAMLWNVGVQTVLPPGYLCCGYPQRGTGDFEKGEKIITDNRVLFHRMANT 1140
            RLFSQVGLATQAMLWNVGVQTVLPPGYLCCGYPQRGTGDFEKGEKIITDNRVLFHRMANT
Sbjct: 1081 RLFSQVGLATQAMLWNVGVQTVLPPGYLCCGYPQRGTGDFEKGEKIITDNRVLFHRMANT 1140

Query: 1141 LNYLDIKTVVVSCGTCYDQLQGYEFEKIFPGCRIIDIHEYLLEKGVKLEGVTGTRYMYHD 1200
            LNYLDIKTVVVSCGTCYDQLQGYEFEKIFPGCRIIDIHEYLLEKGVKLEGVTGTRYMYHD
Sbjct: 1141 LNYLDIKTVVVSCGTCYDQLQGYEFEKIFPGCRIIDIHEYLLEKGVKLEGVTGTRYMYHD 1200

Query: 1201 PCHSPMKQQDPLKTVNSLITTIDAQKIEKNDRCCGESGTFGVSRPDVSTQVRFRKEEEMR 1260
            PCHSPMKQQDPLKTVNSLITTIDAQKIEKNDRCCGESGTFGVSRPDVSTQVRFRKEEEMR
Sbjct: 1201 PCHSPMKQQDPLKTVNSLITTIDAQKIEKNDRCCGESGTFGVSRPDVSTQVRFRKEEEMR 1260

Query: 1261 KGSDKVRADGFTGDVKILTSCPSCFQGLSRYNEDAGTTADYIVVEMARHLLGENWMPEYV 1320
            KGSDKVRADGFTGDVKILTSCPSCFQGLSRYNEDAGTTADYIVVEMARHLLGENWMPEYV
Sbjct: 1261 KGSDKVRADGFTGDVKILTSCPSCFQGLSRYNEDAGTTADYIVVEMARHLLGENWMPEYV 1320

Query: 1321 ERANNGGIERILV 1333
            ERANNGGIERILV
Sbjct: 1321 ERANNGGIERILV 1333


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: 4876
Number of extensions: 156
Number of successful extensions: 1
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: 1333
Length adjustment: 49
Effective length of query: 1284
Effective length of database: 1284
Effective search space:  1648656
Effective search space used:  1648656
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