Alignments for a candidate for serA in Herbaspirillum autotrophicum IAM 14942

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Herbaspirillum autotrophicum IAM 14942

Align Putative phosphoglycerate dehydrogenase (EC:1.1.1.95) (characterized)
to candidate WP_050462791.1 AKL27_RS10575 FAD-linked oxidase

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



>NCBI__GCF_001189915.1:WP_050462791.1
          Length = 1333

 Score = 2476 bits (6417), Expect = 0.0
 Identities = 1212/1333 (90%), Positives = 1274/1333 (95%)

Query: 1    MNAPAQIQALLTDAPHGATPPRLREIPYNYTSFSDREIVIRLLGEESWSLLDELRGKRQT 60
            MNAPA+IQALLTDAPHGA P RLREIPYNYTSFSDREIVIRLLGE++W LLDELRGKRQT
Sbjct: 1    MNAPAKIQALLTDAPHGAVPTRLREIPYNYTSFSDREIVIRLLGEDAWHLLDELRGKRQT 60

Query: 61   GRSARMLYEVLGDIWVVRRNPYLQDDLLDNPKRRAALIEALNHRLGEVDKRRLATDQAEA 120
            GRSARMLYEVLGDIWVVRRNPYLQDD+LDNPKRRAALI+ALNHRLGEVDKRR+ TD AEA
Sbjct: 61   GRSARMLYEVLGDIWVVRRNPYLQDDMLDNPKRRAALIDALNHRLGEVDKRRIVTDLAEA 120

Query: 121  GDAEAQRRSASVEALLKAAKKAIADFAEEFRQTYDLRKRATKVLGRFTAKDNIKFDGLSR 180
            GDA+A RRS +VEALL+AAKKAIADF EEFRQ YDLRKRA KVLGR TAKDNIKFDGLSR
Sbjct: 121  GDADAVRRSTNVEALLRAAKKAIADFGEEFRQIYDLRKRANKVLGRHTAKDNIKFDGLSR 180

Query: 181  VSHVTDATDWRVEYPFVVLTPDTEDEMAGLVKACIELGLTIIPRGGGTGYTGGAIPLTPM 240
            VSHVTDATDWRVEYPFVVLTPD+E+EMAGLVKACIELGLTIIPRGGGTGYTGGAIPLTPM
Sbjct: 181  VSHVTDATDWRVEYPFVVLTPDSEEEMAGLVKACIELGLTIIPRGGGTGYTGGAIPLTPM 240

Query: 241  SAVINTEKLEQLGAVEMEILPGLDKPYATIYSGAGVVTKRVSDAAEKAGFVFAVDPTSAE 300
            SAVINTEKLEQLGAVEM +LPGLDKPYATIYSGAGVVTKRVSDAAEKAGFVFAVDPTSAE
Sbjct: 241  SAVINTEKLEQLGAVEMTVLPGLDKPYATIYSGAGVVTKRVSDAAEKAGFVFAVDPTSAE 300

Query: 301  ASCIGGNVAMNAGGKKAVLWGTALDNLASWRMVDPQGDWLEVTRLDHNLGKIHDVEVARF 360
            ASC+GGNVAMNAGGKKAVLWGTALDNLASWRMVDP GDWL+VTRLDHNLGKIHDV +ARF
Sbjct: 301  ASCVGGNVAMNAGGKKAVLWGTALDNLASWRMVDPNGDWLDVTRLDHNLGKIHDVALARF 360

Query: 361  KLEWSHPGEKGQKTEVFKTEILEISGKKFRKEGLGKDVTDKFLSGLPGVQKEGCDGLITS 420
            +L+W+HP  KGQK   FKTEILEI+G+ FRKEGLGKDVTDKFLSGLPGVQKEGCDGLITS
Sbjct: 361  QLQWTHPAPKGQKNAPFKTEILEIAGRTFRKEGLGKDVTDKFLSGLPGVQKEGCDGLITS 420

Query: 421  ARWILHKMPKQTRTVCLEFFGQARDAIPSIVEIKDYLDAETKKGGAILAGLEHLDERYLR 480
            A WILHKMPK TRTVCLEFFGQARDAIPSIVEIKDYLDAET+KGGAILAGLEHLDERYLR
Sbjct: 421  ATWILHKMPKHTRTVCLEFFGQARDAIPSIVEIKDYLDAETRKGGAILAGLEHLDERYLR 480

Query: 481  AVGYATKSKRGVLPKMVLIGDIVGDDENAVAAAASEVIRMANNRVGEGFVAVSPEARKKF 540
            AVGYATKSKRGVLPKM L GDIVGDDENAVA AASEVIRMANNRVGEGF+AVSPEARKKF
Sbjct: 481  AVGYATKSKRGVLPKMALFGDIVGDDENAVAQAASEVIRMANNRVGEGFIAVSPEARKKF 540

Query: 541  WLDRSRTAAIAKHTNAFKINEDVVIPLNRMGEYTDGIERINIELSIKNKLQLLAELDSFF 600
            WLDRSRTAAIAKHTNAFKINEDVVIPLNRMGEYTDGIERINIELS+KNKLQLL ELDSFF
Sbjct: 541  WLDRSRTAAIAKHTNAFKINEDVVIPLNRMGEYTDGIERINIELSVKNKLQLLGELDSFF 600

Query: 601  VKGNLPLGKSDDAEGDDIPAAEMLEDRVHQAESLLEQTHARWSYLLANLDKPLGEAKGEL 660
              GNLPLGKSDD EG++IPAAEMLEDRVHQA+ L+ +T ARW+YLL NLDKPL  A  EL
Sbjct: 601  AAGNLPLGKSDDGEGEEIPAAEMLEDRVHQAQELIARTQARWTYLLGNLDKPLRAASSEL 660

Query: 661  AALGLEKMLPVFEQRLVDQPEAAVFHVVQDRTVRISWKQEVRAQLRQIFSGAAFKLILEE 720
             ALGL+K+  VFEQRL  QPEA VF VVQDRTVR+SWKQEVRAQLRQIFSGAAFKLILEE
Sbjct: 661  QALGLDKLELVFEQRLQAQPEATVFDVVQDRTVRVSWKQEVRAQLRQIFSGAAFKLILEE 720

Query: 721  CQAIHKRVLRGRVFVALHMHAGDGNVHTNIPVNSDHYEMLQDAHVAVARIMKLARSLNGV 780
            C AIHK++LRGRVFVALHMHAGDGNVHTN+PVNSDHYEMLQDAH AVARIMKLARSL+GV
Sbjct: 721  CSAIHKKILRGRVFVALHMHAGDGNVHTNLPVNSDHYEMLQDAHEAVARIMKLARSLDGV 780

Query: 781  ISGEHGIGITKLEFLTEDEIGEFREYKKRVDPEGRFNKGKLLNLPGMEADLSNAYTPSFG 840
            ISGEHGIGITKLEFLTE+EIG+FR+YK R+DPEGRFNKGKLLNLPGMEADL NAYTPSFG
Sbjct: 781  ISGEHGIGITKLEFLTEEEIGDFRDYKLRIDPEGRFNKGKLLNLPGMEADLRNAYTPSFG 840

Query: 841  LMGHESLIMQQSDIGAIASSVKDCLRCGKCKPVCSTHVPRANLLYSPRNKILATSLLVEA 900
            LMGHESLIMQQSDIGAIA+SVKDCLRCGKCKPVC+THVPRANLLYSPRNKILATSLLVEA
Sbjct: 841  LMGHESLIMQQSDIGAIANSVKDCLRCGKCKPVCATHVPRANLLYSPRNKILATSLLVEA 900

Query: 901  FLYEEQTRRGVSIKHWEEFEDVADHCTVCHKCVTPCPVDIDFGDVSMNMRNLLRKMGKKS 960
            FLYEEQTRRGVSIKHWEEFEDVADHCTVCHKCVTPCPVDIDFGDVSMNMRNLLRKMGKKS
Sbjct: 901  FLYEEQTRRGVSIKHWEEFEDVADHCTVCHKCVTPCPVDIDFGDVSMNMRNLLRKMGKKS 960

Query: 961  FNAGTNAAMFFLNATDPATINATRKVMTQWGFKAQRLGNDLMKKFAKKQTQKPPATVGKP 1020
            FN GT AAMFFLNATDPATINATRKVMT WGFKAQRLG+D++KKFAKKQTQKP ATVGK 
Sbjct: 961  FNPGTTAAMFFLNATDPATINATRKVMTDWGFKAQRLGHDVLKKFAKKQTQKPAATVGKA 1020

Query: 1021 PVKEQVIHFINKKMPGNLPKKTARALLDIEDDKIVPIIRNPKTTTADTEAVFYFPGCGSE 1080
            P+KEQVIHFINKKMPGNLPKKTARALLDIEDDKIVPIIR+PKTTTADTEAVFYFPGCGSE
Sbjct: 1021 PIKEQVIHFINKKMPGNLPKKTARALLDIEDDKIVPIIRDPKTTTADTEAVFYFPGCGSE 1080

Query: 1081 RLFSQVGLATQAMLWNVGVQTVLPPGYLCCGYPQRGTGDFEKGEKIITDNRVLFHRMANT 1140
            RLFSQVGLATQAMLWNVGVQTVLPPGYLCCGYPQRG+GDF+K EKIITDNRVLFHRMANT
Sbjct: 1081 RLFSQVGLATQAMLWNVGVQTVLPPGYLCCGYPQRGSGDFDKAEKIITDNRVLFHRMANT 1140

Query: 1141 LNYLDIKTVVVSCGTCYDQLQGYEFEKIFPGCRIIDIHEYLLEKGVKLEGVTGTRYMYHD 1200
            LNYLDIKTV+VSCGTCYDQLQGY+F+KIFPGCRIIDIHEYLLEKGV+LEGVTGTRYMYHD
Sbjct: 1141 LNYLDIKTVIVSCGTCYDQLQGYQFDKIFPGCRIIDIHEYLLEKGVRLEGVTGTRYMYHD 1200

Query: 1201 PCHSPMKQQDPLKTVNSLITTIDAQKIEKNDRCCGESGTFGVSRPDVSTQVRFRKEEEMR 1260
            PCHSPMK QDP+KTVN+LITT DAQKIEKNDRCCGESGTFGVSRPDVSTQVRFRKEEEMR
Sbjct: 1201 PCHSPMKLQDPMKTVNALITTADAQKIEKNDRCCGESGTFGVSRPDVSTQVRFRKEEEMR 1260

Query: 1261 KGSDKVRADGFTGDVKILTSCPSCFQGLSRYNEDAGTTADYIVVEMARHLLGENWMPEYV 1320
            KG+DKVRADGF G+VKILTSCPSC+QGLSRYNED+GT ADYIVVEMA+HLLGENW+P+YV
Sbjct: 1261 KGADKVRADGFEGEVKILTSCPSCYQGLSRYNEDSGTVADYIVVEMAKHLLGENWLPDYV 1320

Query: 1321 ERANNGGIERILV 1333
             RANNGGIERILV
Sbjct: 1321 ARANNGGIERILV 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: 4689
Number of extensions: 175
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 10 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