Alignments for a candidate for serA in Methylovulum miyakonense HT12

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Methylovulum miyakonense HT12

Align Putative phosphoglycerate dehydrogenase (EC:1.1.1.95) (characterized)
to candidate WP_019866817.1 METMI_RS0113485 FAD-linked oxidase

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



>NCBI__GCF_000384075.1:WP_019866817.1
          Length = 1328

 Score = 1774 bits (4595), Expect = 0.0
 Identities = 902/1339 (67%), Positives = 1051/1339 (78%), Gaps = 40/1339 (2%)

Query: 1    MNAPAQIQALLTDAPHGATPPRLREIPYNYTSFSDREIVIRLLGEESWSLLDELRGKRQT 60
            M+   Q  AL +D      P RLREIPYNYTSFSDREIVIRLLGE++W +LD LR +R T
Sbjct: 24   MSVDLQSPALFSDV----APTRLREIPYNYTSFSDREIVIRLLGEDNWRILDSLRDERVT 79

Query: 61   GRSARMLYEVLGDIWVVRRNPYLQDDLLDNPKRRAALIEALNHRLGEVDKRRLATDQAEA 120
            GRSARML+EVLGDIW V+RNPYL+DDLLDN  RR AL+EAL HRL +++KR    D+ E 
Sbjct: 80   GRSARMLFEVLGDIWAVQRNPYLEDDLLDNRNRRKALLEALRHRLRQMEKRH---DELEN 136

Query: 121  GDAEAQRRSASVEALLKAAKKAIADFAEEFRQTYDLRKRATKVLGRFTAKDNIKFDGLSR 180
             D    RR   V  L+ AA +A+  F   F  T ++R++A  +L + T KDNI FDG +R
Sbjct: 137  EDVGRARR---VALLITAAHQAVNAFEAHFENTREMRRKALALLSKHTRKDNICFDGFAR 193

Query: 181  VSHVTDATDWRVEYPFVVLTPDTEDEMAGLVKACIELGLTIIPRGGGTGYTGGAIPLTPM 240
            VSHVTDATDWRVEYPFVVL P  E+E+  LV+ CI+LGLTIIPRGGGTGYTGGA+PLTP 
Sbjct: 194  VSHVTDATDWRVEYPFVVLYPGNEEEVGQLVRDCIKLGLTIIPRGGGTGYTGGAVPLTPF 253

Query: 241  SAVINTEKLEQLGAVEMEI-LPGLDKPYATIYSGAGVVTKRVSDAAEKAGFVFAVDPTSA 299
            SAVINTEKL ++G VE E  LPG+ + YATI++GAGVVT+RV D A+ AG VFA DPTSA
Sbjct: 254  SAVINTEKLLEIGRVERESSLPGVAQTYATIFTGAGVVTRRVMDVADNAGLVFACDPTSA 313

Query: 300  EASCIGGNVAMNAGGKKAVLWGTALDNLASWRMVDPQGDWLEVTRLDHNLGKIHDVEVAR 359
            +ASCIGGNVAMNAGGKKAVLWGTALDNL SWRMV P G+WLEV R +HNLGKIHD E   
Sbjct: 314  DASCIGGNVAMNAGGKKAVLWGTALDNLLSWRMVTPDGNWLEVERFNHNLGKIHDQEHVS 373

Query: 360  FKLE-WSHPGEKGQKTEVFKTEILEISGKKFRKEGLGKDVTDKFLSGLPGVQKEGCDGLI 418
            F L+ +   G K     +   E L I G +FRK GLGKDVTDKFL GLPG+QKEGCDG+I
Sbjct: 374  FLLKRYDADGRK-----LLSEEPLVIPGAQFRKAGLGKDVTDKFLGGLPGIQKEGCDGII 428

Query: 419  TSARWILHKMPKQTRTVCLEFFGQARDAIPSIVEIKDYLDAETKKGGA--ILAGLEHLDE 476
            TSARWILHKMP  TRT CLEFFGQ R+A+P+IVEI+DYL A  K G A  +LAGLEHLDE
Sbjct: 429  TSARWILHKMPPHTRTFCLEFFGQVREAVPAIVEIRDYLAALPKNGPARVMLAGLEHLDE 488

Query: 477  RYLRAVGYATKSKRGVLPKMVLIGDIVGDDENAVAAAASEVIRMANNRVGEGFVAVSPEA 536
            RY++AVGYA K+KR   PKMVL+GDIVGDDEN VA AASEV+R+ N R  EGF+A SPE 
Sbjct: 489  RYVKAVGYAPKAKRHGRPKMVLVGDIVGDDENQVALAASEVVRLCNARNAEGFIAASPEM 548

Query: 537  RKKFWLDRSRTAAIAKHTNAFKINEDVVIPLNRMGEYTDGIERINIELSIKNKLQLLAEL 596
            RKKFWLDR+RTAAIAKHTNAFKINEDVVIPL RMG+Y DGIERINIELS++NKL+L   L
Sbjct: 549  RKKFWLDRARTAAIAKHTNAFKINEDVVIPLPRMGDYCDGIERINIELSLRNKLRLCDAL 608

Query: 597  DSFFVKGNLPLGKSDDAEGDDIPAAEMLEDRVHQAESLLEQTHARWSYLLANLDKPLGEA 656
             S F+ G+LPL   +D    +   AE++ DR   A   + Q   RW +L  +LD PL +A
Sbjct: 609  -SHFLAGDLPLRSYED----NTNKAELVGDRRSLALDTVAQVRGRWQWLYDHLDLPLLQA 663

Query: 657  KGELAALGLEKMLPVFE-QRLVDQPEAAVFHVVQDRTVRISWKQEVRAQLRQIFSGAAFK 715
            +      G+     V E     DQP   +FH +QD ++R+SWK E+  +L+ IF G  F+
Sbjct: 664  EAAFGDYGIH----VSELTNRADQP--TLFHRIQDHSLRVSWKSELLPRLQDIFEGDNFR 717

Query: 716  LILEECQAIHKRVLRGRVFVALHMHAGDGNVHTNIPVNSDHYEMLQDAHVAVARIMKLAR 775
             ++E  +A+HK +LRGRVFVALHMHAGDGNVHTN+PVNSDHYEMLQ+A+ AV RIM LAR
Sbjct: 718  PVIERVEAVHKEILRGRVFVALHMHAGDGNVHTNLPVNSDHYEMLQEANAAVVRIMGLAR 777

Query: 776  SLNGVISGEHGIGITKLEFLTEDEIGEFREYKKRVDPEGRFNKGKLLNLPGMEADLSNAY 835
            SL GVISGEHGIGITK EFLTE+E+  F +YK+R+DPEGRFN+GKL+  PG  ADL  AY
Sbjct: 778  SLGGVISGEHGIGITKYEFLTEEELASFHDYKQRIDPEGRFNRGKLM--PG--ADLHAAY 833

Query: 836  TPSFGLMGHESLIMQQSDIGAIASSVKDCLRCGKCKPVCSTHVPRANLLYSPRNKILATS 895
            T SF LMG+ESLIMQQSDIGAIA SVKDCLRCGKCKPVCSTHVPRANLLYSPRNKILATS
Sbjct: 834  TTSFSLMGYESLIMQQSDIGAIADSVKDCLRCGKCKPVCSTHVPRANLLYSPRNKILATS 893

Query: 896  LLVEAFLYEEQTRRGVSIKHWEEFEDVADHCTVCHKCVTPCPVDIDFGDVSMNMRNLLRK 955
            LL+EAFLYEEQTRRG+SI HW+EFEDVADHCTVCHKC  PCPVDIDFGDVSMNMRNLLRK
Sbjct: 894  LLIEAFLYEEQTRRGISITHWKEFEDVADHCTVCHKCYNPCPVDIDFGDVSMNMRNLLRK 953

Query: 956  MGKKSFNAGTNAAMFFLNATDPATINATRKVMTQWGFKAQRLGNDLMKKFAKKQTQKPPA 1015
            MGK+SFN    AA+ FL ++ P T+ A RKV+ +W +K QRLGN L+K + K Q  +PP+
Sbjct: 954  MGKQSFNPVKTAALAFLTSSHPNTVKAMRKVLIEWSYKGQRLGNVLLKPWGKAQLSQPPS 1013

Query: 1016 TVGKPPVKEQVIHFINKKMPGNLPKKTARALLDIEDDKIVPIIRNPKTTTADTEAVFYFP 1075
            + GK PV EQV+HF N+KMPG LP KTARALLDIE+D IVPIIR+   T  D+EAVFYFP
Sbjct: 1014 STGKTPVFEQVVHFTNRKMPGKLPNKTARALLDIENDHIVPIIRDRHKTRTDSEAVFYFP 1073

Query: 1076 GCGSERLFSQVGLATQAMLWNVGVQTVLPPGYLCCGYPQRGTGDFEKGEKIITDNRVLFH 1135
            GCGSERLFSQVGLATQAML+ +GVQTVLPPGYLCCGYPQR  G F+K +KI TDNRVLFH
Sbjct: 1074 GCGSERLFSQVGLATQAMLYEIGVQTVLPPGYLCCGYPQRAAGQFDKAQKITTDNRVLFH 1133

Query: 1136 RMANTLNYLDIKTVVVSCGTCYDQLQGYEFEKIFPGCRIIDIHEYLLEKGVKLEGVTGTR 1195
            R+A TLNYLDIKTVVVSCGTC DQL  YEFEKIFPGCR+IDIHEYLLEKGVKLEGV GTR
Sbjct: 1134 RVATTLNYLDIKTVVVSCGTCLDQLVDYEFEKIFPGCRLIDIHEYLLEKGVKLEGVNGTR 1193

Query: 1196 YMYHDPCHSPMKQQDPLKTVNSLITTIDAQKIEKNDRCCGESGTFGVSRPDVSTQVRFRK 1255
            Y+YHDPCHSP+KQQDP+KTVN LI T     + K++RCCGESGT  V+RPD+STQVR RK
Sbjct: 1194 YLYHDPCHSPLKQQDPMKTVNGLIGT----TVNKSERCCGESGTLAVARPDISTQVRSRK 1249

Query: 1256 EEEMRKGSDKVRADGFTGDVKILTSCPSCFQGLSRYNED-AGTTADYIVVEMARHLLGEN 1314
              E+++ + K+R DG+ G VK+LTSCPSC QGL RY +D      DYIVVE+ARH+LG +
Sbjct: 1250 AIELQEDTAKLRTDGYEGPVKMLTSCPSCVQGLLRYQDDLEQMEVDYIVVEIARHILGPD 1309

Query: 1315 WMPEYVERANNGGIERILV 1333
            WM  Y+ +A NGGIER+LV
Sbjct: 1310 WMGNYIGQAANGGIERVLV 1328


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: 4282
Number of extensions: 173
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: 1328
Length adjustment: 49
Effective length of query: 1284
Effective length of database: 1279
Effective search space:  1642236
Effective search space used:  1642236
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