Alignments for a candidate for serA in Methylomicrobium alcaliphilum 20Z

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Methylomicrobium alcaliphilum 20Z

Align Putative phosphoglycerate dehydrogenase (EC:1.1.1.95) (characterized)
to candidate WP_046060990.1 MEALZ_RS04680 FAD-linked oxidase

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



>NCBI__GCF_000968535.2:WP_046060990.1
          Length = 1305

 Score = 1742 bits (4511), Expect = 0.0
 Identities = 868/1337 (64%), Positives = 1053/1337 (78%), Gaps = 36/1337 (2%)

Query: 1    MNAPAQIQALLTDAPHGATPPRLREIPYNYTSFSDREIVIRLLGEESWSLLDELRGKRQT 60
            M+  +++   + DAP      RLREIPYNYTSFSDREIVIRLLGEE+W +++ LRG+R T
Sbjct: 1    MSVDSELSPFVADAPS----ERLREIPYNYTSFSDREIVIRLLGEENWQIIESLRGERMT 56

Query: 61   GRSARMLYEVLGDIWVVRRNPYLQDDLLDNPKRRAALIEALNHRLGEVDKRRLATDQAEA 120
            GRSARML+EVLGDIW V+RNPYL+DDLL+N KRR AL++AL HRL +++KR    +    
Sbjct: 57   GRSARMLFEVLGDIWAVQRNPYLEDDLLNNRKRRKALLDALRHRLRQMEKRHAEYEN--- 113

Query: 121  GDAEAQRRSASVEALLKAAKKAIADFAEEFRQTYDLRKRATKVLGRFTAKDNIKFDGLSR 180
               E   R+  V  L++A  +A+ +F   F +T ++R++A  +  + T KDNI FDG +R
Sbjct: 114  ---EYPDRARRVALLIEATHQAVNEFEAHFDRTREMRRKALALFSKHTHKDNIGFDGFAR 170

Query: 181  VSHVTDATDWRVEYPFVVLTPDTEDEMAGLVKACIELGLTIIPRGGGTGYTGGAIPLTPM 240
            VSHVTDATDWRVEYPFVVL P +E E+  LV+ CI+LGLTIIPRGGGTGYTGGA+PLTP 
Sbjct: 171  VSHVTDATDWRVEYPFVVLYPTSEKEVGQLVRDCIKLGLTIIPRGGGTGYTGGAVPLTPY 230

Query: 241  SAVINTEKLEQLGAVEMEI-LPGLDKPYATIYSGAGVVTKRVSDAAEKAGFVFAVDPTSA 299
            SAVINTEKL  +G +E +  LPG+++ YATI++GAGVVT+RV D AE AG VFA DPTSA
Sbjct: 231  SAVINTEKLLDMGPIEPQSQLPGVEQTYATIHTGAGVVTRRVMDMAENAGLVFACDPTSA 290

Query: 300  EASCIGGNVAMNAGGKKAVLWGTALDNLASWRMVDPQGDWLEVTRLDHNLGKIHDVEVAR 359
            +ASCIGGNVAMNAGGKKAVLWGTALDNL SWRMV P G+WLEV R+ HN GKIHD E+  
Sbjct: 291  DASCIGGNVAMNAGGKKAVLWGTALDNLVSWRMVTPDGNWLEVERIHHNFGKIHDQELVT 350

Query: 360  FKLEWSHPGEKGQKTEVFKTEILEISGKKFRKEGLGKDVTDKFLSGLPGVQKEGCDGLIT 419
            F L+      K    E+   E LEI G KFR++GLGKDVTDKFL GLPG+QKEGCDG+IT
Sbjct: 351  FALKRFDAKAK----ELLSEERLEIPGAKFRRDGLGKDVTDKFLGGLPGIQKEGCDGIIT 406

Query: 420  SARWILHKMPKQTRTVCLEFFGQARDAIPSIVEIKDYLDAETKKGG--AILAGLEHLDER 477
            SARWILHKMP  TRT CLEFFGQ RD++P+IVEI+D+L+A  K G    +LAGLEHLDER
Sbjct: 407  SARWILHKMPAYTRTFCLEFFGQVRDSVPAIVEIRDFLEALPKSGNDRVMLAGLEHLDER 466

Query: 478  YLRAVGYATKSKRGVLPKMVLIGDIVGDDENAVAAAASEVIRMANNRVGEGFVAVSPEAR 537
            Y++AVGYA K+K    PKMVLIGDIVGDD++ VA AASEV+R+ N R  EGFVAVSPE+R
Sbjct: 467  YVKAVGYAGKAKHRGRPKMVLIGDIVGDDDHQVALAASEVVRLCNARGAEGFVAVSPESR 526

Query: 538  KKFWLDRSRTAAIAKHTNAFKINEDVVIPLNRMGEYTDGIERINIELSIKNKLQLLAELD 597
            + FWLDR+RTAAIAKHTNAFKINEDVVIPL RMG+Y DGIERINIELS++NKL+L   L 
Sbjct: 527  RTFWLDRARTAAIAKHTNAFKINEDVVIPLPRMGDYCDGIERINIELSLRNKLRLCDALI 586

Query: 598  SFFVKGNLPLGKSDDAEGDDIPAAEMLEDRVHQAESLLEQTHARWSYLLANLDKPLGEAK 657
              F +G+LPL   +D     +   +++ +R   A  ++ +   RW +L  NLD PL +A+
Sbjct: 587  DLF-EGDLPLRSYEDG----VDKTDLIGERRGHALMVVAEVRERWQWLYDNLDLPLPQAE 641

Query: 658  GELAALGLEKMLPVFEQRLVDQPEAAVFHVVQDRTVRISWKQEVRAQLRQIFSGAAFKLI 717
               +  G+   +      L +QP   +FH +QD ++ +SWKQE+  +L++IF G  F+ +
Sbjct: 642  ALFSQYGI---VAGELTNLTEQP--TLFHRLQDYSLMVSWKQELLPRLKEIFVGDNFRPV 696

Query: 718  LEECQAIHKRVLRGRVFVALHMHAGDGNVHTNIPVNSDHYEMLQDAHVAVARIMKLARSL 777
            +E  +A HK VLRGRVFVALHMHAGDGNVHTN+PVNSD+YEMLQ+A+ AVARIM LARSL
Sbjct: 697  VERIEATHKDVLRGRVFVALHMHAGDGNVHTNLPVNSDNYEMLQEANAAVARIMALARSL 756

Query: 778  NGVISGEHGIGITKLEFLTEDEIGEFREYKKRVDPEGRFNKGKLLNLPGMEADLSNAYTP 837
             GVISGEHGIGITK EFLT++E+  F +YK+R+DPEGRFN+GKL+  PG  +DLS+AYT 
Sbjct: 757  GGVISGEHGIGITKYEFLTDEELAGFHDYKQRIDPEGRFNRGKLM--PG--SDLSSAYTT 812

Query: 838  SFGLMGHESLIMQQSDIGAIASSVKDCLRCGKCKPVCSTHVPRANLLYSPRNKILATSLL 897
            SF LMG ESLIMQQSDIGAI+ SVKDCLRCGKCKPVCSTHVPRANLLYSPRNKILATSLL
Sbjct: 813  SFNLMGFESLIMQQSDIGAISDSVKDCLRCGKCKPVCSTHVPRANLLYSPRNKILATSLL 872

Query: 898  VEAFLYEEQTRRGVSIKHWEEFEDVADHCTVCHKCVTPCPVDIDFGDVSMNMRNLLRKMG 957
            +EAFLYEEQTRRG+SI HW+EFEDV+DHCTVCHKC  PCPVDIDFGDVSMNMRNLLRKMG
Sbjct: 873  IEAFLYEEQTRRGISITHWKEFEDVSDHCTVCHKCFNPCPVDIDFGDVSMNMRNLLRKMG 932

Query: 958  KKSFNAGTNAAMFFLNATDPATINATRKVMTQWGFKAQRLGNDLMKKFAKKQTQKPPATV 1017
            K+SFN    AA+ FL+   P+++   RK++ +W +KAQRLGN  ++ + + Q ++PP++ 
Sbjct: 933  KQSFNPVKTAAIAFLSTGRPSSVKLMRKLLIEWSYKAQRLGNFFLRPWGRAQLKRPPSST 992

Query: 1018 GKPPVKEQVIHFINKKMPGNLPKKTARALLDIEDDKIVPIIRNPKTTTADTEAVFYFPGC 1077
            GKP +KE VIHF N+KMPG LP KT+RALL IE D+IVPIIR+P  T  D+EAVFYFPGC
Sbjct: 993  GKPAMKEYVIHFTNRKMPGKLPSKTSRALLGIESDQIVPIIRDPNKTRTDSEAVFYFPGC 1052

Query: 1078 GSERLFSQVGLATQAMLWNVGVQTVLPPGYLCCGYPQRGTGDFEKGEKIITDNRVLFHRM 1137
            GSERLFSQVGLATQAML+ +GVQTVLPPGYLCCG+PQR  G F+K ++I TDNRVLFHR+
Sbjct: 1053 GSERLFSQVGLATQAMLYEIGVQTVLPPGYLCCGFPQRAAGQFDKAQQITTDNRVLFHRV 1112

Query: 1138 ANTLNYLDIKTVVVSCGTCYDQLQGYEFEKIFPGCRIIDIHEYLLEKGVKLEGVTGTRYM 1197
            A TLNYLDIKTVVVSCGTC DQL  YEF+KIFPGCR+IDIHEYLLEKGVKLEGV G RY+
Sbjct: 1113 ATTLNYLDIKTVVVSCGTCLDQLVDYEFDKIFPGCRMIDIHEYLLEKGVKLEGVNGRRYL 1172

Query: 1198 YHDPCHSPMKQQDPLKTVNSLITTIDAQKIEKNDRCCGESGTFGVSRPDVSTQVRFRKEE 1257
            YHDPCHSPM+QQD +KTVN L+       + K++RCCGESGT  V+RPD+STQVR+RK  
Sbjct: 1173 YHDPCHSPMQQQDAMKTVNGLL----GAPVNKSERCCGESGTLAVARPDISTQVRYRKSV 1228

Query: 1258 EMRKGSDKVRADGFTGDVKILTSCPSCFQGLSRYNEDAG-TTADYIVVEMARHLLGENWM 1316
            E+ + + K+RAD + G VK+LTSCPSC QGL RY  D      DYIVVE+ARH+LGE+WM
Sbjct: 1229 ELHRDTAKLRADDYDGPVKMLTSCPSCLQGLQRYKGDVDQLEVDYIVVEIARHVLGEDWM 1288

Query: 1317 PEYVERANNGGIERILV 1333
              Y+++A  GGIER+LV
Sbjct: 1289 KSYIKQAAKGGIERVLV 1305


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: 4182
Number of extensions: 170
Number of successful extensions: 11
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: 1305
Length adjustment: 48
Effective length of query: 1285
Effective length of database: 1257
Effective search space:  1615245
Effective search space used:  1615245
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