Alignments for a candidate for serA in Azoarcus sp. BH72

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Azoarcus sp. BH72

Align Putative phosphoglycerate dehydrogenase (EC:1.1.1.95) (characterized)
to candidate WP_011764215.1 AZO_RS02425 FAD-linked oxidase

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



>NCBI__GCF_000061505.1:WP_011764215.1
          Length = 1289

 Score = 1731 bits (4483), Expect = 0.0
 Identities = 877/1322 (66%), Positives = 1023/1322 (77%), Gaps = 46/1322 (3%)

Query: 22   RLREIPYNYTSFSDREIVIRLLGEESWSLLDELRGKRQTGRSARMLYEVLGDIWVVRRNP 81
            RLREIPYNYTSFSDREIVIRLLG E+WS+LDELR +R TGRSARMLYEVLGDIWVVRRNP
Sbjct: 4    RLREIPYNYTSFSDREIVIRLLGAEAWSVLDELRSERITGRSARMLYEVLGDIWVVRRNP 63

Query: 82   YLQDDLLDNPKRRAALIEALNHRLGEVDKRRLATDQAEAGDAEAQRRSASVEALLKAAKK 141
            YL+DDLL + +RR AL+ ALNHR+ EV+KRR   D+              V  L+  A++
Sbjct: 64   YLEDDLLASRERREALVGALNHRVSEVEKRRQGNDR--------------VALLIGRARE 109

Query: 142  AIADFAEEFRQTYDLRKRATKVLGRFTAKDNIKFDGLSRVSHVTDATDWRVEYPFVVLTP 201
            A+ADF   F  +   RK   K LGR T +DNI FDG +RVSHVTDATDWRVEYPFVVL P
Sbjct: 110  AVADFERWFDDSARKRKAVLKSLGRLTRRDNICFDGHARVSHVTDATDWRVEYPFVVLYP 169

Query: 202  DTEDEMAGLVKACIELGLTIIPRGGGTGYTGGAIPLTPMSAVINTEKLEQLGAVEMEILP 261
            DTE+EMA LV+ACIELG+TIIPRGGGTGYTGGA+PL   S VINTEKL  + AVE   LP
Sbjct: 170  DTEEEMAPLVRACIELGMTIIPRGGGTGYTGGAVPLDANSVVINTEKLLAMSAVEDIPLP 229

Query: 262  GLD-----KPYATIYSGAGVVTKRVSDAAEKAGFVFAVDPTSAEASCIGGNVAMNAGGKK 316
              D      PYATI +GAGVVT RVS+AA  AG VFAVDPTSA ASCIGGN+AMNAGGKK
Sbjct: 230  DADGKPMAAPYATIRTGAGVVTDRVSEAASAAGRVFAVDPTSASASCIGGNIAMNAGGKK 289

Query: 317  AVLWGTALDNLASWRMVDPQGDWLEVTRLDHNLGKIHDVEVARFKLEWSHPGEKGQKTEV 376
            AVLWGTALDNLA W+MV P G+WLEV RLDHN GKIH+ E  RF+L        G   + 
Sbjct: 290  AVLWGTALDNLAWWKMVTPDGNWLEVERLDHNFGKIHEQETVRFRLRRFD----GISYKP 345

Query: 377  FKTEILEISGKKFRKEGLGKDVTDKFLSGLPGVQKEGCDGLITSARWILHKMPKQTRTVC 436
               EIL + G   RK+GLGKDVTDKFL G+PGVQKEG DGLI +ARW+LHKMP  TRTVC
Sbjct: 346  LGEEILAMPGAACRKDGLGKDVTDKFLGGVPGVQKEGTDGLIVAARWVLHKMPPVTRTVC 405

Query: 437  LEFFGQARDAIPSIVEIKDYLD--AETKKGGAILAGLEHLDERYLRAVGYATKSKRGVLP 494
            LEFFGQ R+A+P+IVEI DY          G +LAGLEHLDERY++AVGY TK+KR   P
Sbjct: 406  LEFFGQVREAVPAIVEITDYFKPGGAGNAAGVLLAGLEHLDERYVKAVGYTTKAKRHGRP 465

Query: 495  KMVLIGDIVGDDENAVAAAASEVIRMANNRVGEGFVAVSPEARKKFWLDRSRTAAIAKHT 554
            KMVLIGDIVG DENAV AAASEV+RM N R  EGF+AVSPE RK+FWL+RSRTAAI++HT
Sbjct: 466  KMVLIGDIVGHDENAVMAAASEVVRMTNVRGAEGFIAVSPEQRKRFWLERSRTAAISRHT 525

Query: 555  NAFKINEDVVIPLNRMGEYTDGIERINIELSIKNKLQLLAELDSFFVKGNLPLGKSDDAE 614
            NAFK+NEDVVIPL RMG+Y DGIERINIELSI+NKL+L   L  F ++G LPL + D   
Sbjct: 526  NAFKVNEDVVIPLPRMGDYCDGIERINIELSIQNKLELCDTLAGF-LRGELPLDQGDA-- 582

Query: 615  GDDIPAAEMLEDRVHQAESLLEQTHARWSYLLANLDKPLGEAKGELAALGLEKMLPVFEQ 674
              ++ + E++ DR   A + +E    RW +LL NLD PL EA+   AA G+     V  +
Sbjct: 583  --NLASEELIGDRREAALNYVEAVRLRWEWLLENLDLPLAEAESRFAAYGI-----VAGE 635

Query: 675  RLVDQPEAAVFHVVQDRTVRISWKQEVRAQLRQIFSGAAFKLILEECQAIHKRVLRGRVF 734
                     +FH +QD ++R+SWK E++ +L +IF G  F+ +L     +HK+VLRGRVF
Sbjct: 636  LSNRAANPRLFHRLQDYSIRVSWKTELKPRLDKIFDGVVFRPVLARIAELHKQVLRGRVF 695

Query: 735  VALHMHAGDGNVHTNIPVNSDHYEMLQDAHVAVARIMKLARSLNGVISGEHGIGITKLEF 794
            VALHMHAGDGNVHTNIPVNSDHYEMLQ A+ AV RIM LARSL+GVISGEHGIGITKL++
Sbjct: 696  VALHMHAGDGNVHTNIPVNSDHYEMLQTANRAVDRIMALARSLDGVISGEHGIGITKLDY 755

Query: 795  LTEDEIGEFREYKKRVDPEGRFNKGKLLNLPGMEADLSNAYTPSFGLMGHESLIMQQSDI 854
            LT+ E+  F  YK++VDPEGRFN+GKL+       +L NAYTPSF LMGHESLIM+Q++I
Sbjct: 756  LTDAEMANFWAYKQKVDPEGRFNRGKLMK----GGNLDNAYTPSFNLMGHESLIMEQTEI 811

Query: 855  GAIASSVKDCLRCGKCKPVCSTHVPRANLLYSPRNKILATSLLVEAFLYEEQTRRGVSIK 914
            G IA  +KDCLRCGKCKPVCSTHVPRANLLYSPRNKIL+TSLLVEA LYEEQTRRGVS+ 
Sbjct: 812  GEIAHDIKDCLRCGKCKPVCSTHVPRANLLYSPRNKILSTSLLVEAMLYEEQTRRGVSLA 871

Query: 915  HWEEFEDVADHCTVCHKCVTPCPVDIDFGDVSMNMRNLLRKMGKKSFNAGTNAAMFFLNA 974
            HW EFEDVADHCTVCHKC  PCPVDIDFGDVS+ MRNLLRK GKKSFN G  AAM FL  
Sbjct: 872  HWAEFEDVADHCTVCHKCEKPCPVDIDFGDVSIKMRNLLRKQGKKSFNPGKAAAMAFLTV 931

Query: 975  TDPATINATRKVMTQWGFKAQRLGNDLMKKFA--KKQTQKPPATVGKPPVKEQVIHFINK 1032
             DPATI   R  M +WGFKAQR  + + K     + Q + PPAT+GK P+K QVIH INK
Sbjct: 932  KDPATIKLIRTGMLEWGFKAQRFAHKVGKSLGLVQPQVKAPPATLGKAPIKAQVIHLINK 991

Query: 1033 KMPGNLPKKTARALLDIEDDKIVPIIRNPKTTTADTEAVFYFPGCGSERLFSQVGLATQA 1092
             MPG LPK+T+RALLDIEDDK++P+IR+P+    D+EAVFYFPGCGSERLFSQVGLATQA
Sbjct: 992  PMPGKLPKRTSRALLDIEDDKVIPVIRDPQKVNGDSEAVFYFPGCGSERLFSQVGLATQA 1051

Query: 1093 MLWNVGVQTVLPPGYLCCGYPQRGTGDFEKGEKIITDNRVLFHRMANTLNYLDIKTVVVS 1152
            ML++VG QTVLPPGYLCCGYPQ   G+ +KG+KI TDNRVLFHR+ANTLNYLDIKTV+VS
Sbjct: 1052 MLYHVGAQTVLPPGYLCCGYPQTSAGEDDKGQKITTDNRVLFHRVANTLNYLDIKTVIVS 1111

Query: 1153 CGTCYDQLQGYEFEKIFPGCRIIDIHEYLLEKGVKLEGVTGTRYMYHDPCHSPMKQQDPL 1212
            CGTC DQLQ YEFEKIFPGCR++DIHEYL+EKGVKLEG+ G  YMYH+PCH+PMK    +
Sbjct: 1112 CGTCMDQLQKYEFEKIFPGCRLLDIHEYLMEKGVKLEGIQGVNYMYHEPCHTPMKVHSGI 1171

Query: 1213 KTVNSLITTIDAQKIEKNDRCCGESGTFGVSRPDVSTQVRFRKEEEMRKGSDKVRADGFT 1272
            K  N+L+ T    +++ NDRCCGESGT  V+RPD+STQVRFRK+EE+ KG  K+R    T
Sbjct: 1172 KVANALMGT----RVDLNDRCCGESGTLAVARPDISTQVRFRKQEEIEKGVAKLRESQPT 1227

Query: 1273 GDVKILTSCPSCFQGLSRYNEDA-GTTADYIVVEMARHLLGENWMPEYVERANNGGIERI 1331
               KILTSCP+C QGL RY +DA G   DYIVVE+A+HLLG+NWMP+YV +AN+GGIER+
Sbjct: 1228 APTKILTSCPACLQGLHRYADDAGGVEPDYIVVEIAKHLLGDNWMPDYVAKANSGGIERV 1287

Query: 1332 LV 1333
            L+
Sbjct: 1288 LL 1289


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: 4190
Number of extensions: 155
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: 1289
Length adjustment: 48
Effective length of query: 1285
Effective length of database: 1241
Effective search space:  1594685
Effective search space used:  1594685
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