Alignments for a candidate for serA in Derxia gummosa DSM 723

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Derxia gummosa DSM 723

Align Putative phosphoglycerate dehydrogenase (EC:1.1.1.95) (characterized)
to candidate WP_028310634.1 H566_RS0105375 FAD-linked oxidase

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



>NCBI__GCF_000482785.1:WP_028310634.1
          Length = 1342

 Score = 2004 bits (5192), Expect = 0.0
 Identities = 998/1354 (73%), Positives = 1137/1354 (83%), Gaps = 33/1354 (2%)

Query: 1    MNAPAQIQAL--LTDAPH--GATPPRLREIPYNYTSFSDREIVIRLLGEESWSLLDELRG 56
            MNAP  + A+    D P    A  PRLREIPYNYTSFSDREIVIRLLGE +W  L+ LRG
Sbjct: 1    MNAPHSLTAVPGTADVPGQPAAERPRLREIPYNYTSFSDREIVIRLLGETAWETLEALRG 60

Query: 57   KRQTGRSARMLYEVLGDIWVVRRNPYLQDDLLDNPKRRAALIEALNHRLGEVDKRRLATD 116
            +R+TGRSARML+EVLGDIWVV+RNPYLQDDLLDNP+RR ALI+AL HR+  ++ RR    
Sbjct: 61   ERRTGRSARMLFEVLGDIWVVQRNPYLQDDLLDNPRRRKALIDALWHRVRGIESRR---- 116

Query: 117  QAEAGDAEAQRRSASVEALLKAAKKAIADFAEEFRQTYDLRKRATKVLGRFTAKDNIKFD 176
                GDA    R A V +L+ +A  AI  FA +F +    R+     LGR TAKDNIKFD
Sbjct: 117  --GGGDAG---RDALVASLVTSASAAIEQFAADFERVGAKRREVLGKLGRITAKDNIKFD 171

Query: 177  GLSRVSHVTDATDWRVEYPFVVLTPDTEDEMAGLVKACIELGLTIIPRGGGTGYTGGAIP 236
            GLSRVSHVTDATDWRVEYPFVVLTPD E EMA LV+AC + GLT+IPRGGGTGYTGGA+P
Sbjct: 172  GLSRVSHVTDATDWRVEYPFVVLTPDNEAEMAPLVRACFDCGLTVIPRGGGTGYTGGAVP 231

Query: 237  LTPMSAVINTEKLEQLGAVEMEILPGLDKPYATIYSGAGVVTKRVSDAAEKAGFVFAVDP 296
            LTP SAVINTEKLE++ AVEM  LPGL +P  T+YS AGVVTKRV++AA+ AGFVFAVDP
Sbjct: 232  LTPWSAVINTEKLEKMSAVEMVDLPGLGRPVPTVYSEAGVVTKRVAEAADSAGFVFAVDP 291

Query: 297  TSAEASCIGGNVAMNAGGKKAVLWGTALDNLASWRMVDPQGDWLEVTRLDHNLGKIHDVE 356
            TS EASCIGGN+AMNAGGKKAVLWGTALDNLA WRMVDP G+WLEVTR++HNLGKIHD +
Sbjct: 292  TSIEASCIGGNIAMNAGGKKAVLWGTALDNLAWWRMVDPSGNWLEVTRINHNLGKIHDAK 351

Query: 357  VARFKLEWSHPGEKGQKTEVFKTEILEISGKKFRKEGLGKDVTDKFLSGLPGVQKEGCDG 416
               F+L W    +     E+ +T  L I G +FRK GLGKDVTDKFL+GLPGVQKEGCDG
Sbjct: 352  DVIFELVWRDGTQPPGAGEIIRTTTLNIDGARFRKTGLGKDVTDKFLAGLPGVQKEGCDG 411

Query: 417  LITSARWILHKMPKQTRTVCLEFFGQARDAIPSIVEIKDYLDAETKKGG------AILAG 470
            LIT+ARW++H+MPK  RTVCLEFFGQARDAIPSIVEIKDYLDA+T+KG        +LAG
Sbjct: 412  LITAARWVVHRMPKHVRTVCLEFFGQARDAIPSIVEIKDYLDAQTRKGAPEGMAPVMLAG 471

Query: 471  LEHLDERYLRAVGYATKSKR--GVLPKMVLIGDIVGDDENAVAAAASEVIRMANNRVGEG 528
            LEHLDERYLRAVGYATKSK   G LPKM L GDIVGDDENAVAAAASEV+R+AN RVGEG
Sbjct: 472  LEHLDERYLRAVGYATKSKAHGGGLPKMALFGDIVGDDENAVAAAASEVVRIANTRVGEG 531

Query: 529  FVAVSPEARKKFWLDRSRTAAIAKHTNAFKINEDVVIPLNRMGEYTDGIERINIELSIKN 588
            F+AVSPE RKKFWLDRSRTAAI++HTNAFK+NEDVVIPL+RM EYTDGIERINIELSI+N
Sbjct: 532  FIAVSPEQRKKFWLDRSRTAAISRHTNAFKVNEDVVIPLHRMDEYTDGIERINIELSIRN 591

Query: 589  KLQLLAELDSFFVKGNLPLGKSDDAEGDDIPAAEMLEDRVHQAESLLEQTHARWSYLLAN 648
            KL+L+AELD   ++G LPLGK+DDA   D+P+A+++E+R  +A  L+E+ HARWS++L +
Sbjct: 592  KLKLVAELDRL-LQGELPLGKTDDAA--DLPSADIIENRAQEARELIEKVHARWSFVLGS 648

Query: 649  LDKPLGEAKGELAALGLEKMLPVFEQRLVDQPEAAVFHVVQDRTVRISWKQEVRAQLRQI 708
            LD+ L EA+ +L   G + +L VF  R+  +P   VF +VQDRT+R+SWK+E+RA+ R+I
Sbjct: 649  LDRRLAEAQADLVRHGYDHLLDVFGPRIAVRPNVRVFDLVQDRTIRVSWKKEIRAEFRRI 708

Query: 709  FSGAAFKLILEECQAIHKRVLRGRVFVALHMHAGDGNVHTNIPVNSDHYEMLQDAHVAVA 768
            F GAAF   L+  +  HK+VLRGRVFVALHMHAGDGNVHTNIPVNSD YEMLQ A+ AVA
Sbjct: 709  FGGAAFDPTLKLFETTHKKVLRGRVFVALHMHAGDGNVHTNIPVNSDDYEMLQTANEAVA 768

Query: 769  RIMKLARSLNGVISGEHGIGITKLEFLTEDEIGEFREYKKRVDPEGRFNKGKLLN----- 823
            RIM LARSL+GVISGEHGIGITKLEFLT++E+  F EYK++VDP+GRFNKGKLL      
Sbjct: 769  RIMTLARSLDGVISGEHGIGITKLEFLTDEELRPFTEYKQKVDPQGRFNKGKLLRGHSFV 828

Query: 824  ---LPGMEADLSNAYTPSFGLMGHESLIMQQSDIGAIASSVKDCLRCGKCKPVCSTHVPR 880
                P   ADL++AYTPSFGLMGHESLIMQQSDIGAIA+SVKDCLRCGKCKPVC+THVPR
Sbjct: 829  EDGRPMAPADLTHAYTPSFGLMGHESLIMQQSDIGAIAASVKDCLRCGKCKPVCATHVPR 888

Query: 881  ANLLYSPRNKILATSLLVEAFLYEEQTRRGVSIKHWEEFEDVADHCTVCHKCVTPCPVDI 940
            A+LLYSPRNKILATSLL+EAFLYEEQTRRGVSIKHW+EF DVADHCTVCHKCVTPCPV I
Sbjct: 889  ASLLYSPRNKILATSLLIEAFLYEEQTRRGVSIKHWDEFSDVADHCTVCHKCVTPCPVKI 948

Query: 941  DFGDVSMNMRNLLRKMGKKSFNAGTNAAMFFLNATDPATINATRKVMTQWGFKAQRLGND 1000
            DFGDVSMNMRNLL K+GK+ FN G+ AAMFFLNATDP TI  TR  M   GFKAQR  ND
Sbjct: 949  DFGDVSMNMRNLLTKLGKRKFNPGSKAAMFFLNATDPDTIKMTRAAMVGIGFKAQRFAND 1008

Query: 1001 LMKKFAKKQTQKPPATVG-KPPVKEQVIHFINKKMPGNLPKKTARALLDIEDDKIVPIIR 1059
            L+KKF +KQT  PPAT G +PP++EQVIHF+NKK+P  LP KTARALLDIED++IVPIIR
Sbjct: 1009 LLKKFTRKQTGHPPATDGGRPPIREQVIHFVNKKLPAGLPTKTARALLDIEDNEIVPIIR 1068

Query: 1060 NPKTTTADTEAVFYFPGCGSERLFSQVGLATQAMLWNVGVQTVLPPGYLCCGYPQRGTGD 1119
            +PK TT DTEAVFYFPGCGSERLFSQVGLATQAMLW+VGVQTVLPPGYLCCGYPQRG G 
Sbjct: 1069 DPKKTTPDTEAVFYFPGCGSERLFSQVGLATQAMLWHVGVQTVLPPGYLCCGYPQRGAGQ 1128

Query: 1120 FEKGEKIITDNRVLFHRMANTLNYLDIKTVVVSCGTCYDQLQGYEFEKIFPGCRIIDIHE 1179
             +K EKI TDNRVLFHR+ANTLNYLDIKTVVVSCGTCYDQL  YEFEKIFPGCRI+DIHE
Sbjct: 1129 ADKAEKIQTDNRVLFHRVANTLNYLDIKTVVVSCGTCYDQLATYEFEKIFPGCRIVDIHE 1188

Query: 1180 YLLEKGVKLEGVTGTRYMYHDPCHSPMKQQDPLKTVNSLITTIDAQKIEKNDRCCGESGT 1239
            YL+EKGVKLEGV GTRYMYHDPCH+PMK QDPLKTVNSLITT DA KI KNDRCCGESGT
Sbjct: 1189 YLMEKGVKLEGVQGTRYMYHDPCHTPMKLQDPLKTVNSLITTADATKIAKNDRCCGESGT 1248

Query: 1240 FGVSRPDVSTQVRFRKEEEMRKGSDKVRADGFTGDVKILTSCPSCFQGLSRYNEDAGTTA 1299
            FGV+RPD++TQVRFRKEE MR  +DK+RADGFTGDVKILTSCPSC QGL+RY+ED+ T A
Sbjct: 1249 FGVTRPDIATQVRFRKEESMRAQADKLRADGFTGDVKILTSCPSCLQGLTRYDEDSDTKA 1308

Query: 1300 DYIVVEMARHLLGENWMPEYVERANNGGIERILV 1333
            DY+V+EMA+HLLG +W+PEYV+ ANNGGIER+LV
Sbjct: 1309 DYVVIEMAKHLLGNDWLPEYVKAANNGGIERVLV 1342


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: 4417
Number of extensions: 175
Number of successful extensions: 8
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: 1342
Length adjustment: 49
Effective length of query: 1284
Effective length of database: 1293
Effective search space:  1660212
Effective search space used:  1660212
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