Alignments for a candidate for serA in Hydrogenovibrio marinus DSM 11271

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Hydrogenovibrio marinus DSM 11271

Align Putative phosphoglycerate dehydrogenase (EC:1.1.1.95) (characterized)
to candidate WP_029908112.1 P166_RS0101595 DUF3683 domain-containing protein

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



>NCBI__GCF_000711315.1:WP_029908112.1
          Length = 1283

 Score = 1432 bits (3708), Expect = 0.0
 Identities = 722/1318 (54%), Positives = 932/1318 (70%), Gaps = 44/1318 (3%)

Query: 22   RLREIPYNYTSFSDREIVIRLLGEESWSLLDELRGKRQTGRSARMLYEVLGDIWVVRRNP 81
            R+REIPYNYTSFSD+EI +R +G E W  ++ LR  R TGRSARML+EVLGD+WVV RNP
Sbjct: 4    RIREIPYNYTSFSDKEIALRFVGMEGWKCIESLRDSRNTGRSARMLFEVLGDMWVVSRNP 63

Query: 82   YLQDDLLDNPKRRAALIEALNHRLGEVDKRRLATDQAEAGDAEAQRRSASVEALLKAAKK 141
            Y+QDDL++NPKRR ALI+AL HRL +V+ R     +AE               LL + + 
Sbjct: 64   YIQDDLIENPKRRDALIKALEHRLKQVESRLNGNQKAEE--------------LLSSIRG 109

Query: 142  AIADFAEEFRQTYDLRKRATKVLGRFTAKDNIKFDGLSRVSHVTDATDWRVEYPFVVLTP 201
            A+  F E F    +LR +  K L + T  DNI F GL+RVSH TDATDWRVE P VV++P
Sbjct: 110  AVNKFTEWFPHQIELRSKVRKKLSKHTRLDNIDFGGLARVSHATDATDWRVELPLVVVSP 169

Query: 202  DTEDEMAGLVKACIELGLTIIPRGGGTGYTGGAIPLTPMSAVINTEKLEQLGAVEMEILP 261
            DTE+E+A LV  CI+LGLTIIPRGGGTGYTGGAIPL   S VINTEKLE +  VE   LP
Sbjct: 170  DTEEEVAYLVDGCIQLGLTIIPRGGGTGYTGGAIPLYQDSVVINTEKLEYMSLVEHVDLP 229

Query: 262  GLDKPYATIYSGAGVVTKRVSDAAEKAGFVFAVDPTSAEASCIGGNVAMNAGGKKAVLWG 321
            G+ K   TI +GAGVVT+RVS+ AE+ G+ FAVDPTS +ASCIGGN+AMNAGGKKAVLWG
Sbjct: 230  GIGK-VPTIQTGAGVVTRRVSEQAERFGYAFAVDPTSQDASCIGGNIAMNAGGKKAVLWG 288

Query: 322  TALDNLASWRMVDPQGDWLEVTRLDHNLGKIHDVEVARFKLEWSHPGEKGQKTEVFKTEI 381
            T LDNLASW+MV P  +WLEV R++HNLGK+ D    +F++   +  EK  KT V KTE 
Sbjct: 289  TTLDNLASWKMVTPDAEWLEVERINHNLGKLQDQNTVKFRI---NRYEKDGKTPVGKTET 345

Query: 382  LEISGKKFRKEGLGKDVTDKFLSGLPGVQKEGCDGLITSARWILHKMPKQTRTVCLEFFG 441
            LE+ G  FR  GLGKDVTDKFLSGLPG+QKEGCDGLITSAR+++H+MP   RTVCLEFFG
Sbjct: 346  LEMPGSAFRHAGLGKDVTDKFLSGLPGIQKEGCDGLITSARFVVHRMPSHIRTVCLEFFG 405

Query: 442  -QARDAIPSIVEIKDYLDAETKKGGAILAGLEHLDERYLRAVGYATKSKRGVLPKMVLIG 500
                 A+P+IVEI DY++++ K  G +L+GLEHLDERY++AV Y TK+ R  LPKM+L+ 
Sbjct: 406  TDLSKAVPAIVEITDYIESK-KAHGILLSGLEHLDERYIKAVNYNTKANRKGLPKMILLA 464

Query: 501  DIVGDDENAVAAAASEVIRMANNRVGEGFVAVSPEARKKFWLDRSRTAAIAKHTNAFKIN 560
            DI G++   VA  A E++ +A  R  EGF+AVS EARK+FW DRSRTAAI+KHTNAFKIN
Sbjct: 465  DIAGENGFEVANTAQEIVELAKKRDAEGFIAVSEEARKRFWADRSRTAAISKHTNAFKIN 524

Query: 561  EDVVIPLNRMGEYTDGIERINIELSIKNKLQLLAELDSFFVKGNLP-LGKSDDAEGDDIP 619
            EDVVIPL  + EY   IERINIE SIKNKLQ+L +L+++F  G +P     DD E  +  
Sbjct: 525  EDVVIPLENLNEYNTEIERINIEESIKNKLQILDQLNAYFA-GEIPEYTLEDDFENSEGQ 583

Query: 620  AAEMLEDRVHQAESLLEQTHARWSYLLANLDKPLGEAKGELAALGLEKMLPVFEQRLVDQ 679
             A   +D+V      + +T ARW  +L NLD  +   K EL   G         + L   
Sbjct: 584  PASYFKDKVAATLGHIGKTKARWEGILQNLDVQV-LTKPELLLEG---------EALKLS 633

Query: 680  PEAAVFHVVQDRTVRISWKQEVRAQLRQIFSGAAFKLILEECQAIHKRVLRGRVFVALHM 739
             +     ++  R ++IS+K E+   L+++F G  F+ +    + +H  +   R+FVALHM
Sbjct: 634  ADDTFVSLLLKREIKISYKSEMVTFLQEVFMGHDFEALHTRLKKLHFEIRNARLFVALHM 693

Query: 740  HAGDGNVHTNIPVNSDHYEMLQDAHVAVARIMKLARSLNGVISGEHGIGITKLEFLTEDE 799
            HAGDGN+HTNIPV+S++YEM+  A V V RIM++A+ LNGVISGEHGIG+TK ++L +D+
Sbjct: 694  HAGDGNIHTNIPVHSNNYEMIHQAEVIVDRIMEIAKRLNGVISGEHGIGLTKFQYLDKDK 753

Query: 800  IGEFREYKKRVDPEGRFNKGKLLNLPGMEADLSNAYTPSFGLMGHESLIMQQSDIGAIAS 859
            I  F +YK +VDP G FNKGKL+  PG  + L NAYTPS  L+  E+LI++ +D+  +  
Sbjct: 754  IQAFVDYKNKVDPHGHFNKGKLM--PG--SGLQNAYTPSLHLVEQEALILEANDLDLLNK 809

Query: 860  SVKDCLRCGKCKPVCSTHVPRANLLYSPRNKILATSLLVEAFLYEEQTRRGVSIKHWEEF 919
             +KDCLRCGKCKPVC TH+PRANLLYSPRNKILAT  ++EAFLYEEQTRRG+S+ H++  
Sbjct: 810  DIKDCLRCGKCKPVCQTHIPRANLLYSPRNKILATGQVIEAFLYEEQTRRGISLHHFDAM 869

Query: 920  EDVADHCTVCHKCVTPCPVDIDFGDVSMNMRNLLRKMGKKSFNAGTNAAMFFLNATDPAT 979
             DVADHCT CHKC TPCPVDIDFGDVS++MR +L  MG+K  +     A++FLN   P T
Sbjct: 870  NDVADHCTTCHKCETPCPVDIDFGDVSIHMRTILTNMGQKRSSIMVKLALYFLNTKHPFT 929

Query: 980  INATRKVMTQWGFKAQRLGNDLMKKFA--KKQTQKPPATVGKPPVKEQVIHFINKKMPGN 1037
            IN  RK M  WG  A  +G+   + F   +++   P +T    P+++ VI+F+ K +   
Sbjct: 930  INFLRKTMIGWGAVAMTIGHRFARLFGLVERKNALPASTSEPAPIQQHVINFVRKPLDTG 989

Query: 1038 LPKKTARALLDIEDDKIVPIIRNPKTTTADTEAVFYFPGCGSERLFSQVGLATQAMLWNV 1097
              + + R++L +ED   VPI+R+P  TT DTEAVFYFPGCGSERLFS +GLAT + L++ 
Sbjct: 990  PNQSSYRSVLGLEDATQVPIVRDPNKTTEDTEAVFYFPGCGSERLFSDIGLATISSLYDA 1049

Query: 1098 GVQTVLPPGYLCCGYPQRGTGDFEKGEKIITDNRVLFHRMANTLNYLDIKTVVVSCGTCY 1157
            GVQTVLPPGYLCCGYPQ   G  +K  +I T+NR LFHR+ANTLNY+DI TV+VSCGTCY
Sbjct: 1050 GVQTVLPPGYLCCGYPQAAAGLAQKSSQITTENRALFHRVANTLNYMDINTVIVSCGTCY 1109

Query: 1158 DQLQGYEFEKIFPGCRIIDIHEYLLEKGVKLEGVTGTRYMYHDPCHSPMKQQDPLKTVNS 1217
            DQL  YEFE+IFPGCR++DIHE+L E+G+ LE  TG +Y+YH PCH PMK+ D       
Sbjct: 1110 DQLTKYEFERIFPGCRLMDIHEFLTERGMGLESPTGKQYLYHTPCHDPMKKMDGTTVAKD 1169

Query: 1218 LITTIDAQKIEKNDRCCGESGTFGVSRPDVSTQVRFRKEEEMRKGSDKVRADG--FTGDV 1275
            L+ +    ++  +DRCC E+GT   SRPD++ Q+RFRKEEE+ KG  ++  +     G+V
Sbjct: 1170 LLQS----EVLFSDRCCAEAGTLATSRPDIANQLRFRKEEELTKGIVELTGESKVKNGEV 1225

Query: 1276 KILTSCPSCFQGLSRYNEDAGTTADYIVVEMARHLLGENWMPEYVERANNGGIERILV 1333
            K+LTSCP+C QGL+RY+++ G   DYIVVE+ ++  G  W  E+ E+  NGG+E++L+
Sbjct: 1226 KLLTSCPACQQGLNRYHDNTGLDTDYIVVELMKNRYGNTWNKEFYEKLKNGGVEKVLL 1283


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: 3849
Number of extensions: 161
Number of successful extensions: 13
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: 1283
Length adjustment: 48
Effective length of query: 1285
Effective length of database: 1235
Effective search space:  1586975
Effective search space used:  1586975
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 Jul 25 2024. The underlying query database was built on Jul 25 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