Alignments for a candidate for serA in Hydrogenovibrio kuenenii DSM 12350

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Hydrogenovibrio kuenenii DSM 12350

Align Putative phosphoglycerate dehydrogenase (EC:1.1.1.95) (characterized)
to candidate WP_038070594.1 N745_RS0103470 DUF3683 domain-containing protein

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



>NCBI__GCF_000526715.1:WP_038070594.1
          Length = 1283

 Score = 1426 bits (3691), Expect = 0.0
 Identities = 717/1317 (54%), Positives = 932/1317 (70%), Gaps = 42/1317 (3%)

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

Query: 82   YLQDDLLDNPKRRAALIEALNHRLGEVDKRRLATDQAEAGDAEAQRRSASVEALLKAAKK 141
            Y+QDDL+++PKRR ALI AL HRL +V+ R     +AE               LL+  + 
Sbjct: 64   YIQDDLIESPKRRDALIGALEHRLKQVEARLNGNKKAEE--------------LLRTIRN 109

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

Query: 202  DTEDEMAGLVKACIELGLTIIPRGGGTGYTGGAIPLTPMSAVINTEKLEQLGAVEMEILP 261
            DTE+E+A LV  CI+LGLTIIPRGGGTGYTGGAIPL   S VINTEKLE +  VE   L 
Sbjct: 170  DTEEEVAYLVDDCIQLGLTIIPRGGGTGYTGGAIPLYQDSVVINTEKLEYMSLVEQVELS 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 + E+
Sbjct: 289  TTLDNLASWKMVTPDAEWLEVERINHNLGKLQDQQTVSFRI---NRFEKDGKTPVGEPEM 345

Query: 382  LEISGKKFRKEGLGKDVTDKFLSGLPGVQKEGCDGLITSARWILHKMPKQTRTVCLEFFG 441
            LE+ G  FRK GLGKDVTDKFLSGLPGVQKEGCDGLITSAR+++H+MP  TRTVCLEFFG
Sbjct: 346  LEMPGSAFRKAGLGKDVTDKFLSGLPGVQKEGCDGLITSARFVVHRMPSHTRTVCLEFFG 405

Query: 442  -QARDAIPSIVEIKDYLDAETKKGGAILAGLEHLDERYLRAVGYATKSKRGVLPKMVLIG 500
                 A+P+IVEI +Y++++ K  G +L+GLEHLD+RY++AV Y TK+ R  LPKM+L+ 
Sbjct: 406  TDLSKAVPAIVEITEYIESK-KLHGILLSGLEHLDDRYIKAVNYNTKANRKGLPKMILLA 464

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

Query: 561  EDVVIPLNRMGEYTDGIERINIELSIKNKLQLLAELDSFFVKGNLPLGKSDDAEGDDIPA 620
            EDVVIPL  + EY   IERINIE SIKNKLQ+L +L ++F    L     DD E  +   
Sbjct: 525  EDVVIPLENLNEYNTEIERINIEESIKNKLQILDQLHAYFAGEILEYTLEDDFENSEGQP 584

Query: 621  AEMLEDRVHQAESLLEQTHARWSYLLANLDKPLGEAKGELAALGLEKMLPVFEQRLVDQP 680
            A   +D+V      +++T ARW+ +L +LD  +  A+ +L   G         + L    
Sbjct: 585  ASYFKDKVSTTLEHIDKTKARWAGILESLDTQVS-AQPDLLLEG---------EALKLSA 634

Query: 681  EAAVFHVVQDRTVRISWKQEVRAQLRQIFSGAAFKLILEECQAIHKRVLRGRVFVALHMH 740
            +     ++  R ++IS+K E+   L+++F G  F+ +    + +H  +   R+FVALHMH
Sbjct: 635  DDTFATLLLKREIKISYKDEIVTFLQEVFMGHDFEALHIRLKKLHFDIRNARLFVALHMH 694

Query: 741  AGDGNVHTNIPVNSDHYEMLQDAHVAVARIMKLARSLNGVISGEHGIGITKLEFLTEDEI 800
            AGDGN+HTNIPV+S++YEM+  A V V RIM++A+ LNGVISGEHGIG+TK ++L ED++
Sbjct: 695  AGDGNIHTNIPVHSNNYEMVHQAEVLVDRIMEIAKRLNGVISGEHGIGLTKFQYLDEDKV 754

Query: 801  GEFREYKKRVDPEGRFNKGKLLNLPGMEADLSNAYTPSFGLMGHESLIMQQSDIGAIASS 860
              F EYK +VDP GRFNKGKL+  PG  + L NAYTPS  L+  E+LI++ +D+  +   
Sbjct: 755  QAFVEYKNKVDPHGRFNKGKLM--PG--SGLDNAYTPSLHLVEQEALILEANDLDLLNKD 810

Query: 861  VKDCLRCGKCKPVCSTHVPRANLLYSPRNKILATSLLVEAFLYEEQTRRGVSIKHWEEFE 920
            +KDCLRCGKCKPVC TH+PRANLLYSPRNKILAT  ++EAFLYEEQTRRG+S+ H++   
Sbjct: 811  IKDCLRCGKCKPVCQTHIPRANLLYSPRNKILATGQVIEAFLYEEQTRRGISLHHFDAMN 870

Query: 921  DVADHCTVCHKCVTPCPVDIDFGDVSMNMRNLLRKMGKKSFNAGTNAAMFFLNATDPATI 980
            DVADHCT CHKC +PCPVDIDFGDVS+ MR +L  MG+K  +     A++FLN   P TI
Sbjct: 871  DVADHCTTCHKCESPCPVDIDFGDVSIRMRTILTNMGQKKTSIMVKLAIYFLNTKSPFTI 930

Query: 981  NATRKVMTQWGFKAQRLGNDLMKKFA--KKQTQKPPATVGKPPVKEQVIHFINKKMPGNL 1038
               RK M  WG  A  LG+   K F   +++   P +T    P+++ VI+F+ K +    
Sbjct: 931  GLLRKTMIGWGAIAMTLGHRFAKLFGLVERKNALPASTSEPAPLQQHVINFVRKPLDTGP 990

Query: 1039 PKKTARALLDIEDDKIVPIIRNPKTTTADTEAVFYFPGCGSERLFSQVGLATQAMLWNVG 1098
             + + R++L +ED   VPI+R+P  TT D+EAVFYFPGCGSERLFS +GLAT + L++ G
Sbjct: 991  NQSSYRSVLGLEDATQVPIVRDPNKTTEDSEAVFYFPGCGSERLFSDIGLATISSLYDAG 1050

Query: 1099 VQTVLPPGYLCCGYPQRGTGDFEKGEKIITDNRVLFHRMANTLNYLDIKTVVVSCGTCYD 1158
            VQT+LPPGYLCCGYPQ   G  +K  +I T+NR LFHR+ANTLNY+DI TV+VSCGTCYD
Sbjct: 1051 VQTILPPGYLCCGYPQAAAGLAQKSSQITTENRALFHRVANTLNYMDITTVIVSCGTCYD 1110

Query: 1159 QLQGYEFEKIFPGCRIIDIHEYLLEKGVKLEGVTGTRYMYHDPCHSPMKQQDPLKTVNSL 1218
            QL  YEFE+IFPGCR++DIHEYL EKG+ LE  TG +Y+YH PCH PMK+ D  +    L
Sbjct: 1111 QLTKYEFERIFPGCRLMDIHEYLTEKGLGLENATGKQYLYHAPCHDPMKKMDGTQVAKDL 1170

Query: 1219 ITTIDAQKIEKNDRCCGESGTFGVSRPDVSTQVRFRKEEEMRKGSDKVRADG--FTGDVK 1276
            + +    ++  +DRCC E+GT   SRPD++ Q+RFRKEEE+ KG  ++  +     G+VK
Sbjct: 1171 LKS----EVLFSDRCCAEAGTLATSRPDIANQLRFRKEEELTKGIVELTGESKVKNGEVK 1226

Query: 1277 ILTSCPSCFQGLSRYNEDAGTTADYIVVEMARHLLGENWMPEYVERANNGGIERILV 1333
            +LTSCP+C QGL+RY+++ G   DYIVVE+ ++  G+ W  E+ E+  NGG+E++L+
Sbjct: 1227 LLTSCPACQQGLNRYHDNTGLDTDYIVVELMKNRYGKAWNKEFYEKLKNGGVEKVLL 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: 3869
Number of extensions: 176
Number of successful extensions: 12
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