Alignments for a candidate for trpB in Geobacter uraniireducens Rf4

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpB in Geobacter uraniireducens Rf4

Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_011939393.1 GURA_RS12870 TrpB-like pyridoxal phosphate-dependent enzyme

Query= uniprot:P50383
         (425 letters)



>NCBI__GCF_000016745.1:WP_011939393.1
          Length = 434

 Score =  404 bits (1038), Expect = e-117
 Identities = 206/414 (49%), Positives = 277/414 (66%), Gaps = 4/414 (0%)

Query: 8   LPKYWYNIIPDLPKPLPPPRDPQGAYFSRIDLLRSILPKEVLRQQFTIERYIKIPEEVRD 67
           +P+ WYN   DLP+ LPPPRDP+G   SRI  +R I PK +  Q    ER++ IPEE+ +
Sbjct: 13  VPRRWYNSRKDLPEELPPPRDPEGTD-SRIQKIREITPKTLQEQDVMEERWLDIPEEILE 71

Query: 68  RYLSIGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAKEEGIEHV 127
           +YL IGRPTPL+RA+ LE YL TPARIYFK E    TGS K NT++ QAY+ K+EG + V
Sbjct: 72  KYLVIGRPTPLYRARNLERYLDTPARIYFKREDLLCTGSFKPNTSLAQAYYVKKEGYKGV 131

Query: 128 VTETGAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPTNLTEY 187
           VT+TGAGQWGT+VALA + Y +  T+FM +VS+ QKP RR   Q++GA    SP+  T+ 
Sbjct: 132 VTQTGAGQWGTSVALACAQYGLSCTVFMPEVSFNQKPYRRIHSQIFGAEFLPSPSRHTKS 191

Query: 188 GRKILETNPQHPGSLGIAMSEAIEYALKNE-FRYLVGSVLDVVLLHQSVIGQETITQLDL 246
           GR +LE  P HPGS+   +S+A+E+A++NE   YL GS     LLH +VIG ET  QL L
Sbjct: 192 GRALLEKMPDHPGSVNSGISDALEFAMENEGICYLNGSNAMHTLLHNTVIGLETEVQLKL 251

Query: 247 LGEDADILIGCVGGGSNFGGFTYPFIGNK--KGKRYIAVSSAEIPKFSKGEYKYDFPDSA 304
            GE  D+LI CVGGGSN GGF  PF+ ++     R++AV S   P+ ++G Y+Y+  D  
Sbjct: 252 AGEKPDVLIACVGGGSNLGGFMMPFLKDRLQNKLRFLAVESTAAPRLTQGTYRYEHGDPG 311

Query: 305 GLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIVEWREYNEREIFEAAKIF 364
            L PL K  TLG D+VPP ++ GGLR HG +P +SLL   G +E   Y + ++F   +IF
Sbjct: 312 KLTPLNKAYTLGTDFVPPRMHVGGLRQHGGSPLVSLLRHLGYLEAVAYEQSDVFACGRIF 371

Query: 365 IENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGLLDLSNYESMM 418
            + +GI+PAPE+ HAI+ V  EA EA++  + +VIV   SGHG LDL  YE+++
Sbjct: 372 TKVEGILPAPETCHAIKGVFHEAYEAKEEGKERVIVACFSGHGFLDLEGYEAVL 425


Lambda     K      H
   0.318    0.138    0.403 

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: 481
Number of extensions: 24
Number of successful extensions: 5
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: 425
Length of database: 434
Length adjustment: 32
Effective length of query: 393
Effective length of database: 402
Effective search space:   157986
Effective search space used:   157986
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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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