GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpB in Desulfatibacillum aliphaticivorans DSM 15576

Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_028316557.1 G491_RS0125530 TrpB-like pyridoxal phosphate-dependent enzyme

Query= uniprot:P50383
         (425 letters)



>NCBI__GCF_000429905.1:WP_028316557.1
          Length = 458

 Score =  398 bits (1023), Expect = e-115
 Identities = 205/424 (48%), Positives = 290/424 (68%), Gaps = 11/424 (2%)

Query: 1   MVKEDEILPKYWYNIIPDLPKPLPPPRDPQGAYFSRIDLLRSILPKEVLRQQFTIERYIK 60
           ++ EDE +P+ WYNI+ D+   + PP  P G   S  D L  + P  ++ Q+ + ER+I 
Sbjct: 7   LLTEDE-MPRQWYNILADIK--MNPPLGPDGNPVSP-DQLAPVFPMNLIEQEVSQERWID 62

Query: 61  IPEEVRDRYLSIGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAK 120
           IP+EV D Y ++ RP+PL RA RLE+ L TPARIYFK EG +P GSHK NTA+PQAY+ K
Sbjct: 63  IPQEVMDIY-TLWRPSPLVRATRLEKALGTPARIYFKNEGVSPAGSHKPNTAVPQAYYNK 121

Query: 121 EEGIEHVVTETGAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYAS 180
           E GI+ + TETGAGQWG+A++ A + + ++ T++MV++S++QKP R+S+M ++G    AS
Sbjct: 122 EFGIKKITTETGAGQWGSALSFACAQFGLQCTVYMVRISFDQKPYRKSMMGVWGGKCIAS 181

Query: 181 PTNLTEYGRKILETNPQHPGSLGIAMSEAIEYALKN---EFRYLVGSVLDVVLLHQSVIG 237
           P+ LT+ GR  LE +P  PGSLGIA+SEA+E A+ +   E RY +GSVL+ V+LHQ+VIG
Sbjct: 182 PSTLTKAGRDALERDPNTPGSLGIAISEAVEAAVSDETGETRYSLGSVLNHVMLHQTVIG 241

Query: 238 QETITQLDLLGEDADILIGCVGGGSNFGGFTYPFIGNKKGKRYI---AVSSAEIPKFSKG 294
            E   QL+ +GE  DI+IGC GGGSNF G  +PF  +K   +++    V  A  P  +K 
Sbjct: 242 LEAKKQLEKVGEYPDIVIGCAGGGSNFAGLAFPFAQDKINGKHVEIYPVEPAACPTLTKA 301

Query: 295 EYKYDFPDSAGLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIVEWREYNE 354
            + YD  D AG  PL+ M +LG  +VP PI+AGGLRYHG+APT+S L  EG+++ +  N+
Sbjct: 302 PFVYDHGDVAGYTPLLPMHSLGHAFVPAPIHAGGLRYHGMAPTVSQLVDEGLMDAKSVNQ 361

Query: 355 REIFEAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGLLDLSNY 414
            + +EA  IF  ++G +PAPE+ HAI  V+ EA +A++  + KVI+FN SGHG LDL  Y
Sbjct: 362 LDCYEAGLIFARSEGHIPAPETTHAIAQVIKEANKAKEEGKEKVILFNWSGHGALDLGAY 421

Query: 415 ESMM 418
           E  +
Sbjct: 422 EKYL 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: 509
Number of extensions: 22
Number of successful extensions: 6
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: 458
Length adjustment: 32
Effective length of query: 393
Effective length of database: 426
Effective search space:   167418
Effective search space used:   167418
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:

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:

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:

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:

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