GapMind for Amino acid biosynthesis

 

Alignments for a candidate for CBS in Pseudomonas simiae WCS417

Align Putative cystathionine beta-synthase MT1108; EC 4.2.1.22; Beta-thionase; Serine sulfhydrase (uncharacterized)
to candidate GFF1476 PS417_07505 cysteine synthase

Query= curated2:P9WP50
         (464 letters)



>FitnessBrowser__WCS417:GFF1476
          Length = 324

 Score =  228 bits (581), Expect = 2e-64
 Identities = 140/328 (42%), Positives = 187/328 (57%), Gaps = 36/328 (10%)

Query: 2   RIAQHISELIGGTPLVRLNSVVPDGAGTVAAKVEYLNPGGSSKDRIAVKMIEAAEASGQL 61
           RI    +  IG TPLV++N + P G  T+ AK+E  NPG S K RI   MI  AE++G+L
Sbjct: 3   RIFADNAHSIGNTPLVQINRIAPRGV-TILAKIEGRNPGYSVKCRIGANMIWDAESTGKL 61

Query: 62  KPGGTIVEPTSGNTGVGLALVAQRRGYKCVFVCPDKVSEDKRNVLIAYGAEVVVCPTA-- 119
           KPG TIVEPTSGNTG+GLA VA  RGYK +   P  +S ++R VL A GAE+V+   A  
Sbjct: 62  KPGMTIVEPTSGNTGIGLAFVAAARGYKLLLTMPASMSIERRKVLKALGAELVLTEPAKG 121

Query: 120 ----------VPPHDPASYYSVSDRLVRDIDGAWKPDQYANPEGPASHYVTTGPEIWADT 169
                     +   DPA+Y+               P Q+ NP  PA H  TTGPEIW DT
Sbjct: 122 MKGAIEKAGEIVASDPATYF--------------MPAQFENPANPAIHEKTTGPEIWNDT 167

Query: 170 EGKVTHFVAGIGTGGTITGAGRYLKEVSGGRVRIVGADPEGS--VYSGGAGR-----PYL 222
           +G V   VAG+GTGGTITG  RY+K ++G  +  V  +P  S  +    AG      P+ 
Sbjct: 168 DGAVDVLVAGVGTGGTITGVSRYIKNIAGKPILSVAVEPIVSPVITQALAGEEIKPSPHK 227

Query: 223 VEGVGEDFWPAAYDPSVPDEIIAVSDSDSFDMTRRLAREEAMLVGGSCGMAVVAALKVAE 282
           ++G+G  F P   D S+ D +  V+D +S  M  RL +EE +L G SCG A+  A+++AE
Sbjct: 228 IQGIGAGFVPKNLDLSMVDRVELVTDDESKAMALRLMQEEGILCGISCGAAMAVAVRLAE 287

Query: 283 EAGPDA-LIVVLLPDGGRGYMSK-IFND 308
           +       IVV+LPD G  Y+S  +F+D
Sbjct: 288 KPEMQGKTIVVILPDSGERYLSSMLFSD 315


Lambda     K      H
   0.316    0.135    0.398 

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: 420
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: 464
Length of database: 324
Length adjustment: 30
Effective length of query: 434
Effective length of database: 294
Effective search space:   127596
Effective search space used:   127596
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 (21.6 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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