GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpB in Azospirillum thiophilum BV-S

Align isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate WP_045583683.1 AL072_RS23510 isocitrate lyase

Query= BRENDA::P9WKK7
         (428 letters)



>NCBI__GCF_001305595.1:WP_045583683.1
          Length = 425

 Score =  538 bits (1387), Expect = e-158
 Identities = 272/412 (66%), Positives = 319/412 (77%), Gaps = 6/412 (1%)

Query: 22  RWKDVTRTYSAEDVVALQGSVVEEHTLARRGAEVLWEQLHDLEWVNALGALTGNMAVQQV 81
           R++ + R ++ +DV  L GSV  E+TLA  GA  LWE L+   ++N LGALTGN A+Q V
Sbjct: 15  RYEGIRRDFTMDDVKRLSGSVKIEYTLAELGARRLWELLNTEPYINTLGALTGNQAMQAV 74

Query: 82  RAGLKAIYLSGWQVAGDANLSGHTYPDQSLYPANSVPQVVRRINNALQRADQIAKIEGDT 141
           +AGLKAIYLSGWQVAGDAN +G  YPDQSLYP NSVP VV RINN  +RAD+I   EG  
Sbjct: 75  KAGLKAIYLSGWQVAGDANTAGQMYPDQSLYPVNSVPAVVERINNTFKRADEIQTSEGKG 134

Query: 142 SVENWLAPIVADGEAGFGGALNVYELQKALIAAGVAGSHWEDQLASEKKCGHLGGKVLIP 201
               W API+AD EAGFGG LN +EL KA+I AG AG HWEDQLASEKKCGHLGGKVLIP
Sbjct: 135 DTY-WFAPIIADAEAGFGGPLNAFELMKAMIKAGAAGVHWEDQLASEKKCGHLGGKVLIP 193

Query: 202 TQQHIRTLTSARLAADVADVPTVVIARTDAEAATLITSDVDERDQPFITGE--RTREGFY 259
           TQQHIRTL +ARLAADV    T+VIARTDAE+A LITSD+DERD PFI  +  RT EGFY
Sbjct: 194 TQQHIRTLNAARLAADVCGTSTLVIARTDAESAQLITSDIDERDHPFIDFDSGRTTEGFY 253

Query: 260 RTKNG--IEPCIARAKAYAPFADLIWMETGTPDLEAARQFSEAVKAEYPDQMLAYNCSPS 317
           R K G  +E CIAR  +YAP++DL+W ET  P+L+ AR+F+EAV  ++P +MLAYNCSPS
Sbjct: 254 RLKKGLGVEHCIARGLSYAPYSDLMWWETSKPNLDEARRFAEAVHKQFPGKMLAYNCSPS 313

Query: 318 FNWKKHLDDATIAKFQKELAAMGFKFQFITLAGFHALNYSMFDLAYGYAQNQMSAYVELQ 377
           FNWK +LDDATIAK+Q+EL AMG+KFQF+TLAGFH+LNYS F LA GYA+  M+AY ELQ
Sbjct: 314 FNWKANLDDATIAKYQRELGAMGYKFQFVTLAGFHSLNYSAFTLAKGYAERGMAAYSELQ 373

Query: 378 EREFAAEERGYTATKHQREVGAGYFDRIATTVD-PNSSTTALTGSTEEGQFH 428
           + EFAAE+ GYTATKHQREVG GYFD +AT +    SSTTA   STE  QFH
Sbjct: 374 QAEFAAEKDGYTATKHQREVGTGYFDAVATAISGGTSSTTAYKDSTEADQFH 425


Lambda     K      H
   0.316    0.130    0.384 

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: 608
Number of extensions: 26
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: 428
Length of database: 425
Length adjustment: 32
Effective length of query: 396
Effective length of database: 393
Effective search space:   155628
Effective search space used:   155628
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: 51 (24.3 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 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