GapMind for catabolism of small carbon sources

 

Aligments for a candidate for prpB in Azospirillum brasilense Sp245

Align isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate AZOBR_RS02405 AZOBR_RS02405 isocitrate lyase

Query= BRENDA::P9WKK7
         (428 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS02405 AZOBR_RS02405 isocitrate
           lyase
          Length = 425

 Score =  534 bits (1375), Expect = e-156
 Identities = 268/412 (65%), Positives = 320/412 (77%), Gaps = 6/412 (1%)

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

Query: 82  RAGLKAIYLSGWQVAGDANLSGHTYPDQSLYPANSVPQVVRRINNALQRADQIAKIEGDT 141
           +AGLKAIYLSGWQVAGDANL+G  YPDQSLYPANSVP VV RINN  +RAD+I   EG  
Sbjct: 75  KAGLKAIYLSGWQVAGDANLAGQMYPDQSLYPANSVPAVVERINNTFKRADEIQTAEGKG 134

Query: 142 SVENWLAPIVADGEAGFGGALNVYELQKALIAAGVAGSHWEDQLASEKKCGHLGGKVLIP 201
               W API+AD EAGFGG LNV+EL KA+I AG +G H+EDQLASEKKCGHLGGKVLIP
Sbjct: 135 DTY-WFAPIIADAEAGFGGPLNVFELMKAMIKAGASGVHFEDQLASEKKCGHLGGKVLIP 193

Query: 202 TQQHIRTLTSARLAADVADVPTVVIARTDAEAATLITSDVDERDQPFITGE--RTREGFY 259
           TQQHIRTL +ARLAAD     T+V+ RTDAE+A LITSDVDERD PFI  +  RT EGF+
Sbjct: 194 TQQHIRTLNAARLAADTMGTSTIVLCRTDAESAQLITSDVDERDHPFIDFDAGRTSEGFF 253

Query: 260 RTKNG--IEPCIARAKAYAPFADLIWMETGTPDLEAARQFSEAVKAEYPDQMLAYNCSPS 317
           R K G  ++ CIAR  +YAP++DL+W ET  P+LE A++F+EA++ E+P+++LAYNCSPS
Sbjct: 254 RLKKGTGVDHCIARGLSYAPYSDLLWWETSRPNLEEAKRFAEAIRKEFPNKLLAYNCSPS 313

Query: 318 FNWKKHLDDATIAKFQKELAAMGFKFQFITLAGFHALNYSMFDLAYGYAQNQMSAYVELQ 377
           FNWK +LD+A IAKFQ+E+ AMG+KFQF+TLAGFH+LNYS F LA GYA   M+AY ELQ
Sbjct: 314 FNWKANLDEADIAKFQREIGAMGYKFQFVTLAGFHSLNYSAFKLAKGYAARGMAAYSELQ 373

Query: 378 EREFAAEERGYTATKHQREVGAGYFDRIATTVD-PNSSTTALTGSTEEGQFH 428
           E EFAAE  GYTATKHQREVG GYFD +AT +    SSTTA   STE  QFH
Sbjct: 374 EAEFAAEAEGYTATKHQREVGTGYFDAVATAISGGQSSTTAYKDSTEADQFH 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: 587
Number of extensions: 23
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 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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