Aligments for a candidate for prpB in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Aligments for a candidate for prpB in Shewanella loihica PV-4

Align isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate 5208774 Shew_1276 isocitrate lyase (RefSeq)

Query= BRENDA::P9WKK7
         (428 letters)



>FitnessBrowser__PV4:5208774
          Length = 450

 Score =  536 bits (1380), Expect = e-157
 Identities = 275/434 (63%), Positives = 335/434 (77%), Gaps = 10/434 (2%)

Query: 4   VGTPKSAEQIQQEWDTNPRWKDVTRTYSAEDVVALQGSVVEEHTLARRGAEVLWEQLHD- 62
           +   +  + I+Q+W  NPRW  V R YSAEDVVAL+GS+V E+TLA RGAE LW+ ++  
Sbjct: 17  ISRQQQIDAIKQDWAENPRWAGVRRPYSAEDVVALRGSIVPENTLATRGAEKLWQLVNGG 76

Query: 63  --LEWVNALGALTGNMAVQQVRAGLKAIYLSGWQVAGDANLSGHTYPDQSLYPANSVPQV 120
               +VN+LGALTG  AVQQ +AG++AIYLSGWQVA DANL+G  YPDQSLYPANSVP V
Sbjct: 77  AKKGYVNSLGALTGGQAVQQAKAGIEAIYLSGWQVAADANLAGTMYPDQSLYPANSVPAV 136

Query: 121 VRRINNALQRADQIA---KIEG-DTSVENWLAPIVADGEAGFGGALNVYELQKALIAAGV 176
           V+RINN+ +RADQI    +I+  D    ++  PIVAD EAGFGG LN YEL K +I AG 
Sbjct: 137 VQRINNSFRRADQIQWSNEIDPQDERYTDYFLPIVADAEAGFGGVLNAYELMKNMIDAGA 196

Query: 177 AGSHWEDQLASEKKCGHLGGKVLIPTQQHIRTLTSARLAADVADVPTVVIARTDAEAATL 236
           AG H+EDQLAS KKCGH+GGKVL+PTQ+ ++ L SARLAADV+ VPT+VIARTDA AA L
Sbjct: 197 AGVHFEDQLASVKKCGHMGGKVLVPTQEAVQKLVSARLAADVSGVPTLVIARTDANAADL 256

Query: 237 ITSDVDERDQPFITGERTREGFYRTKNGIEPCIARAKAYAPFADLIWMETGTPDLEAARQ 296
           +TSD D  D+ FITGERT EGFYR   GI+  I+R  AYAP+ADLIW ET  PDLE AR+
Sbjct: 257 LTSDCDPYDRDFITGERTSEGFYRVNAGIDQAISRGLAYAPYADLIWCETAKPDLEEARR 316

Query: 297 FSEAVKAEYPDQMLAYNCSPSFNWKKHLDDATIAKFQKELAAMGFKFQFITLAGFHALNY 356
           F+EA+ A+YPDQ+LAYNCSPSFNWKK+LDDATIA+FQ+EL+ MG+K+QFITLAG H + Y
Sbjct: 317 FAEAIHAQYPDQLLAYNCSPSFNWKKNLDDATIARFQQELSDMGYKYQFITLAGIHNMWY 376

Query: 357 SMFDLAYGYAQNQ-MSAYVE-LQEREFAAEERGYTATKHQREVGAGYFDRIATTVD-PNS 413
           +MFDLAY YA+ + M  YVE +QE EFAA ++GYT   HQ+EVG GYFD++   +    S
Sbjct: 377 NMFDLAYDYARGEGMKHYVEKVQEVEFAAAKKGYTFVAHQQEVGTGYFDKVTNVIQGGES 436

Query: 414 STTALTGSTEEGQF 427
           S TALTGSTEE QF
Sbjct: 437 SVTALTGSTEEEQF 450


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: 615
Number of extensions: 18
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: 450
Length adjustment: 32
Effective length of query: 396
Effective length of database: 418
Effective search space:   165528
Effective search space used:   165528
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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, 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

GapMind for catabolism of small carbon sources