GapMind for catabolism of small carbon sources

 

Alignments 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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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