GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Pseudomonas stutzeri RCH2

Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate GFF3249 Psest_3312 ABC-type (unclassified) transport system, ATPase component

Query= TCDB::Q8DQH8
         (254 letters)



>FitnessBrowser__psRCH2:GFF3249
          Length = 241

 Score =  146 bits (368), Expect = 4e-40
 Identities = 86/258 (33%), Positives = 147/258 (56%), Gaps = 25/258 (9%)

Query: 1   MALLEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTV 60
           MA+L+ + L K +     V DV+L +  G++VGL+GPNGAGKTT F ++ G+    +G V
Sbjct: 1   MAVLKAQHLAKSYKSRQVVRDVSLSIESGQIVGLLGPNGAGKTTCFYMIVGLVNADQGRV 60

Query: 61  TLDGHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTSFLRLPA 120
            +D + +     +  A  G+G   Q   +F+ L+V DN++                   A
Sbjct: 61  LIDQNDVTHLPMHGRARAGIGYLPQEASIFRKLSVADNIM-------------------A 101

Query: 121 FYKSEKEL----KAKALE-LLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFL 175
             ++ K+L    + +ALE LL+ F ++   ++L  +LS G++RR+EI RALAT PK + L
Sbjct: 102 ILETRKDLDRSGRQQALEGLLQEFHINHIRDSLGMSLSGGERRRVEIARALATAPKFILL 161

Query: 176 DEPAAGMNPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGT 235
           DEP AG++P    ++ ++I  +K +  I +++ +H++   +++ E  Y++  G+LIA+G 
Sbjct: 162 DEPFAGVDPISVGDIKQIIHHLKAK-GIGVLITDHNVRETLDICETAYIVNDGQLIAEGD 220

Query: 236 PDEIKTNKRVIEAYLGGE 253
              I +N+ V E YLG E
Sbjct: 221 AQTILSNQLVKEVYLGHE 238


Lambda     K      H
   0.319    0.139    0.385 

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: 151
Number of extensions: 8
Number of successful extensions: 3
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: 254
Length of database: 241
Length adjustment: 24
Effective length of query: 230
Effective length of database: 217
Effective search space:    49910
Effective search space used:    49910
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 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