GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztC in Herbaspirillum seropedicae SmR1

Align BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate HSERO_RS07530 HSERO_RS07530 amino acid ABC transporter permease

Query= TCDB::Q52665
         (434 letters)



>FitnessBrowser__HerbieS:HSERO_RS07530
          Length = 216

 Score =  101 bits (251), Expect = 2e-26
 Identities = 67/223 (30%), Positives = 121/223 (54%), Gaps = 23/223 (10%)

Query: 216 LPEVDSDQFGGFLLA----LVIGVTAIVVSLPLGILLALGRQSDMLIVKSLSVGIIEFVR 271
           L E   D F   L A    L++   A +     G ++AL R S +  ++ LS   I+ ++
Sbjct: 2   LAEFSFDNFVFLLEAARWTLLLSALAFLGGGIAGFIVALMRTSHLAPLRLLSAVYIQIIQ 61

Query: 272 GVPLITLLFTASLLLQYF---LPPGTNFDLILRVVILVTLFAAAYIAEVIRGGLAALPRG 328
           G P++ LLF +   L  F   LPP      ++   I +T++++AY+ E+ RG + A+P  
Sbjct: 62  GTPVLILLFLSFYGLAIFGYKLPP------MVAATIAMTIYSSAYLGEIWRGCIEAVPVP 115

Query: 329 QYEAADALGLDYWQAQRLIIMPQALKISIPGIVSSFIGLFKDTTLVAFVGLFDPLKGISN 388
           Q+EA+ AL +  WQ  R +I+PQA++IS+P  V   + + K+T++ + +GL +       
Sbjct: 116 QWEASTALAMTRWQQLRYVILPQAVRISLPPTVGFLVQIVKNTSIASIIGLVE------- 168

Query: 389 VVRSDMAWKGTYWEPYI---FVALIFFLFNFSMSRYSMYLERK 428
           + ++        ++P++    VA I+F+F + +SR++  LERK
Sbjct: 169 LAQAGKLVSNATFQPFLVFPIVAGIYFVFCYPLSRFAFALERK 211


Lambda     K      H
   0.329    0.143    0.457 

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: 264
Number of extensions: 17
Number of successful extensions: 2
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: 434
Length of database: 216
Length adjustment: 27
Effective length of query: 407
Effective length of database: 189
Effective search space:    76923
Effective search space used:    76923
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 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