GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_17605 in Phaeobacter inhibens BS107

Align ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale)
to candidate GFF1143 PGA1_c11580 octopine permease ATP-binding protein P

Query= uniprot:A0A1N7U8S3
         (276 letters)



>FitnessBrowser__Phaeo:GFF1143
          Length = 259

 Score =  258 bits (660), Expect = 7e-74
 Identities = 137/248 (55%), Positives = 169/248 (68%), Gaps = 2/248 (0%)

Query: 27  LQVEGIHKRYGEHEVLKGVSLNARQGDVISLIGASGSGKSTMLRCINFLEQPDAGVITLD 86
           L++ G+HK YGE EV+KGV + A +GDV+SLIG+SGSGKST+LRC N LE    G I   
Sbjct: 8   LEIRGLHKSYGELEVIKGVDITAHRGDVVSLIGSSGSGKSTLLRCCNLLEDSQEGDILFK 67

Query: 87  GISIEMRQGRAGTRAPHQDQLQNLRTRLAMVFQHFNLWSHMTVLENITMAPRRVLDVSAA 146
           G  I         R     Q+  +RT L+MVFQ FNLW+HMT+L+N+  AP  VL    A
Sbjct: 68  GEPINWSGTGLARRPSDAKQVLRIRTNLSMVFQQFNLWAHMTILQNVMEAPLTVLGRDRA 127

Query: 147 EAEKRARMYLDKVGLPSRVADQYPAFLSGGQQQRVAIARALAMEPEIILFDEPTSALDPE 206
           E E  AR YL KVG+  +  D YPA LSGGQQQR AIARAL MEPE +LFDEPTSALDPE
Sbjct: 128 EVEDAARKYLTKVGIGDK-CDAYPAQLSGGQQQRAAIARALCMEPEALLFDEPTSALDPE 186

Query: 207 LVGEVLKVIQTLAEEGRTMLMVTHEMGFARQVSSQVLFLHQGRVEEHG-DARILDQPNSE 265
           L  EV+KVI+ LA EGRTM++VTH+M  A  VSS ++FLH+G +EE G    +     SE
Sbjct: 187 LEQEVVKVIKDLAAEGRTMIIVTHDMNMAADVSSHIVFLHKGLIEEEGCPDEVFGSTRSE 246

Query: 266 RLQQFLSN 273
           RL+ FL++
Sbjct: 247 RLRGFLAS 254


Lambda     K      H
   0.319    0.133    0.372 

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: 219
Number of extensions: 8
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: 276
Length of database: 259
Length adjustment: 25
Effective length of query: 251
Effective length of database: 234
Effective search space:    58734
Effective search space used:    58734
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 (21.8 bits)
S2: 47 (22.7 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