GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuF in Phaeobacter inhibens BS107

Align MalF, component of Maltose/trehalose porter (characterized)
to candidate GFF508 PGA1_c05200 putative ABC transporter, inner membrane component

Query= TCDB::O51924
         (300 letters)



>FitnessBrowser__Phaeo:GFF508
          Length = 287

 Score =  120 bits (300), Expect = 5e-32
 Identities = 85/283 (30%), Positives = 149/283 (52%), Gaps = 12/283 (4%)

Query: 18  EAKLGYLMILPLLTVVLVFIILPVMGTFWISLHRDVTFIPEKPF-VGLRNYLRVLSAREF 76
           E +  +  +LP+L +V    ++P+M     S+    TF     F  GL  + ++L +  F
Sbjct: 4   ENQKAWFFVLPVLLLVAFNALIPMMTVVNYSVQE--TFGDNVFFWQGLDWFQQILRSDRF 61

Query: 77  WYSTFVTVSFSFVSVSLETILGLSFALILNERLKGRGVLRAIVLIPWAVPTIISARTWEL 136
             +      F+F+ + +E  LG++ AL +  +     V   ++ +P  +P  +    W +
Sbjct: 62  HAALGRQFMFTFLILIIEIPLGIAIALSMPRKGFWVPVCLVLMALPMLIPWNVVGAMWNI 121

Query: 137 MYNYSYGLFNWILS-ILGVSPVNWLGTPISAFFAIVIADVWKTTPLMTLLLLAGLQAIPQ 195
                 GL  + L+  LG++  +    PI+A+  I+  DVW  T L+ LL  AGL +IP 
Sbjct: 122 FTLPDIGLLGYFLNHTLGIN-YDMTQDPIAAWVTIITMDVWHWTSLVVLLSYAGLVSIPD 180

Query: 196 DLYEAALIDGASMFERFKSITLPLLKPVLIVALILRTIDALRVFDIIYVLTGGGPGGATT 255
             Y+AA IDGAS +  F+ I LP +K VL +A++LR +D+  ++   +VLTGGGPG +TT
Sbjct: 181 AYYQAAKIDGASNWAVFRFIQLPKMKTVLTIAILLRFMDSFNIYTEPFVLTGGGPGNSTT 240

Query: 256 SISL----LAFNYYNLGDYGIGSAISILTFVLVLSFTIVYLKV 294
            +S+    +A   ++LG     +A+S++ F + L  + ++  V
Sbjct: 241 LLSIDLVKIALGQFDLGP---AAAMSLIYFAITLLVSWLFYTV 280


Lambda     K      H
   0.329    0.145    0.436 

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: 260
Number of extensions: 19
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: 300
Length of database: 287
Length adjustment: 26
Effective length of query: 274
Effective length of database: 261
Effective search space:    71514
Effective search space used:    71514
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