GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_17600 in Phaeobacter inhibens BS107

Align ABC transporter permease; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine ABC transporter permease HisM; SubName: Full=Histidine transport system permease protein; SubName: Full=Histidine/lysine/arginine/ornithine ABC transporter permease HisM (characterized, see rationale)
to candidate GFF3834 PGA1_262p02380 putative histidine transport system permease protein HisM

Query= uniprot:A0A1N7U128
         (237 letters)



>FitnessBrowser__Phaeo:GFF3834
          Length = 258

 Score =  121 bits (303), Expect = 1e-32
 Identities = 74/215 (34%), Positives = 119/215 (55%), Gaps = 13/215 (6%)

Query: 20  LSGVAMTLWLFIISVVLGFFLSIPLALARVSEHVWLRWPVEVYTYLFRGTPLYIQLLICY 79
           L G+  T+W+ +++ +LGF L++PL LA+     +L  P  ++  + RGTPL +Q+ + Y
Sbjct: 43  LEGLWTTIWILVVTSILGFALAVPLGLAQAVGPWYLSTPARIFCTVIRGTPLLLQIWLLY 102

Query: 80  TGLYSL----EIVQDNALLNQFFRNALNCTLLAFVLNTCAYTVEIFAGAIRNIPHGEIEA 135
            GL SL      ++ + L   + R A    +LA  L+   Y  E+  GA   +  G++EA
Sbjct: 103 YGLGSLFPQFPWIRSSELW-PYLRQAWPYAVLALTLSYAGYEGEVMRGAFSGVAKGQLEA 161

Query: 136 ARAYGLHGWRLNLF--VVVPAALRRALPAYSNEMILMLHATSLAFTATVADILKVARDAN 193
           A+AYG+   RL +F  + +P A+R  LP    E IL L AT L  T TV DI  V+    
Sbjct: 162 AKAYGMP--RLTMFRRIWLPQAVRNVLPTLGGETILQLKATPLVATITVLDIYAVSSRVR 219

Query: 194 AETFLTFQAFGIAALLYMLLSFALVGLFRLAERRW 228
           ++TF+ ++   + AL+YM    A+ G+  LA +R+
Sbjct: 220 SDTFIVYEPLLLLALVYM----AIAGVITLAFKRF 250


Lambda     K      H
   0.332    0.143    0.443 

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: 186
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: 237
Length of database: 258
Length adjustment: 24
Effective length of query: 213
Effective length of database: 234
Effective search space:    49842
Effective search space used:    49842
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (22.0 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