GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisM in Lutibaculum baratangense AMV1

Align Amino acid ABC transporter, membrane protein (characterized, see rationale)
to candidate WP_081718345.1 N177_RS02595 ABC transporter permease

Query= uniprot:Q88GX2
         (236 letters)



>NCBI__GCF_000496075.1:WP_081718345.1
          Length = 248

 Score =  251 bits (641), Expect = 9e-72
 Identities = 125/222 (56%), Positives = 160/222 (72%)

Query: 14  DLLERYGPRFIDGLLVTAKLVAISFSLGAVLGLLLALARLSRSLVLQRMAAGYVYFFRGS 73
           D  +RYG R + G   T +LV +S  +GA + L +A  RLS + V+  +A GYVYFFRG+
Sbjct: 22  DFAQRYGFRMLSGFWTTIELVTLSLLIGAAISLPVAAGRLSPNPVIGALAYGYVYFFRGT 81

Query: 74  PLLAQLFLLYYGLGSLKGFWQDVGLWWFFRDAWFCTLLAFTLNTAAYQAEIFRGSLMAVA 133
           PLLAQ FL+YYG GS +     VGLW FFRDAWFC +  F+LNT+AYQAEI  G++  V 
Sbjct: 82  PLLAQTFLVYYGAGSFRAELDAVGLWTFFRDAWFCAVFTFSLNTSAYQAEILAGAIRTVP 141

Query: 134 PGQHEAARALNLKRSTTFFKVILPQSLLVAIGPLGNELILMIKASAIASLVTIYDLMGVT 193
             Q EA +AL L R     +++LPQ+L+VA+ P GNE++LMIK SAIAS++TIYDLMG T
Sbjct: 142 RSQIEAGQALGLSRYVIATRIVLPQALVVALRPYGNEVVLMIKGSAIASIITIYDLMGET 201

Query: 194 KLAFSRSFDFQIYLWAAVLYLVIVELVRRLLKHLEARLGRHL 235
           + AFSRSFDFQ Y+WAA+LYLV+VE +RRL   +E RL RHL
Sbjct: 202 RRAFSRSFDFQTYIWAAILYLVLVETLRRLWDVMERRLTRHL 243


Lambda     K      H
   0.331    0.144    0.433 

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: 181
Number of extensions: 10
Number of successful extensions: 1
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: 236
Length of database: 248
Length adjustment: 23
Effective length of query: 213
Effective length of database: 225
Effective search space:    47925
Effective search space used:    47925
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 (21.9 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 24 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