GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21720 in Methanospirillum lacunae Ki8-1

Align ABC transporter for D-glucosamine, permease component 2 (characterized)
to candidate WP_109969962.1 DK846_RS15735 amino acid ABC transporter permease

Query= reanno::pseudo3_N2E3:AO353_21720
         (220 letters)



>NCBI__GCF_003173355.1:WP_109969962.1
          Length = 225

 Score =  138 bits (347), Expect = 1e-37
 Identities = 73/204 (35%), Positives = 124/204 (60%), Gaps = 1/204 (0%)

Query: 18  LWSGFLTSVQCSVLAIMLGTLIGIVAGLVLTYGTLWMRAPFRFYVDLIRGTPVFVLVLAC 77
           L SG   +V    +A+++G ++G+   L   YG   +R+    YV   RG PV VL+   
Sbjct: 14  LLSGIFITVGLVAVALLIGIILGLPMALGQVYGKHLIRSVISIYVWFFRGLPVLVLLFLF 73

Query: 78  FY-MAPALGWQIDAFQAGVLGLTLFCGSHVAEIVRGALQALPRGQMEASKAIGLTFYQAL 136
           ++ + P LG  + AF  G + L L   ++ ++I RGA+Q++  GQM A++++G++  QA+
Sbjct: 74  YFGIFPGLGLDLPAFVVGAVVLGLRGAAYQSQIFRGAIQSIAEGQMTAARSLGMSRAQAI 133

Query: 137 AYVLLPQALRQILPTWVNSSTEIVKASTLLSVIGVAELLLSTQQIIARTFMTLEFYLFAG 196
             ++LPQA+R  LP W N   EI+  S++   IGVAELL  + QI+++T++T+  YL   
Sbjct: 134 RSIILPQAMRIALPGWSNEYPEILTESSICYAIGVAELLTRSSQIVSQTYVTMPIYLACA 193

Query: 197 FLFFIINYAIELLGRHIEKRVALP 220
            +F +++YA   L + +EKR+A+P
Sbjct: 194 VMFILLSYAGTHLIQRLEKRIAIP 217


Lambda     K      H
   0.330    0.142    0.440 

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: 185
Number of extensions: 7
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: 220
Length of database: 225
Length adjustment: 22
Effective length of query: 198
Effective length of database: 203
Effective search space:    40194
Effective search space used:    40194
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 (21.9 bits)
S2: 45 (21.9 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