GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21720 in Marinobacter adhaerens HP15

Align ABC transporter for D-glucosamine, permease component 2 (characterized)
to candidate GFF2975 HP15_2919 amino acid ABC transporter, permease protein

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



>FitnessBrowser__Marino:GFF2975
          Length = 223

 Score =  122 bits (307), Expect = 4e-33
 Identities = 66/185 (35%), Positives = 107/185 (57%), Gaps = 1/185 (0%)

Query: 33  IMLGTLIGIVAGLVLTYGTLWMRAPFRFYVDLIRGTPVFVLVLACFYMAPAL-GWQIDAF 91
           +++G  +GI  GL+      ++R P   Y+++ RGTP+ V VL  FY  P L G  ID  
Sbjct: 34  LLIGFALGIFFGLLSINKKWFLRWPATAYIEIFRGTPILVQVLFIFYGLPDLIGGPIDPL 93

Query: 92  QAGVLGLTLFCGSHVAEIVRGALQALPRGQMEASKAIGLTFYQALAYVLLPQALRQILPT 151
            AG+  + L  G++++E+VRG +Q++ +GQ EA  ++GL+  Q    V+ PQA R+++P 
Sbjct: 94  TAGIAAIALNSGAYISEVVRGGVQSIDKGQTEAGLSLGLSRTQTFWSVVWPQAFRRMIPP 153

Query: 152 WVNSSTEIVKASTLLSVIGVAELLLSTQQIIARTFMTLEFYLFAGFLFFIINYAIELLGR 211
             N +   +K ++L SVIGV EL+   Q  IA TF   E Y     L+  I  ++ ++ R
Sbjct: 154 LGNQAIVSIKDTSLFSVIGVGELVRQGQIYIANTFTAFEVYFVVAILYLAITLSLSIILR 213

Query: 212 HIEKR 216
            +E+R
Sbjct: 214 FVERR 218


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: 149
Number of extensions: 9
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: 223
Length adjustment: 22
Effective length of query: 198
Effective length of database: 201
Effective search space:    39798
Effective search space used:    39798
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 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