GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Bb in Pedobacter sp. GW460-11-11-14-LB5

Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate CA265_RS15880 CA265_RS15880 sugar ABC transporter ATP-binding protein

Query= uniprot:Q6MNM2
         (347 letters)



>FitnessBrowser__Pedo557:CA265_RS15880
          Length = 330

 Score =  147 bits (370), Expect = 5e-40
 Identities = 88/253 (34%), Positives = 146/253 (57%), Gaps = 10/253 (3%)

Query: 4   IQFSNIKKSFGS--ADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTIS 61
           I   N+ K + +  A  +K +  +I  G+ + ++G SG GKSTLL+++ GL   D G I 
Sbjct: 6   ISVKNLTKQYQAEQAGGIKNVSFEIKQGDVVAIIGESGSGKSTLLKSIYGLLKTDEGEIF 65

Query: 62  IDGKKIN----DIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEI 117
            + K++      + P ++ + MV Q ++L  +  V +N+    +L N       ++  +I
Sbjct: 66  FEDKRVKGPDEQLIPGHKQMKMVTQDFSLNIYAKVYDNIAS--QLSNTDLKTKAEKTLQI 123

Query: 118 SELLQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIK 177
            E L+I  L ++K  ELSGG++QRVA+ +A+   T V+L DEP S +DA L++Q+R +IK
Sbjct: 124 MEHLRILPLQNKKIIELSGGEQQRVAIAKAMVADTQVLLLDEPFSQVDALLKNQLRADIK 183

Query: 178 RLHHNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSP 237
           R+   +  T+I V+HD  +   L D++ +LK+G + Q G PSEIY  PK+ + A  +G+ 
Sbjct: 184 RVASETGVTVILVSHDPADGLFLADQLLILKNGELLQTGKPSEIYQHPKHIYTAQILGNA 243

Query: 238 EMNFLEGAVLEKI 250
            +  L  A  EKI
Sbjct: 244 VV--LSQADAEKI 254


Lambda     K      H
   0.318    0.136    0.383 

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: 250
Number of extensions: 6
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: 347
Length of database: 330
Length adjustment: 28
Effective length of query: 319
Effective length of database: 302
Effective search space:    96338
Effective search space used:    96338
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 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