GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Pedobacter sp. GW460-11-11-14-LB5

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate CA265_RS15880 CA265_RS15880 sugar ABC transporter ATP-binding protein

Query= reanno::Phaeo:GFF2754
         (331 letters)



>FitnessBrowser__Pedo557:CA265_RS15880
          Length = 330

 Score =  137 bits (345), Expect = 4e-37
 Identities = 85/273 (31%), Positives = 153/273 (56%), Gaps = 12/273 (4%)

Query: 2   TALQLTNVCKSFGPVEV--LKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGE 59
           T + + N+ K +   +   +K+++  ++ G+ V  +G SG GKSTLL+ I GL     GE
Sbjct: 4   TIISVKNLTKQYQAEQAGGIKNVSFEIKQGDVVAIIGESGSGKSTLLKSIYGLLKTDEGE 63

Query: 60  ISIGGQTVTTTP----PAKRGIAMVFQSYALYPHLSVRENMALALKQ-ERQPKEEIAARV 114
           I    + V        P  + + MV Q ++L  +  V +N+A  L   + + K E   ++
Sbjct: 64  IFFEDKRVKGPDEQLIPGHKQMKMVTQDFSLNIYAKVYDNIASQLSNTDLKTKAEKTLQI 123

Query: 115 AEASRMLSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRL 174
            E  R+L L++   ++  ELSGG++QRVAI +A+V + ++ L DEP S +DA L+   R 
Sbjct: 124 MEHLRILPLQN---KKIIELSGGEQQRVAIAKAMVADTQVLLLDEPFSQVDALLKNQLRA 180

Query: 175 EIARLHRQLSASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFI 234
           +I R+  +   ++I V+HD  + + LAD++++L++G + Q G P E+Y +P + + A+ +
Sbjct: 181 DIKRVASETGVTVILVSHDPADGLFLADQLLILKNGELLQTGKPSEIYQHPKHIYTAQIL 240

Query: 235 G-APAMNFVPAQRLG-GNPGQFIGIRPEYARIS 265
           G A  ++   A+++G       +   PE+A IS
Sbjct: 241 GNAVVLSQADAEKIGLKTERNSVVFYPEWAEIS 273


Lambda     K      H
   0.320    0.137    0.391 

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: 197
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: 331
Length of database: 330
Length adjustment: 28
Effective length of query: 303
Effective length of database: 302
Effective search space:    91506
Effective search space used:    91506
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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