GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatM in Desulfovibrio vulgaris Miyazaki F

Align Glutamate/aspartate import permease protein GltK (characterized)
to candidate 8502447 DvMF_3153 polar amino acid ABC transporter, inner membrane subunit (RefSeq)

Query= SwissProt::P0AER5
         (224 letters)



>FitnessBrowser__Miya:8502447
          Length = 233

 Score =  132 bits (331), Expect = 7e-36
 Identities = 76/227 (33%), Positives = 133/227 (58%), Gaps = 21/227 (9%)

Query: 2   YEFDWSSIVPS--LPYLLDGLVITLKITVTAVVIGILWGTMLAVMRLSSFAPVAWFAKAY 59
           Y FDW  ++    L +++DG+V+T +I+  ++V+ +  GT++AVMRLS+  P+ WF+  +
Sbjct: 3   YNFDWKLVLSGEYLQWIIDGVVVTCQISALSLVLAMALGTLIAVMRLSAVRPLVWFSAGF 62

Query: 60  VNVFRSIPL-VMVLLWFY---LIVPGFLQNVLGLSPKNDIRLISAMVAFSMFEAAYYSEI 115
              FR+ PL V +  W++    ++P  +   L    K +    + +++ +++ AA+ +E 
Sbjct: 63  TEFFRNTPLLVQIFFWYFGSDAVLPTAVNQWLY---KQNFEFAAGVISLAVYTAAFIAEE 119

Query: 116 IRAGIQSISRGQSSAALALGMTHWQSMKLIILPQAFRAMVPLLLTQGIVLFQDTSLVYVL 175
           IR+GI SI R Q  A+ A G+T  Q+M+ ++LPQAFR +VP L++Q + LF+++SL   +
Sbjct: 120 IRSGIFSIPRTQLEASRACGLTFLQAMRYVVLPQAFRIIVPPLISQALNLFKNSSLCMTI 179

Query: 176 SLADFFRTASTIGERDGTQVEMILFAGFVYFVIS----LSASLLVSY 218
            + +    A         Q+E   F GF  F +S    L+ SLLVS+
Sbjct: 180 GVMELTYMA--------RQIESYTFHGFEAFTVSTLIYLTISLLVSF 218


Lambda     K      H
   0.330    0.140    0.412 

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: 150
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: 224
Length of database: 233
Length adjustment: 23
Effective length of query: 201
Effective length of database: 210
Effective search space:    42210
Effective search space used:    42210
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: 46 (22.3 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