GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PGA1_c12640 in Desulfovibrio vulgaris Miyazaki F

Align D-lactate transporter, ATP-binding component (characterized)
to candidate 8502040 DvMF_2753 ABC transporter related (RefSeq)

Query= reanno::Phaeo:GFF1248
         (251 letters)



>lcl|FitnessBrowser__Miya:8502040 DvMF_2753 ABC transporter related
           (RefSeq)
          Length = 255

 Score =  179 bits (453), Expect = 6e-50
 Identities = 96/252 (38%), Positives = 153/252 (60%), Gaps = 6/252 (2%)

Query: 1   MGILEVKNVGKRFGGLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSV 60
           M +L ++N+ K FGGL A+++V   V E ++  +IGPNGAGK+T+ N + G   PD+G +
Sbjct: 1   MSLLALRNLTKTFGGLVAVNNVTFDVAEGSIVGLIGPNGAGKTTVFNLITGNYKPDSGDI 60

Query: 61  MFDGKSVLGRAPYEINQMGISRVFQTPEIFGDLSVLENMMIPCFAKRDGAFEMNAISAVS 120
            FDG+++ G   + I Q GI+R FQT  +F ++SV+EN++  C  +      ++A+    
Sbjct: 61  FFDGRTIKGLPTHRIVQQGIARTFQTIRLFQNMSVIENVLAGCHCRMQSGM-LSAMLRTP 119

Query: 121 GQR----DILEKAEHMLEEMNMADKRHMNAASMSRGDKRRLEIGMCLSQEPRLLLLDEPT 176
            QR      L +A   LE + +A++    A ++S G++R LEI   L+ +PR ++LDEP 
Sbjct: 120 AQRAEEQRALLRATRELEFVGLANEHANLAKNLSYGNQRLLEIARALATDPRFIILDEPA 179

Query: 177 AGMARADTNNTIDLLKQIKSERDITIAIIEHDMHVVFSLADRITVLAQGTPLVEDDPQNI 236
            GM   +T   ID ++ I+ +R IT+ +IEHDM +V  + +++ VL  G  L E  P  I
Sbjct: 180 GGMNDQETAALIDTIRAIR-DRGITVLLIEHDMSLVMKVCEKLVVLEYGALLAEGVPAAI 238

Query: 237 KGNPKVREAYLG 248
           K +P+V EAYLG
Sbjct: 239 KDDPRVIEAYLG 250


Lambda     K      H
   0.318    0.135    0.379 

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: 10
Number of successful extensions: 3
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: 251
Length of database: 255
Length adjustment: 24
Effective length of query: 227
Effective length of database: 231
Effective search space:    52437
Effective search space used:    52437
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: 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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