GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natC in Desulfovibrio vulgaris Miyazaki F

Align NatC aka SLL0146, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate 8501894 DvMF_2609 inner-membrane translocator (RefSeq)

Query= TCDB::P74455
         (372 letters)



>FitnessBrowser__Miya:8501894
          Length = 415

 Score = 89.7 bits (221), Expect = 1e-22
 Identities = 69/212 (32%), Positives = 104/212 (49%), Gaps = 9/212 (4%)

Query: 5   YLIFLITSAATYGIFALGLNLQWGFAGLINFGHVAFMTLGAYATTLLSLR-GLPIPLAVL 63
           Y   ++ SA  Y +  LGLN+  G +G +  G+VAF  +GAY+  +L+   GL     + 
Sbjct: 111 YQTNIMISALLYVMLGLGLNIVVGLSGQLVLGYVAFYAVGAYSYAILNSNFGLGFWSVLP 170

Query: 64  VGMGLAMALGLLIGTSTLRLREDYLAIVTIGVSELIRLIANNEEWLTQGTFGVQSFPWPM 123
           +G  +A   G+L+G   LRLR DYLAIVT+G  E+IRL+  N    +QG  G+ +   P 
Sbjct: 171 IGGAMAALFGILLGFPVLRLRGDYLAIVTLGFGEIIRLVLENWSSFSQGPSGIANIERPG 230

Query: 124 DFNPTL-LSRIVFVIWLTVLTIYAESILIKSLLKQWKEGKKIQGKSYQPRKPLALLIWGI 182
                L +S     I+  +L     +IL  + LK  + G+  Q         +A    GI
Sbjct: 231 LLGMQLSVSDATTYIYYLILAAVIVTILAVTRLKNSRIGRAWQALR---EDEIACQAMGI 287

Query: 183 ITTALILTAYVPGVVSLYNYSGKAGLMLLALT 214
             T   LTA+  G      ++G AG++  A T
Sbjct: 288 DITTTKLTAFALGAC----WAGFAGVIFAAKT 315



 Score = 72.4 bits (176), Expect = 2e-17
 Identities = 51/154 (33%), Positives = 82/154 (53%), Gaps = 16/154 (10%)

Query: 211 LALTLLALTYAGLEFWVHSPWGRILKAIREDEEIPRALGKNVFWYKLQAFMGGGAIAGLA 270
           L L  + +T   +    +S  GR  +A+REDE   +A+G ++   KL AF  G   AG A
Sbjct: 248 LILAAVIVTILAVTRLKNSRIGRAWQALREDEIACQAMGIDITTTKLTAFALGACWAGFA 307

Query: 271 GALFAWQLTSIYPSNFDTLLTFNAWIIVVLGGAGSNAGTVLGTIIFWAYDSLTRFLLPQI 330
           G +FA + T I P++F  L +     +VVLGG GS  G  +G ++          LLP+ 
Sbjct: 308 GVIFAAKTTFINPASFTFLESAMVLAMVVLGGMGSVIGVSVGALVL--------ILLPEY 359

Query: 331 --AFLDQSQAGALRVMVIGLILMVLMVWRPQGIL 362
             AF +       R+++ G  ++++MV+RPQG++
Sbjct: 360 LRAFSE------YRMLIFGATMVLMMVFRPQGLV 387


Lambda     K      H
   0.327    0.143    0.442 

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: 398
Number of extensions: 23
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 372
Length of database: 415
Length adjustment: 31
Effective length of query: 341
Effective length of database: 384
Effective search space:   130944
Effective search space used:   130944
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 (21.7 bits)
S2: 50 (23.9 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