GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natC in Desulfovibrio vulgaris Hildenborough

Align NatC aka SLL0146, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate 209488 DVU0549 high-affinity branched-chain amino acid ABC transporter, permease protein

Query= TCDB::P74455
         (372 letters)



>MicrobesOnline__882:209488
          Length = 407

 Score = 91.3 bits (225), Expect = 4e-23
 Identities = 70/212 (33%), Positives = 103/212 (48%), Gaps = 9/212 (4%)

Query: 5   YLIFLITSAATYGIFALGLNLQWGFAGLINFGHVAFMTLGAYATTLLSLR-GLPIPLAVL 63
           Y   ++ SA  Y +  LGLN+  G +G +  G+VAF  +GAYA  LL+   GL     + 
Sbjct: 110 YQTNIMISALLYVMLGLGLNIVVGLSGQLVLGYVAFYAVGAYAYALLNADFGLGFWTVLP 169

Query: 64  VGMGLAMALGLLIGTSTLRLREDYLAIVTIGVSELIRLIANNEEWLTQGTFGVQSFPWPM 123
           +G  LA   G+L+G   LRL+ DYLAIVT+G  E++RL+  N   +T+G  G+     P 
Sbjct: 170 IGGALAAVFGILLGFPVLRLKGDYLAIVTLGFGEIVRLVLENWGSVTRGPSGISKIARPG 229

Query: 124 DFNPTL-LSRIVFVIWLTVLTIYAESILIKSLLKQWKEGKKIQGKSYQPRKPLALLIWGI 182
            F   L +S     I+  +L     +I     LK  + G+  Q         +A    GI
Sbjct: 230 LFGMELSVSEATTYIYYLILAAVIFTIFAVGRLKDSRIGRAWQALR---EDEIACEAMGI 286

Query: 183 ITTALILTAYVPGVVSLYNYSGKAGLMLLALT 214
             T   LTA+  G      ++G AG++  A T
Sbjct: 287 DLTTTKLTAFALGAC----WAGFAGVIFAAKT 314



 Score = 74.3 bits (181), Expect = 5e-18
 Identities = 49/133 (36%), Positives = 74/133 (55%), Gaps = 16/133 (12%)

Query: 232 GRILKAIREDEEIPRALGKNVFWYKLQAFMGGGAIAGLAGALFAWQLTSIYPSNFDTLLT 291
           GR  +A+REDE    A+G ++   KL AF  G   AG AG +FA + T I P++F  L +
Sbjct: 268 GRAWQALREDEIACEAMGIDLTTTKLTAFALGACWAGFAGVIFAAKTTFINPASFTFLES 327

Query: 292 FNAWIIVVLGGAGSNAGTVLGTIIFWAYDSLTRFLLPQI--AFLDQSQAGALRVMVIGLI 349
                +VVLGG GS  G VLG ++          LLP+   AF +       R+++ G  
Sbjct: 328 AMILAMVVLGGMGSTLGVVLGALVL--------ILLPEYLRAFSE------YRMLIFGAA 373

Query: 350 LMVLMVWRPQGIL 362
           ++++MV+RPQG++
Sbjct: 374 MVLMMVFRPQGLV 386


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: 395
Number of extensions: 19
Number of successful extensions: 5
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: 407
Length adjustment: 30
Effective length of query: 342
Effective length of database: 377
Effective search space:   128934
Effective search space used:   128934
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