GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1694 in Desulfovibrio vulgaris Hildenborough

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 209488 DVU0549 high-affinity branched-chain amino acid ABC transporter, permease protein

Query= uniprot:A0A165KER0
         (358 letters)



>MicrobesOnline__882:209488
          Length = 407

 Score =  254 bits (648), Expect = 4e-72
 Identities = 155/351 (44%), Positives = 207/351 (58%), Gaps = 55/351 (15%)

Query: 13  VALLVLPLILQSFGNAWVRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYLFA 72
           V   VLP+++ ++      I   ALLYV+L LGLNIVVG +G L LGYVAFYAVGAY +A
Sbjct: 98  VVFAVLPMLVSTYQT---NIMISALLYVMLGLGLNIVVGLSGQLVLGYVAFYAVGAYAYA 154

Query: 73  LMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYLAIVT 132
           L+         A F   F        W V+P+   LAA FG +LG P L+L+GDYLAIVT
Sbjct: 155 LLN--------ADFGLGF--------WTVLPIGGALAAVFGILLGFPVLRLKGDYLAIVT 198

Query: 133 LGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDINSVTLY-YY 191
           LGFGEI+R+ L N     ++T GP G+ +I    +FG++L          ++  T Y YY
Sbjct: 199 LGFGEIVRLVLENWG---SVTRGPSGISKIARPGLFGMELS---------VSEATTYIYY 246

Query: 192 LFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGASFGGVS 251
           L L  V+ ++    RL+DSRIGRAW A+REDEIA +AMGI+    KL AF +GA + G +
Sbjct: 247 LILAAVIFTIFAVGRLKDSRIGRAWQALREDEIACEAMGIDLTTTKLTAFALGACWAGFA 306

Query: 252 GAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEVLRYVAGPL 311
           G +F A   F++P SF+ +ES MI+AMVVLGG+G   GV+LGA++L  LPE LR  +   
Sbjct: 307 GVIFAAKTTFINPASFTFLESAMILAMVVLGGMGSTLGVVLGALVLILLPEYLRAFSE-- 364

Query: 312 QAMTDGRLDSAILRQLLIALAMIIIMLLRPRGLWP---------SPEHGKS 353
                        R L+   AM+++M+ RP+GL            PE GKS
Sbjct: 365 ------------YRMLIFGAAMVLMMVFRPQGLVSCRSREYDVNDPEAGKS 403


Lambda     K      H
   0.328    0.144    0.430 

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: 406
Number of extensions: 17
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: 1
Length of query: 358
Length of database: 407
Length adjustment: 30
Effective length of query: 328
Effective length of database: 377
Effective search space:   123656
Effective search space used:   123656
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