GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livM in Desulfovibrio vulgaris Hildenborough

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 208248 DVU2742 high-affinity branched chain amino acid ABC transporter, permease protein

Query= uniprot:A0A165KER0
         (358 letters)



>MicrobesOnline__882:208248
          Length = 358

 Score =  156 bits (394), Expect = 9e-43
 Identities = 107/361 (29%), Positives = 189/361 (52%), Gaps = 30/361 (8%)

Query: 1   MKNTKTNWIIGAVALLVLPLILQSFGNAWVRIADLALLYV----LLALGLNIVVGYAGLL 56
           M+N   N ++ A+ LLV+ L    FG    + ++  L+++    + A  LNIV GY G  
Sbjct: 1   MRNYTLNIVLAALCLLVVGL--SQFG-VLDQYSETVLMFIGINIIFAASLNIVNGYMGEF 57

Query: 57  DLGYVAFYAVGAYLFALMASPHLADNFAAFAAMFPNGLHTSLW-IVIPVAALLAAFFGAM 115
             G+  F  VGAY+ +L++     +N    AA+ P  L   L+ +VI +   +AA FG +
Sbjct: 58  SCGHAGFMCVGAYVSSLLSVTLFTNNKLLGAALLPPELAPLLFPVVIAIGGFVAAGFGLL 117

Query: 116 LGAPTLKLRGDYLAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKR 175
           +  P+ + RGDYLAI+T+    I+   + NL+       GP+G   +  V + G+     
Sbjct: 118 VALPSFRTRGDYLAIITIAANYIVISLIENLE----FIGGPRGFHGMKKV-INGMR---- 168

Query: 176 LEVFGFDINSVTLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRN 235
                 D+  +       L+  + S+ +  RL  S  G+   A+ +DE+AA+ M ++T +
Sbjct: 169 ------DLADIPWMLIWVLLGTLFSLWLLRRLVTSTYGKGISAVCQDEVAAEIMSVDTNH 222

Query: 236 MKLLAFGMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAV 295
           +KL AF + +   GV+G ++    G+V+P++F++++S   + MV LGG+  + G ++ A+
Sbjct: 223 IKLTAFMVSSGLAGVAGGLYAHIFGYVNPQAFNILKSTEGLVMVYLGGMASLSGSVMSAI 282

Query: 296 LLSALPEVLRYVAGPLQA-------MTDGRLDSAILRQLLIALAMIIIMLLRPRGLWPSP 348
           L + L E LR+V   L +       + DG   S I + ++I L +I++M  RP G+  + 
Sbjct: 283 LFTLLIESLRFVIPGLDSVLHSVGLLPDGYELSQIWKWVIIPLILILLMQFRPEGIMGNR 342

Query: 349 E 349
           E
Sbjct: 343 E 343


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: 333
Number of extensions: 24
Number of successful extensions: 4
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: 358
Length of database: 358
Length adjustment: 29
Effective length of query: 329
Effective length of database: 329
Effective search space:   108241
Effective search space used:   108241
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: 49 (23.5 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