GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livM in Phaeobacter inhibens BS107

Align High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M (characterized)
to candidate GFF248 PGA1_c02600 putative high-affinity branched-chain amino acid transport system permease protein LivM

Query= SwissProt::P22729
         (425 letters)



>FitnessBrowser__Phaeo:GFF248
          Length = 361

 Score =  139 bits (350), Expect = 1e-37
 Identities = 101/323 (31%), Positives = 161/323 (49%), Gaps = 35/323 (10%)

Query: 95  ALLVLAVAWPFMVSRGTVDIATLTMIYIILGLGLNVVVGLSGLLVLGYGGFYAIGAYTFA 154
           AL++LA+A P +++   +   T  +I+ I GLGL ++ G +G   LG+  F AIG Y   
Sbjct: 27  ALVMLALALPLLINEFYIGEVTNVLIWAIAGLGLMLLTGQTGQASLGHAAFLAIGCYANT 86

Query: 155 LLNHYYGLGFWTCLPIAGLMAAAAGFLLGFPVLRLRGDYLAIVTLGFGEIVRILLLNNTE 214
           +L    GL F    P+AG++    G ++  P LRL G YLAI T+    +   +++    
Sbjct: 87  ILIEQ-GLPFIVAFPLAGVITGIVGGIIAIPALRLHGIYLAIATIALSILADDIIVLLEP 145

Query: 215 ITGGPNGISQIPKPT-LFGLEFSRTAREGGWDTFSNFFGLKYDPSDRVIFLYLVALLLVV 273
            TGG +G  + P    LFG+E  R                       V F YLV  + V+
Sbjct: 146 WTGGVSG--KFPDVIRLFGIEIERWTMP-------------------VRFYYLVFGVTVI 184

Query: 274 LSLFVINRLLRMPLGRAWEALREDEIACRSLGLSPRRIKLTAFTISAAFAGFAGTLFAAR 333
            +LF  N LLR PLGRA+ A+R+ E++  ++G+   R K TAF +S    G+AG L    
Sbjct: 185 CTLFYRN-LLRSPLGRAFAAVRDSEVSATAMGVHIARTKATAFGLSCMITGWAGALMGYY 243

Query: 334 QGFVSPESFTFAESAFVLAIVVLGGMGSQFAVILAAIL---LVVSRELMRDFNEYSMLML 390
            G  + E+F+   S  +L ++V+GG+GS       A++   L     +++D    S + +
Sbjct: 244 AGAFNNETFSLVISITLLMMIVIGGLGSIHGAFFGAVVVAFLPQGLSILKDSVLGSGVAI 303

Query: 391 GGL--------MVLMMIWRPQGL 405
            GL        ++L +++ P GL
Sbjct: 304 PGLETGVFGMILILFILFEPMGL 326


Lambda     K      H
   0.330    0.145    0.436 

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: 289
Number of extensions: 11
Number of successful extensions: 2
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: 425
Length of database: 361
Length adjustment: 31
Effective length of query: 394
Effective length of database: 330
Effective search space:   130020
Effective search space used:   130020
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 (21.8 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