GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livM in Desulfovibrio vulgaris Miyazaki F

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate 8500844 DvMF_1582 inner-membrane translocator (RefSeq)

Query= uniprot:Q1MCU1
         (463 letters)



>FitnessBrowser__Miya:8500844
          Length = 313

 Score =  139 bits (350), Expect = 1e-37
 Identities = 97/328 (29%), Positives = 158/328 (48%), Gaps = 40/328 (12%)

Query: 117 LYPMVVVAIKGPQ---GSLTYVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVG 173
           L P+VV+A+       G  +YV +  I  +++ +     N++ G  G +  G+ AF+ +G
Sbjct: 5   LVPLVVLAMLAGLPLLGLNSYVMHILILSIMWTLAGMAWNLLGGYCGQVSFGHAAFFGMG 64

Query: 174 AYSYALLSSYFGLSFWVLLPLSGIFAALWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVL 233
           AYS  L+  + GLS W    +S    AL  + +G  VLRLRG Y  + TLA GE++R+  
Sbjct: 65  AYSAGLIHLHLGLSPWWGFLVSLPLVALVALAMGSVVLRLRGPYFVLATLAIGEVLRITC 124

Query: 234 INWTDVTKGTFGISSIPKATLFGIPFDATAGGFAKLFHLPISSAYYKIFLFYLILALCML 293
            N TD TKGT GI                      +    +    Y    +Y+IL L +L
Sbjct: 125 ENLTDFTKGTLGIM---------------------ITRTWVEKTQY----YYIILGLALL 159

Query: 294 TAYVTIRLRRMPIGRAWEALREDEIACRSLGINTVTTKLTAFATGAMFAGFAGSFFAARQ 353
              V   +     G  + A+RED+ A  S+GI+T   K  A    AM  G AG+F+    
Sbjct: 160 GFVVCRAIVHSRWGYYFVAIREDQDAAESMGIDTTRYKTIALTVSAMLTGLAGAFYTNYM 219

Query: 354 GFVSPESFVFLE--SAVILAIVVLGGMGSLTGIAIAAIVMVGGTELLREMSFLKLIFGPD 411
           G++ P     L   S +I+ +V++GG+ +  G A+ A +MV   E +R +  + + +   
Sbjct: 220 GYIDPGVVFSLGEISILIIMVVMVGGVATEWGPALGAGIMVILAEYIRSLPLIGVAY--- 276

Query: 412 FTPELYRMLIFGLAMVVVMLFKPRGFVG 439
                    +FG+ ++V++++ P G VG
Sbjct: 277 -------QTMFGVLLIVIIIYLPNGLVG 297


Lambda     K      H
   0.330    0.145    0.432 

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: 456
Number of extensions: 32
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: 463
Length of database: 313
Length adjustment: 30
Effective length of query: 433
Effective length of database: 283
Effective search space:   122539
Effective search space used:   122539
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