GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisM in Desulfovibrio vulgaris Miyazaki F

Align Histidine transport system permease protein HisM (characterized)
to candidate 8500595 DvMF_1343 polar amino acid ABC transporter, inner membrane subunit (RefSeq)

Query= SwissProt::P0A2I7
         (235 letters)



>FitnessBrowser__Miya:8500595
          Length = 337

 Score =  105 bits (261), Expect = 1e-27
 Identities = 69/218 (31%), Positives = 116/218 (53%), Gaps = 15/218 (6%)

Query: 17  GYRFTGVAITLWLLISSVVMGGLLAVILAVGRVSSNKFIRFPIWLFTYIFRGTPLYVQLL 76
           G    G+ ITL + + +++ G ++ V+  + R+S N  +R+    +  I RG+PL VQ+ 
Sbjct: 125 GILLEGLWITLEVSVLAIIGGIVIGVVTGLCRISINPMLRWGAITYIEIIRGSPLLVQIF 184

Query: 77  VFYSGMYTLEIVKGTDLLNAFFR-------SGLNCTVLALTLNTCAYTTEIFAGAIRSVP 129
           ++Y        V GT L+NA          S L   V+AL L T AY  EI    I+SV 
Sbjct: 185 LWY-------FVVGT-LINALLEHVGLGGISPLWYGVMALALFTGAYVAEIVRAGIQSVH 236

Query: 130 HGEIEAARAYGFSSFKMYRCIILPSALRIALPAYSNEVILMLHSTALAFTATVPDLLKIA 189
            G++EAAR+ G +  +  R +ILP A R  +P  + + I ++  ++L     + +L K  
Sbjct: 237 RGQMEAARSLGMNYAQAMRKVILPQAFRRIMPPLAGQFISLIKDSSLLGVIAIRELTKAT 296

Query: 190 RDINSATYQPFTAFGIAAVLYLLISYVLISLFRRAERR 227
           R++ + + QPF  + + AVLYL++++ L    +  ERR
Sbjct: 297 REVVTTSLQPFELWIVCAVLYLVLTFTLSLFVQYLERR 334


Lambda     K      H
   0.330    0.141    0.429 

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: 215
Number of extensions: 8
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: 235
Length of database: 337
Length adjustment: 26
Effective length of query: 209
Effective length of database: 311
Effective search space:    64999
Effective search space used:    64999
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 (21.9 bits)
S2: 47 (22.7 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