GapMind for catabolism of small carbon sources

 

Alignments for a candidate for larD in Desulfovibrio vulgaris Miyazaki F

Align D/L-lactic acid transporter; Lactate racemization operon protein LarD; Lactic acid channel (characterized)
to candidate 8500047 DvMF_0810 major intrinsic protein (RefSeq)

Query= SwissProt::F9UST3
         (238 letters)



>FitnessBrowser__Miya:8500047
          Length = 252

 Score =  109 bits (272), Expect = 6e-29
 Identities = 81/236 (34%), Positives = 123/236 (52%), Gaps = 17/236 (7%)

Query: 4   QLIAEFMGTALMIIFGVGVHCSSVLKGTKYRGSGHIFAITTWGFGISVALFIFGNVC--- 60
           ++++EFMGT ++IIFG G    +VL G   +G    +   T+G+G++V L I   +    
Sbjct: 9   EMVSEFMGTMVLIIFGAGNVAMTVLFG---KGLNITWDNITFGWGLAVLLGIMAGLPSGA 65

Query: 61  -INPAMVLAQCLLGNIAWSLFIPYSVAEVLGGVVGSVIVWIMYADHFKASTDEISPITIR 119
            INPA+ +A    G   W   +PYS A+V GG  G+ IV+I +  H K    +    +  
Sbjct: 66  HINPAVTVALAATGRFPWKKVLPYSAAQVAGGFAGAAIVFIDF--HAKWVGVDPQLASTA 123

Query: 120 NLFCTAPAVRN--LPRNFFVELFDTFIFISGILAISEIKTPG----IVPIGVGLLVWAIG 173
            +FCT PA+    LP  F  ++  T   + GILAI +  +      I  I V LLV AIG
Sbjct: 124 GIFCTFPAITTSYLP-GFIDQIIGTAALMFGILAIGDFASKNNIGWIGGILVALLVVAIG 182

Query: 174 MGLGGPTGFAMNLARDMGPRIAHAILPIANKADSDWQYGIIVPGIAPFVGAAIAAW 229
           M LG   G+A+N ARD GPR   A++    + +      ++VP + P +G  + A+
Sbjct: 183 MSLGAMHGYAINPARDFGPRF-FALVAGFTQPNLMEPGIVLVPIVGPLIGGPLGAF 237


Lambda     K      H
   0.330    0.145    0.470 

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: 241
Number of extensions: 20
Number of successful extensions: 3
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: 238
Length of database: 252
Length adjustment: 24
Effective length of query: 214
Effective length of database: 228
Effective search space:    48792
Effective search space used:    48792
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: 46 (22.3 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