GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lutA in Desulfovibrio vulgaris Miyazaki F

Align Lactate utilization protein A (characterized)
to candidate 8501127 DvMF_1863 protein of unknown function DUF224 cysteine-rich region domain protein (RefSeq)

Query= SwissProt::O07020
         (238 letters)



>FitnessBrowser__Miya:8501127
          Length = 430

 Score =  124 bits (312), Expect = 2e-33
 Identities = 75/238 (31%), Positives = 123/238 (51%), Gaps = 5/238 (2%)

Query: 2   KVSLFVTCLVDMFQTNVGKATVELLERLGCEVDFPEGQICCGQPAYNSGYVHDAKKAMKR 61
           +V+ F  CL D    +V +A +++ E  G  V  PEGQ CCG PA +SG      K +K 
Sbjct: 187 RVAFFPGCLGDKMFVSVAEACLKVFEHHGVGVYMPEGQACCGIPAISSGDRVAYDKLVKI 246

Query: 62  MIETFQDS--EYVVSPSGSCTTMFRE-YPHLFQDDPK-WADKAKKLADKTYELTDFIVNV 117
            ++ F     +Y+V+P  +CT   +E +P L  + P    D+ + L DK  ++  F+V+V
Sbjct: 247 NLDLFSKGGFDYLVTPCATCTATIKEIWPKLMDEYPATMRDQIRALHDKVMDVNQFVVDV 306

Query: 118 LGVE-DVGATLHTKATLHTSCHMTRLLGVRKEPMKLLSHVKGLQFTELPGKHNCCGFGGT 176
           LGV+ +  A    K T H SCHM + LGV  +P  L+      +  E+     CCG GG+
Sbjct: 307 LGVKPEAPAKGGVKVTFHDSCHMKKSLGVTSQPRALIGMNPKYELVEMAECDRCCGSGGS 366

Query: 177 FSVKMAQISEQMVDEKVECVEETGAEVLIGADCGCLMNIGGRLGRKDKNVKVMHIAEV 234
           F++    +S+Q+ + K + +  TGA+++      C++ +   L +    V V H  E+
Sbjct: 367 FNLYHYDLSKQIGERKRDNILATGAQIVSTGCPACMLQMTDMLSQHGAKVAVKHSIEL 424


Lambda     K      H
   0.321    0.136    0.411 

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: 283
Number of extensions: 18
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: 238
Length of database: 430
Length adjustment: 27
Effective length of query: 211
Effective length of database: 403
Effective search space:    85033
Effective search space used:    85033
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 48 (23.1 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