GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1A in Desulfovibrio vulgaris Miyazaki F

Align major cell-binding factor (characterized)
to candidate 8502446 DvMF_3152 extracellular solute-binding protein family 3 (RefSeq)

Query= CharProtDB::CH_021449
         (259 letters)



>FitnessBrowser__Miya:8502446
          Length = 271

 Score =  131 bits (330), Expect = 1e-35
 Identities = 87/256 (33%), Positives = 135/256 (52%), Gaps = 14/256 (5%)

Query: 9   KLAVFALGACVAFSNANAAEGKLESIKSKGQLIVGVKNDVPHYALLDQATGEIKGFEVDV 68
           +L + A+  CV  +   A  GK+E IK++G L+ GVK+    +  +D+ + +I GF++D+
Sbjct: 3   RLVLLAVALCVVLTGTMAHAGKIEDIKARGALVCGVKDSTVPFGYIDEQSKQIVGFDIDI 62

Query: 69  AKLLAKSILGDDKKIKLVAVNAKTRGPLLDNGSVDAVIATFTITPERKRIYNFSEPYYQD 128
            K +A  +     K++L  V + TR P+L  GSVD V AT T   ER  + +FS  Y+ D
Sbjct: 63  CKAVADKL---GVKLELKTVTSATRIPMLTQGSVDMVAATMTHKFERDDVIDFSITYFMD 119

Query: 129 AIGLLVLKEKKYKSLADMKGANIGVAQAATTKKAIGEAAKKIGIDVKFSEFPDYPSIKAA 188
              LLV K    KS AD+KG  +  A+ +T++K I +AA+     V F E   YP    A
Sbjct: 120 GQKLLVKKGGGVKSAADLKGKKVATAKGSTSEKNI-KAAQPEATVVSFDE---YPQAFLA 175

Query: 189 LDAKRVDAFSVDKSILLGYVD-----DKSEILPDSFEPQSYGIVTKKDDPAFAKYVDDFV 243
           L   + +A + D +ILLG  +     DK EI+ D   P+ YG+   ++D  F   V+  +
Sbjct: 176 LKQGKAEAVTTDSTILLGLRNSDPEPDKWEIVGDYISPEPYGLGLAENDSKFRDLVNRTL 235

Query: 244 KE--HKNEIDALAKKW 257
            +  +  E   L  KW
Sbjct: 236 VDLWNSGEYVKLYDKW 251


Lambda     K      H
   0.316    0.135    0.372 

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: 164
Number of extensions: 11
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: 259
Length of database: 271
Length adjustment: 25
Effective length of query: 234
Effective length of database: 246
Effective search space:    57564
Effective search space used:    57564
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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