GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutV in Desulfovibrio vulgaris Hildenborough

Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate 209324 DVU0388 amino acid ABC transporter, ATP-binding protein

Query= TCDB::Q9KKE1
         (275 letters)



>MicrobesOnline__882:209324
          Length = 255

 Score =  150 bits (380), Expect = 2e-41
 Identities = 100/229 (43%), Positives = 138/229 (60%), Gaps = 11/229 (4%)

Query: 43  LNDVSLKIGAGKIFVIMGLSGSGKSTLVRHINRLIEPTSGEVLFDGDNILDLGAKA-LRA 101
           L DVSL +  G++ V++G SG+GKSTL++ IN LI P +G V  +G   +D   KA L A
Sbjct: 24  LRDVSLDVDRGQLKVLIGPSGAGKSTLLQCINHLILPDAGTVSLEG-RAVDAHRKADLYA 82

Query: 102 FRMRRVSMVFQSFALMPHRTVLQNVVYGQR-VRGVSKDDAREIGMKWIDTVGLSGYDAKF 160
           FR ++V M+FQ F L  H   L NV    R VRG+S+  ARE  M  ++ VGLS   A +
Sbjct: 83  FR-QQVGMIFQEFNLFDHLDALSNVSIALRKVRGMSRAAARERAMAELERVGLSSRHALY 141

Query: 161 PHQLSGGMKQRVGLARALAADTDVILMDEAFSALDPLIRGDMQDQLLQLQRNLAK---TI 217
           P QLSGG KQRV +ARALA D  V+L+DE  SALDP + G    ++L + R+LAK   T+
Sbjct: 142 PAQLSGGQKQRVAIARALAMDPKVMLLDEPTSALDPELVG----EVLAVIRDLAKGGMTM 197

Query: 218 VFITHDLDEALRIGSEIAILRDGQVVQVGTPNDILDNPANDYVARFVQR 266
           V  TH +D A  + +EI  +  G +++ G+P ++L   A      F  R
Sbjct: 198 VMATHQMDFARALANEIVFMERGAIIERGSPAELLAPGAGTRTQDFCSR 246


Lambda     K      H
   0.323    0.139    0.397 

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: 175
Number of extensions: 12
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: 275
Length of database: 255
Length adjustment: 25
Effective length of query: 250
Effective length of database: 230
Effective search space:    57500
Effective search space used:    57500
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: 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