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 206400 DVU0968 amino acid ABC transporter, ATP-binding protein

Query= TCDB::Q9KKE1
         (275 letters)



>MicrobesOnline__882:206400
          Length = 246

 Score =  153 bits (386), Expect = 4e-42
 Identities = 89/218 (40%), Positives = 132/218 (60%), Gaps = 10/218 (4%)

Query: 43  LNDVSLKIGAGKIFVIMGLSGSGKSTLVRHINRLIEPTSGEVLFDGDNILDLGAKALRAF 102
           L DVSL +  G++ VI+G SGSGKST +R +NRL    SGE+L +G +ILD   +     
Sbjct: 22  LRDVSLDVAPGEVVVIIGPSGSGKSTFLRCLNRLEYADSGEILIEGRDILDPKCEINEV- 80

Query: 103 RMRRVSMVFQSFALMPHRTVLQNVVYGQR-VRGVSKDDAREIGMKWIDTVGLSGYDAKFP 161
               V MVFQSF L PH +VL+NV   Q  VR  S+ ++ + GM+ +  VG++   A +P
Sbjct: 81  -RAEVGMVFQSFNLFPHLSVLENVALAQMTVRKRSRAESEKKGMELLTKVGIADKHAVYP 139

Query: 162 HQLSGGMKQRVGLARALAADTDVILMDEAFSALDPLIRGDMQDQLLQLQRNLAK---TIV 218
            QLSGG +QRV +AR+LA D  ++L DE  SALDP    +M  ++L + RNLA+   T+V
Sbjct: 140 DQLSGGQQQRVAIARSLAMDPKIMLFDEPTSALDP----EMVGEVLDVMRNLAREGMTMV 195

Query: 219 FITHDLDEALRIGSEIAILRDGQVVQVGTPNDILDNPA 256
            +TH++  A  +   +  +  G ++++ TP D+    A
Sbjct: 196 VVTHEMGFAREVADRVVFMDHGAILEIATPKDLFTTGA 233


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: 186
Number of extensions: 8
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: 246
Length adjustment: 24
Effective length of query: 251
Effective length of database: 222
Effective search space:    55722
Effective search space used:    55722
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