GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutV in Desulfovibrio vulgaris Miyazaki F

Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate 8500289 DvMF_1045 glycine betaine/L-proline ABC transporter, ATPase subunit (RefSeq)

Query= TCDB::Q9KKE1
         (275 letters)



>FitnessBrowser__Miya:8500289
          Length = 397

 Score =  303 bits (775), Expect = 5e-87
 Identities = 160/264 (60%), Positives = 195/264 (73%)

Query: 1   MADIEIRNVYKIFGHDAKKALTMVEDGLDKADILSRSGCTVGLNDVSLKIGAGKIFVIMG 60
           MA IEIR++ KIFG   +KAL MV  G  K +I  R+   VG+N  +  +  G+I V+MG
Sbjct: 1   MAKIEIRDLTKIFGPVPEKALAMVRAGKPKDEIYKRTKHAVGVNRATFDVDEGEIVVVMG 60

Query: 61  LSGSGKSTLVRHINRLIEPTSGEVLFDGDNILDLGAKALRAFRMRRVSMVFQSFALMPHR 120
           LSGSGKSTLVR +NRLIEPT G V  DG ++  L  K LRA R R   MVFQ+FAL PHR
Sbjct: 61  LSGSGKSTLVRCLNRLIEPTDGTVRIDGTDVTTLSVKDLRALRQRTFGMVFQNFALFPHR 120

Query: 121 TVLQNVVYGQRVRGVSKDDAREIGMKWIDTVGLSGYDAKFPHQLSGGMKQRVGLARALAA 180
           TVL+N  YG  V G +K   R+   + +  VGL+G++A  P QLSGGM+QRVGLARALA 
Sbjct: 121 TVLENAEYGLEVMGAAKATRRDKAAEALARVGLAGWEAARPGQLSGGMQQRVGLARALAL 180

Query: 181 DTDVILMDEAFSALDPLIRGDMQDQLLQLQRNLAKTIVFITHDLDEALRIGSEIAILRDG 240
           D D++LMDEAFSALDPLIR DMQD+LL+LQ ++ KTIVFI+HDLDEAL+IG  I ++RDG
Sbjct: 181 DPDILLMDEAFSALDPLIRRDMQDELLRLQDDVRKTIVFISHDLDEALKIGDRIVLMRDG 240

Query: 241 QVVQVGTPNDILDNPANDYVARFV 264
            VVQVGTP DIL +PA+DYVARFV
Sbjct: 241 AVVQVGTPEDILTSPADDYVARFV 264


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: 379
Number of extensions: 15
Number of successful extensions: 1
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: 397
Length adjustment: 28
Effective length of query: 247
Effective length of database: 369
Effective search space:    91143
Effective search space used:    91143
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: 49 (23.5 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