GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutW in Desulfovibrio vulgaris Hildenborough

Align HutW aka HISW, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate 207785 DVU2298 glycine/betaine/L-proline ABC transporter, permease protein

Query= TCDB::Q9KKE2
         (285 letters)



>MicrobesOnline__882:207785
          Length = 283

 Score =  246 bits (629), Expect = 3e-70
 Identities = 134/275 (48%), Positives = 183/275 (66%), Gaps = 4/275 (1%)

Query: 11  RAPVNDFIQALVTNY----GWVFKAISGVILKAVLFIEWILRGLPWWLVILAFMALACRS 66
           R P+  +++A   N         +A S V    +  +E +L  +P W  I     LA R+
Sbjct: 8   RIPLGAWLEAFTDNMVEWCSGATRAFSTVAGNGIDMLESLLGSIPPWAFIPVVALLAWRA 67

Query: 67  SRRWSLTLAVCALLETVGVLGIWDLTMQTLALMLMATIVSVVIGVPMGILVAKSRVVRNI 126
           +R+  +          +  LG+W+ TM T+AL+L+AT ++VV GVP+GI  A +  VR +
Sbjct: 68  TRKPGIGAFALLGFGLIWNLGLWEATMSTIALVLVATALAVVTGVPLGIAAAVNVTVRKV 127

Query: 127 TLPVLDVMQTMPSFVYLIPALMLFGLGKVPAILATIIYAVPPLIRLTDLGIRQVDAEVVE 186
            +PVLD+MQTMP+FVYLIPA+  FGLGKV A+ AT+++A+PP IR T LGIRQV  ++VE
Sbjct: 128 LMPVLDLMQTMPAFVYLIPAIPFFGLGKVAAVFATVVFAMPPAIRFTCLGIRQVPDDLVE 187

Query: 187 AATAFGGSPGQILFGVELPLATPTIMAGLNQTIMMALSMVVVASMIGARGLGEQVLNGIQ 246
            A AFG S  Q L  +ELPLA PTI+AG+NQTIM+ALSMVV+A+MIGARGLG +V   IQ
Sbjct: 188 CAEAFGTSRWQRLVKLELPLAAPTILAGVNQTIMLALSMVVIAAMIGARGLGGEVWKAIQ 247

Query: 247 TLDVGKGLEAGIGIVILAVVLDRITQGFGKPRTED 281
            L++G G EAGIGIVI+A+ LDR+ Q  G+  + D
Sbjct: 248 RLELGSGFEAGIGIVIVAICLDRVLQHIGRRSSVD 282


Lambda     K      H
   0.327    0.142    0.422 

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: 263
Number of extensions: 13
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: 285
Length of database: 283
Length adjustment: 26
Effective length of query: 259
Effective length of database: 257
Effective search space:    66563
Effective search space used:    66563
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 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