GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Desulfovibrio vulgaris Hildenborough

Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate 207786 DVU2299 glycine/betaine/L-proline ABC transporter, ATP binding protein

Query= reanno::WCS417:GFF4321
         (386 letters)



>MicrobesOnline__882:207786
          Length = 397

 Score =  165 bits (418), Expect = 2e-45
 Identities = 111/355 (31%), Positives = 177/355 (49%), Gaps = 37/355 (10%)

Query: 1   MATLELRNVNKTYGAGLPDTLKNIE----------------------LSIKEGEFLILVG 38
           M+ L +RN+ K +G      L  +E                        ++EGE ++++G
Sbjct: 1   MSKLSIRNLTKIFGPHPEKALGLLEQGLGKEEIHRRTSHAVGVDRASFDVEEGEIVVVMG 60

Query: 39  PSGCGKSTLMNCIAGLETITGGAIMIGDQDVSGMSP------KDRDIAMVFQSYALYPTM 92
            SG GKSTL+ C+  L   T G + +  +DV+ M        + R   MVFQ++AL+P  
Sbjct: 61  LSGSGKSTLVRCLNRLIEPTAGTVTVDGRDVTSMPVDELRRLRQRSFGMVFQNFALFPHR 120

Query: 93  SVRENIEFGLKIRKMPQADIDAEVARVAKLLQIEHLLNRKPGQLSGGQQQRVAMGRALAR 152
           +V +N  FGL+   +P+A+ + +     + + +      +P QLSGG QQRV + RAL+ 
Sbjct: 121 TVLQNAAFGLEAMGVPRAERERQAMVSLERVGLAEWAASRPAQLSGGMQQRVGLARALSL 180

Query: 153 RPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDG 212
            P I L DE  S LD  +R +M+ E+  +   L+ T V+++HD  EA+ LGD++ +M+DG
Sbjct: 181 DPDILLMDEAFSALDPLIRRDMQDELLRLQDDLQKTIVFISHDLDEALKLGDRIVLMRDG 240

Query: 213 IIQQFGTPKEIYNNPANQFVASFIGSPPMNFV-PLRLQRKDGRLVALLDSGQARCELALN 271
            + Q GTP++I  NPA+ +VA F+G   +  V       K    VA+L     R  L   
Sbjct: 241 AVVQIGTPEDILTNPADDYVARFVGEADVTKVLTAGSVMKRSEAVAVLGIDGPRTALRKM 300

Query: 272 TTEA-----GLEDRDVILGL--RPEQIMLAA-GEGDSASSIRAEVQVTEPTGPDT 318
              A      L++R  ++GL    +   LAA G  +  S +R ++    P  P T
Sbjct: 301 RRNAIATLFVLDERHRLVGLITADDAARLAAEGVRELGSIVRRDIATVPPEAPAT 355


Lambda     K      H
   0.318    0.135    0.382 

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: 318
Number of extensions: 17
Number of successful extensions: 2
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: 386
Length of database: 397
Length adjustment: 31
Effective length of query: 355
Effective length of database: 366
Effective search space:   129930
Effective search space used:   129930
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 (21.7 bits)
S2: 50 (23.9 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