GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araV in Dechlorosoma suillum PS

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate Dsui_2943 Dsui_2943 ABC-type spermidine/putrescine transport system, ATPase component

Query= TCDB::Q97UF2
         (371 letters)



>FitnessBrowser__PS:Dsui_2943
          Length = 356

 Score =  187 bits (475), Expect = 4e-52
 Identities = 108/278 (38%), Positives = 163/278 (58%), Gaps = 13/278 (4%)

Query: 23  VDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTSGYIYFDNEAVSSPRRVMMSPE 82
           VD +   I++G+   +LGPSG GKTT LR IAG E+  +G I  D E VS P    ++PE
Sbjct: 19  VDGIGFHIEAGVIACLLGPSGCGKTTLLRCIAGFEDIAAGSIALDGELVSRPG-FKLAPE 77

Query: 83  KRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIENKVKEVSEELGLSGVLNRYPKE 142
           +R I MVFQ++AL+P++TV DNIAF LK     +   + +V  + + +GL+G   +YP E
Sbjct: 78  QRRIGMVFQDYALFPHLTVADNIAFGLKTKGGER---QQRVAAMLDLVGLAGQGEKYPHE 134

Query: 143 LSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRESARALVRKIQRERKLTTLIVSHD 202
           LSGGQ QR A+ARAL   P+++LLDEPFSNLD  +RE     VR+I ++   T ++V+HD
Sbjct: 135 LSGGQQQRVALARALAPAPRLVLLDEPFSNLDVDLRERLSLEVREILKKAGTTAILVTHD 194

Query: 203 PADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIARLTGEINLIQAKIIENNAIIAN 262
             + FA+A++ GV+  G+  Q  TP  +Y  PA   +A   G+   +   ++  N +   
Sbjct: 195 QHEAFAMADEIGVMHEGRIQQWDTPYNLYHQPANRFVADFVGQGVFVPGTVLAGNRVQME 254

Query: 263 LKVPLNNMELKGQS---------NIVIGLRPDDLTLSD 291
           L +  + + ++  +          + I LRPDD+   D
Sbjct: 255 LGILESGVPVECSAGCGVCGKGCGVDILLRPDDVVHDD 292


Lambda     K      H
   0.317    0.136    0.374 

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: 10
Number of successful extensions: 3
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: 371
Length of database: 356
Length adjustment: 29
Effective length of query: 342
Effective length of database: 327
Effective search space:   111834
Effective search space used:   111834
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 (21.6 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