GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araV in Tatumella morbirosei LMG 23360

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate WP_038022060.1 HA49_RS08470 sulfate/thiosulfate ABC transporter ATP-binding protein CysA

Query= TCDB::Q97UF2
         (371 letters)



>NCBI__GCF_000757425.2:WP_038022060.1
          Length = 362

 Score =  191 bits (485), Expect = 3e-53
 Identities = 113/292 (38%), Positives = 171/292 (58%), Gaps = 14/292 (4%)

Query: 3   TIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTSG 62
           +I +  ++K F  GKT V  ++++ + I SG    +LGPSG GKTT LR+IAGLE   SG
Sbjct: 2   SINIHQINKSF--GKTPV--LNDIDLDISSGEMVALLGPSGSGKTTLLRIIAGLEHQNSG 57

Query: 63  YIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLA----KVPKDK 118
            I F +  VS      +    R +  VFQ++AL+ +MTVFDNIAF L +     +  +  
Sbjct: 58  RISFRDRDVSH-----LHARDRHVGFVFQHYALFRHMTVFDNIAFGLTVLPRRERPSQAD 112

Query: 119 IENKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIR 178
           I  KV  + E + LS +  RYP +LSGGQ QR A+ARAL  DP +LLLDEPF  LDAQ+R
Sbjct: 113 IRKKVLNLLEMVQLSHLAGRYPAQLSGGQKQRVALARALAVDPHILLLDEPFGALDAQVR 172

Query: 179 ESARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDL 238
           +  R  +R++  E + T++ V+HD  +   +A++  V+  G   Q GTP ++++ PA+  
Sbjct: 173 KELRRWLRQLHEELQFTSVFVTHDQEEAMEVADRIVVMSQGNVEQTGTPEQVWKQPASRF 232

Query: 239 IARLTGEINLIQAKIIENNAIIANLKVPLNNMELKGQSNIVIGLRPDDLTLS 290
           +    GEIN +Q +++ N   +A  + PL +     Q  + + LRP +  +S
Sbjct: 233 VLEFLGEINRLQGQLVGNKLQVAGHQWPL-DFTPAVQGEVDLFLRPWETDIS 283


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: 260
Number of extensions: 11
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: 371
Length of database: 362
Length adjustment: 30
Effective length of query: 341
Effective length of database: 332
Effective search space:   113212
Effective search space used:   113212
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 24 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