GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araV in Escherichia coli BW25113

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate 17511 b3450 ATP-binding component of sn-glycerol 3-phosphate transport system (VIMSS)

Query= TCDB::Q97UF2
         (371 letters)



>FitnessBrowser__Keio:17511
          Length = 356

 Score =  201 bits (512), Expect = 2e-56
 Identities = 115/297 (38%), Positives = 185/297 (62%), Gaps = 16/297 (5%)

Query: 1   MTTIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPT 60
           M  ++++ ++K +  GKT+V  +  +++ +  G    ++GPSG GK+T LR++AGLE  T
Sbjct: 1   MAGLKLQAVTKSWD-GKTQV--IKPLTLDVADGEFIVMVGPSGCGKSTLLRMVAGLERVT 57

Query: 61  SGYIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIE 120
            G I+ +++ V+      M P+ RGIAMVFQN+ALYP+M+V +N+A+ LK+  + K +I 
Sbjct: 58  EGDIWINDQRVTE-----MEPKDRGIAMVFQNYALYPHMSVEENMAWGLKIRGMGKQQIA 112

Query: 121 NKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRES 180
            +VKE +  L L G+L R P+ELSGGQ QR A+ RA+V+DP V L DEP SNLDA++R  
Sbjct: 113 ERVKEAARILELDGLLKRRPRELSGGQRQRVAMGRAIVRDPAVFLFDEPLSNLDAKLRVQ 172

Query: 181 ARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIA 240
            R  ++++ R  K T+L V+HD  +   +A +  V+  G   QIGTP E+YE PA+  +A
Sbjct: 173 MRLELQQLHRRLKTTSLYVTHDQVEAMTLAQRVMVMNGGVAEQIGTPVEVYEKPASLFVA 232

Query: 241 RLTGE--INLIQAKIIENNA---IIANLKVPLNN--MELKGQSNIVIGLRPDDLTLS 290
              G   +NL+  ++        +   +++PLN    +  G+  + +G+RP+ + LS
Sbjct: 233 SFIGSPAMNLLTGRVNNEGTHFELDGGIELPLNGGYRQYAGR-KMTLGIRPEHIALS 288


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: 296
Number of extensions: 13
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: 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