GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araV in Pseudomonas simiae WCS417

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate GFF4321 PS417_22130 sugar ABC transporter ATPase

Query= TCDB::Q97UF2
         (371 letters)



>FitnessBrowser__WCS417:GFF4321
          Length = 386

 Score =  194 bits (492), Expect = 4e-54
 Identities = 127/379 (33%), Positives = 202/379 (53%), Gaps = 21/379 (5%)

Query: 1   MTTIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPT 60
           M T+ + N++K +  G  +   + N+ ++I  G    ++GPSG GK+T +  IAGLE  T
Sbjct: 1   MATLELRNVNKTYGAGLPDT--LKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETIT 58

Query: 61  SGYIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIE 120
            G I   ++ VS      MSP+ R IAMVFQ++ALYP M+V +NI F LK+ K+P+  I+
Sbjct: 59  GGAIMIGDQDVSG-----MSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADID 113

Query: 121 NKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRES 180
            +V  V++ L +  +LNR P +LSGGQ QR A+ RAL + PK+ L DEP SNLDA++R  
Sbjct: 114 AEVARVAKLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVE 173

Query: 181 ARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIA 240
            R  ++ + +  K TT+ V+HD  +   + +K  V+ +G   Q GTP EIY  PA   +A
Sbjct: 174 MRTEMKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVA 233

Query: 241 RLTGE--INLIQAKIIENNAII--------ANLKVPLNNMELKGQS-NIVIGLRPDDLTL 289
              G   +N +  ++   +  +        A  ++ LN  E   +  ++++GLRP+ + L
Sbjct: 234 SFIGSPPMNFVPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIML 293

Query: 290 SDTLLDKYIDMGIVKVKLVSYGAGIFKIVVSPITDENIDIIVDAEEPLETGIETHLLAKP 349
           +    D      I     V+   G   +V   + D  +   +  +   + G    L   P
Sbjct: 294 AAGEGDS--ASSIRAEVQVTEPTGPDTLVFVQLNDTKVCCRLAPDVAPQVGETLTLQFDP 351

Query: 350 NKVKIFDLN-GSNLITSKT 367
           +KV +FD N G  L T+ +
Sbjct: 352 SKVLLFDANTGERLGTASS 370


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: 304
Number of extensions: 10
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: 386
Length adjustment: 30
Effective length of query: 341
Effective length of database: 356
Effective search space:   121396
Effective search space used:   121396
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: 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