GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araV in Bacteroides thetaiotaomicron VPI-5482

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate 351279 BT1751 Glycine betaine transport ATP-binding protein (NCBI ptt file)

Query= TCDB::Q97UF2
         (371 letters)



>FitnessBrowser__Btheta:351279
          Length = 408

 Score =  154 bits (388), Expect = 5e-42
 Identities = 97/305 (31%), Positives = 170/305 (55%), Gaps = 13/305 (4%)

Query: 11  KIFKKGKTEVK---------AVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTS 61
           K+ K+GKT+ +         AV + +++I+ G  F ++G SG GK+T LR I  L  PTS
Sbjct: 22  KMLKEGKTKSEILKATGCTVAVKDANLSINEGEIFVIMGLSGSGKSTLLRCINRLIRPTS 81

Query: 62  GYIYFDNEAVSSPR-RVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIE 120
           G +  +   ++    + ++   ++ +AMVFQN+ L P+ +V  NIAF L+L  V K + E
Sbjct: 82  GEVIINGTDIAKVSDKELLQIRRKELAMVFQNFGLLPHRSVLHNIAFGLELQGVKKGERE 141

Query: 121 NKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRES 180
            K  E  + +GL G  N+   ELSGG  QR  +ARAL  +P+VLL+DE FS LD  IR  
Sbjct: 142 QKAMESMQLVGLKGYENQMVSELSGGMQQRVGLARALANNPEVLLMDEAFSALDPLIRVQ 201

Query: 181 ARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIA 240
            +  +  +Q + K T + ++HD ++   + ++  ++ +G+  QIGT  EI   PA   + 
Sbjct: 202 MQDELLTLQSKMKKTIVFITHDLSEAIKLGDRIAIMKDGEIVQIGTSEEILTEPANAYVE 261

Query: 241 RLTGEINLIQAKIIENNAIIANLKVPLNNMELKGQSNIVIGLRPDDLTLSDTLLDKYIDM 300
           R     N+ ++KII  ++++ + K  +  ++ +G   ++  +R  +LT+   +    + +
Sbjct: 262 RFVE--NVDRSKIITASSVMVD-KPIVARLKKEGPEVLIRKMRERNLTVLPVVDSNNLLV 318

Query: 301 GIVKV 305
           G V++
Sbjct: 319 GEVRL 323


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: 297
Number of extensions: 11
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: 408
Length adjustment: 30
Effective length of query: 341
Effective length of database: 378
Effective search space:   128898
Effective search space used:   128898
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