GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araV in Sinorhizobium meliloti 1021

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate SMc01608 SMc01608 ABC transporter ATP-binding protein

Query= TCDB::Q97UF2
         (371 letters)



>FitnessBrowser__Smeli:SMc01608
          Length = 353

 Score =  208 bits (530), Expect = 2e-58
 Identities = 121/292 (41%), Positives = 179/292 (61%), Gaps = 18/292 (6%)

Query: 1   MTTIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPT 60
           M  +++ N+ K F      V+ V N  + ID G     LGPSG GKTT LR+IAG E P+
Sbjct: 1   MAFLQLTNIQKSFGP----VQVVHNFDMGIDKGEFVSFLGPSGCGKTTILRMIAGFETPS 56

Query: 61  SGYIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIE 120
            G I+ D +   +     + P +R I MVFQ +AL+PNM V DN+AF LK+A   + +IE
Sbjct: 57  GGSIFIDGKDQGA-----LKPNQRNIGMVFQAYALFPNMNVHDNVAFGLKVAGASRTEIE 111

Query: 121 NKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRES 180
            +VK++   + L  + +R+P +LSGGQ QR A+ARAL   P+VLLLDEP S LDA+IR S
Sbjct: 112 ARVKQMLGLIKLEHLADRFPYQLSGGQQQRVALARALAVKPQVLLLDEPLSALDAKIRIS 171

Query: 181 ARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIA 240
            R  +R+IQ++  +TT+ V+HD  +  +I+++  V+ +G+  QIGTP EIY  PAT  +A
Sbjct: 172 LREEIRQIQQQLGITTVFVTHDQEEALSISDRIVVMNSGRADQIGTPFEIYNTPATRFVA 231

Query: 241 RLTGEINLIQAKIIE--NNAII-----ANLKVPLNNMELKGQSNIVIGLRPD 285
              G +N+I+ K+ +  + A+       +LK P+     KG  +I + LRP+
Sbjct: 232 SFVGTLNIIEGKVADPASGAVTIGGQRISLKEPIAG--AKGGDSISLALRPE 281


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: 268
Number of extensions: 8
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: 353
Length adjustment: 29
Effective length of query: 342
Effective length of database: 324
Effective search space:   110808
Effective search space used:   110808
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