GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araV in Pontibacter ramchanderi LP43

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate WP_101442772.1 BD749_RS02395 ABC transporter ATP-binding protein

Query= TCDB::Q97UF2
         (371 letters)



>NCBI__GCF_002846395.1:WP_101442772.1
          Length = 231

 Score =  125 bits (315), Expect = 9e-34
 Identities = 71/234 (30%), Positives = 123/234 (52%), Gaps = 11/234 (4%)

Query: 2   TTIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTS 61
           T + + NL K +  G   +  ++ ++IT+ +G    ++GPSG GKTT L L AGL+  +S
Sbjct: 3   TILEINNLKKTYNSGDRHLTVLEGINITLQAGDTCAIVGPSGSGKTTLLGLCAGLDRASS 62

Query: 62  GYIYFDN---EAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDK 118
           G +  +    + +S   R  +    + +  +FQN+ L P +T  +N+  PL+L    +  
Sbjct: 63  GSVVLNGVQLDNLSEDARAQV--RNQYVGFIFQNFQLIPTLTALENVMVPLELRG--ERN 118

Query: 119 IENKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIR 178
           ++ +  E+   +GL+   + YP +LSGG+ QR ++ARA    P +L  DEP  NLD +  
Sbjct: 119 VQGQAMELLARVGLAERHDHYPTQLSGGEQQRVSLARAFSNRPTILFADEPTGNLDEETG 178

Query: 179 ESARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYE 232
           E    L+ ++ RE   T ++V+HD      +A K   I+  K   + + T+  E
Sbjct: 179 EKVEKLLFELNREAGTTLVLVTHD----LELAEKTQRIIRIKGGHVVSDTKTAE 228


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: 184
Number of extensions: 9
Number of successful extensions: 3
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: 231
Length adjustment: 26
Effective length of query: 345
Effective length of database: 205
Effective search space:    70725
Effective search space used:    70725
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: 48 (23.1 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