GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araV in Gallaecimonas xiamenensis 3-C-1

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate WP_156804435.1 B3C1_RS03280 polyamine ABC transporter ATP-binding protein

Query= TCDB::Q97UF2
         (371 letters)



>NCBI__GCF_000299915.1:WP_156804435.1
          Length = 375

 Score =  186 bits (473), Expect = 7e-52
 Identities = 101/263 (38%), Positives = 162/263 (61%), Gaps = 9/263 (3%)

Query: 4   IRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTSGY 63
           + +E +SK F     +VKAVDNVS+ I  G  F +LG SG GK+T LR++AG E+P+SG 
Sbjct: 17  LTIEGVSKFFG----QVKAVDNVSLEIRKGEIFALLGGSGSGKSTLLRMLAGFEQPSSGR 72

Query: 64  IYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIENKV 123
           I+ D + ++      + P KR I M+FQ++AL+P+MTV  NIA+ LK   +PK +I  +V
Sbjct: 73  IFIDGQDITE-----LPPYKRPINMMFQSYALFPHMTVAQNIAYGLKQDGLPKAEIGPRV 127

Query: 124 KEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRESARA 183
            E+   + ++    R P++LSGGQ QR A+AR+L K PK+LLLDEP   LD ++R   + 
Sbjct: 128 DEMLRLVRMTDYAQRKPQQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRTQMQL 187

Query: 184 LVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIARLT 243
            + +I     +T ++V+HD  +   +A +  ++  G   Q GTP +IYE P + + A   
Sbjct: 188 ELVQIIESVGVTCVMVTHDQEEAMTMAQRIAIMNEGWIVQQGTPLDIYESPNSRMTAEFI 247

Query: 244 GEINLIQAKIIENNAIIANLKVP 266
           G +N+ + +++++    A ++VP
Sbjct: 248 GSVNMFEGELVDDAPDHALIQVP 270


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: 283
Number of extensions: 9
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: 375
Length adjustment: 30
Effective length of query: 341
Effective length of database: 345
Effective search space:   117645
Effective search space used:   117645
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 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