GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araV in Caulobacter crescentus NA1000

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate CCNA_03235 CCNA_03235 spermidine/putrescine transport ATP-binding protein potA

Query= TCDB::Q97UF2
         (371 letters)



>FitnessBrowser__Caulo:CCNA_03235
          Length = 381

 Score =  213 bits (542), Expect = 7e-60
 Identities = 114/263 (43%), Positives = 170/263 (64%), Gaps = 9/263 (3%)

Query: 4   IRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTSGY 63
           I  EN++K F K    + AVDNVS+T++ G  F +LGPSG GKTT LR++AG E PT G 
Sbjct: 15  ITFENVTKRFGK----LAAVDNVSLTVNEGEFFALLGPSGCGKTTLLRMLAGFETPTEGR 70

Query: 64  IYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIENKV 123
           I  D + +S+     + P KR + MVFQ++A++P+MTV DN+A+ LK+  VPK + E +V
Sbjct: 71  ILIDGQDISN-----VPPNKRPVNMVFQSYAVFPHMTVADNVAYGLKVDNVPKAEREARV 125

Query: 124 KEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRESARA 183
            E  E + L G+  R P +LSGGQ QR A+ARALVK P+VLLLDEP S LDA++RE  R 
Sbjct: 126 AEALELVQLGGLGGRKPDQLSGGQRQRVALARALVKRPRVLLLDEPLSALDAKLREQMRT 185

Query: 184 LVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIARLT 243
            +  +Q +  +T ++V+HD  +  A+A++  V+  G   Q+ TP+++YE+P +  +A   
Sbjct: 186 ELCTLQEKVGITFIMVTHDQDEALALASRCAVMSKGLLQQVATPSDLYEFPNSRFVADFI 245

Query: 244 GEINLIQAKIIENNAIIANLKVP 266
           G++NL +  +  +    A +K P
Sbjct: 246 GQVNLFEGVLAVDEPSHAVIKSP 268


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: 313
Number of extensions: 7
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: 381
Length adjustment: 30
Effective length of query: 341
Effective length of database: 351
Effective search space:   119691
Effective search space used:   119691
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