GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araV in Echinicola vietnamensis KMM 6221, DSM 17526

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate Echvi_3653 Echvi_3653 ABC-type sulfate/molybdate transport systems, ATPase component

Query= TCDB::Q97UF2
         (371 letters)



>FitnessBrowser__Cola:Echvi_3653
          Length = 290

 Score =  148 bits (373), Expect = 2e-40
 Identities = 94/237 (39%), Positives = 137/237 (57%), Gaps = 11/237 (4%)

Query: 14  KKGKTEVKAVD-NVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTSGYIYFDNEA-- 70
           K  K    A+D ++ +TI  G    + GPSG GKT+ LR+I+GL  P  G++  + E   
Sbjct: 8   KSLKANGPAMDLDIKLTISQGEFITLFGPSGSGKTSTLRMISGLLTPDKGHLSVNGEQWF 67

Query: 71  -VSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIENKVKEVSEE 129
             S  + V  SP +R +  +FQ+++L+PNMTV +NIAF LK AK   DK    + E+ E 
Sbjct: 68  DASFGKNV--SPGRRKLGYLFQDYSLFPNMTVKENIAFALKNAK---DKAY--LMELLES 120

Query: 130 LGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRESARALVRKIQ 189
           +GL  + +  PK LSGGQ QR A+ARAL   P +LLLDEP S LD  +RE  +  +  I 
Sbjct: 121 MGLLHLQDTLPKHLSGGQQQRVALARALALKPDILLLDEPLSALDPSMREKLQEYILAIH 180

Query: 190 RERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIARLTGEI 246
           R+  LTT++VSHD  +I  ++++   + +GK  +  TP E +    T    +  GEI
Sbjct: 181 RKYALTTILVSHDAGEIIKLSDRIIELDHGKVLRQCTPKEFFGTGLTSAKFQFQGEI 237


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: 235
Number of extensions: 8
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: 290
Length adjustment: 28
Effective length of query: 343
Effective length of database: 262
Effective search space:    89866
Effective search space used:    89866
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.

Links

Downloads

Related tools

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