GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araV in Rhizorhabdus wittichii RW1

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate WP_012048833.1 SWIT_RS13320 amino acid ABC transporter ATP-binding protein

Query= TCDB::Q97UF2
         (371 letters)



>NCBI__GCF_000016765.1:WP_012048833.1
          Length = 241

 Score =  132 bits (332), Expect = 1e-35
 Identities = 74/214 (34%), Positives = 124/214 (57%), Gaps = 3/214 (1%)

Query: 22  AVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTSGYIYFDNEAVSSPRRVMMSP 81
           A+ NVS+ +  G    + GPSG GK+T +R I GLE    G I    + V   RRV+   
Sbjct: 16  ALRNVSLDVARGERIVICGPSGSGKSTLIRCINGLETHDEGVIRIGEDEVRPDRRVLQRI 75

Query: 82  EKRGIAMVFQNWALYPNMTVFDNIAF-PLKLAKVPKDKIENKVKEVSEELGLSGVLNRYP 140
             R + MVFQ++ L+P++T+ +N A  P+K+  + +D  E   +E+ E + ++   ++YP
Sbjct: 76  RAR-VGMVFQDFNLFPHLTILENCALAPMKVRGLARDAAEALARELLERVRIADQADKYP 134

Query: 141 KELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRESARALVRKIQRERKLTTLIVS 200
            +LSGGQ QRTAIARAL   P+++L DEP S LDA++ +    +++ +  E  +T L V+
Sbjct: 135 AQLSGGQQQRTAIARALAMQPEIILFDEPTSALDAEMVKEVLDIMKALATE-GITMLCVT 193

Query: 201 HDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYP 234
           H+      +A++   +  G+  + G+P + +  P
Sbjct: 194 HEMGFAREVADRIIFMDAGQIVETGSPRDFFTAP 227


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: 186
Number of extensions: 12
Number of successful extensions: 4
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: 241
Length adjustment: 27
Effective length of query: 344
Effective length of database: 214
Effective search space:    73616
Effective search space used:    73616
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 Apr 09 2024. 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