GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araV in Megamonas funiformis YIT 11815

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate WP_008538413.1 HMPREF9454_RS05390 ABC transporter ATP-binding protein

Query= TCDB::Q97UF2
         (371 letters)



>NCBI__GCF_000245775.1:WP_008538413.1
          Length = 260

 Score =  186 bits (473), Expect = 5e-52
 Identities = 103/249 (41%), Positives = 153/249 (61%), Gaps = 11/249 (4%)

Query: 11  KIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTSGYIYFDNEA 70
           K  +K    ++ + N+++ I+ G    +LGPSG GKTT L LI GL + + G I FD E 
Sbjct: 5   KKIRKSYEGIEVLKNINLKIEKGEIVSILGPSGCGKTTLLNLILGLTQVSEGRIIFDGED 64

Query: 71  VSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIENKVKEVSEEL 130
           ++      M  EKRG  +VFQ++AL+PN+ V++NI + LK    P      +V+++   L
Sbjct: 65  ITQ-----MPMEKRGFNIVFQDYALFPNLNVYENIVYGLK--NKPNISTTKEVQDLINLL 117

Query: 131 GLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRESARALVRKIQR 190
           GL   L +  +ELSGGQ QRTA+AR LV  PK+LLLDEP S LD  I+ES +  +++I R
Sbjct: 118 GLGKHLTKKIEELSGGQKQRTALARTLVMKPKILLLDEPLSALDGVIKESIKQKIKEIAR 177

Query: 191 ERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIARLTGEINLIQ 250
           + KLTT+IV+HDP +   +++K  ++  G+ +Q GTP EI + PA D ++    E  L Q
Sbjct: 178 DFKLTTIIVTHDPEEALTLSDKVLIVNEGQISQFGTPEEIIKKPANDFVS----EFILRQ 233

Query: 251 AKIIENNAI 259
            +I  NN +
Sbjct: 234 LEIKRNNIL 242


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: 242
Number of extensions: 15
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: 260
Length adjustment: 27
Effective length of query: 344
Effective length of database: 233
Effective search space:    80152
Effective search space used:    80152
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.

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