GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araV in Paucidesulfovibrio gracilis DSM 16080

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate WP_200806763.1 B5D49_RS03200 ABC transporter ATP-binding protein

Query= TCDB::Q97UF2
         (371 letters)



>NCBI__GCF_900167125.1:WP_200806763.1
          Length = 406

 Score =  204 bits (520), Expect = 3e-57
 Identities = 111/253 (43%), Positives = 160/253 (63%), Gaps = 11/253 (4%)

Query: 4   IRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTSGY 63
           +R++ L K F  GKT   AV    +TI++G    +LGPSG GKTT LR+IAGLE PT G 
Sbjct: 45  VRLQGLMKRF--GKTV--AVQETDLTIETGELVTLLGPSGCGKTTILRMIAGLETPTKGD 100

Query: 64  IYFDNEAVSSPRRVMMSP-EKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIENK 122
           IY         RR+  +P  KR + M+FQN+AL+P+ T+F+N+AF LK   V ++++  K
Sbjct: 101 IYIKG------RRINDTPIHKRNLGMIFQNYALFPHKTIFENVAFGLKYRNVSREEMREK 154

Query: 123 VKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRESAR 182
           V +  E + L GV  RY  +LSGGQ QR A+ARA+V +P VLL+DEP S LD ++RE  R
Sbjct: 155 VAQALEMVRLPGVEKRYASQLSGGQQQRIALARAIVIEPDVLLMDEPLSALDEKLREEMR 214

Query: 183 ALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIARL 242
             +  IQ++  LTTL V+HD  +  +++NK  V+ +G+  Q GTP ++Y+YP    +A  
Sbjct: 215 MEIDNIQQQLNLTTLFVTHDQREALSMSNKIVVMKDGRKQQEGTPEDVYDYPDNYFVADF 274

Query: 243 TGEINLIQAKIIE 255
            G  N   A+++E
Sbjct: 275 LGHANFFDARVLE 287


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: 319
Number of extensions: 12
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: 406
Length adjustment: 30
Effective length of query: 341
Effective length of database: 376
Effective search space:   128216
Effective search space used:   128216
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 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