GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araV in Marinomonas arctica 328

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate WP_111608342.1 DK187_RS16035 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= TCDB::Q97UF2
         (371 letters)



>NCBI__GCF_003259225.1:WP_111608342.1
          Length = 355

 Score =  217 bits (553), Expect = 3e-61
 Identities = 122/294 (41%), Positives = 184/294 (62%), Gaps = 14/294 (4%)

Query: 1   MTTIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPT 60
           MT + +E + K +  G     A+ +V ++I+ G    ++GPSG GK+T LR++AGLE  +
Sbjct: 1   MTDVILEKVGKTYPNG---YHAIPSVDLSIEEGEFIVLVGPSGCGKSTLLRMVAGLESIS 57

Query: 61  SGYIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIE 120
           +G +    E ++        P  R IAMVFQN+ALYP+MTV+DN+A+ LK   + KD I 
Sbjct: 58  TGELRIRGERMNEKE-----PADRDIAMVFQNYALYPHMTVYDNMAYGLKNRGMAKDLIA 112

Query: 121 NKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRES 180
            KV +V+  LGL+ +L R P++LSGGQ QR A+ RA+V+DPKV L DEP SNLDA++R  
Sbjct: 113 EKVSDVAAMLGLTELLQRKPRQLSGGQRQRVAMGRAMVRDPKVFLFDEPLSNLDAKLRVQ 172

Query: 181 ARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIA 240
            R  +R++QR+   TTL V+HD  +   +A++  V+  GK  QIGTP ++Y  PAT  +A
Sbjct: 173 MRVEIRQLQRKLGTTTLYVTHDQVEAMTLADRLVVLNKGKAEQIGTPMDLYNKPATPFVA 232

Query: 241 RLTG--EINLIQAKIIENNAIIAN-LKVPLNNMELKGQSNIVIGLRPDDLTLSD 291
              G   +NL+ A + E    +++ L +PL++     +  IV G+RP+ L +SD
Sbjct: 233 AFIGSPSMNLLDAHLTEQGITVSDELTLPLSHPH---RGAIVWGIRPEHLDVSD 283


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: 306
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: 355
Length adjustment: 29
Effective length of query: 342
Effective length of database: 326
Effective search space:   111492
Effective search space used:   111492
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 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