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.
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:
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