Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate SMc03065 SMc03065 alpha-glucoside ABC transporter ATP-binding protein
Query= TCDB::Q97UF2 (371 letters) >FitnessBrowser__Smeli:SMc03065 Length = 362 Score = 207 bits (526), Expect = 5e-58 Identities = 131/365 (35%), Positives = 198/365 (54%), Gaps = 22/365 (6%) Query: 9 LSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTSGYIYFDN 68 L K +K V + + + I G +GPSG GK+T LR+IAGLEE T G ++ D Sbjct: 5 LLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDMFIDG 64 Query: 69 EAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIENKVKEVSE 128 E V+ + P KRGIAMVFQ++ALYP+MTV+DN+AF +++A+ K++I+ +V+ ++ Sbjct: 65 ERVND-----VPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAAD 119 Query: 129 ELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRESARALVRKI 188 L L+ L+R PK LSGGQ QR AI RA+ ++PKV L DEP SNLDA +R + R + K+ Sbjct: 120 MLQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKL 179 Query: 189 QRERKLTTLI-VSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIARLTGE-- 245 TT+I V+HD + +A++ V+ G Q+G P E+YE PA +AR G Sbjct: 180 SERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPA 239 Query: 246 INLIQAKIIENNAIIA---------NLKVPLNNMELKGQSNIVIGLRPDDLTLSDTLLDK 296 +N+I A I A L VP N E G+RP+DL +++ D Sbjct: 240 MNVIPATITATGQQTAVSLAGGKSVTLDVPTNASE--NGKTASFGVRPEDLRVTEA--DD 295 Query: 297 YIDMGIVKVKLVSYGAGIFKIVVSPITDENIDIIVDAEEPLETGIETHLLAKPNKVKIFD 356 ++ G V + + + G + + +E I + + G + A K+ +FD Sbjct: 296 FLFEGTVSI-VEALGEVTLLYIEGLVENEPIIAKMPGIARVGRGDKVRFTADKAKLHLFD 354 Query: 357 LNGSN 361 NG + Sbjct: 355 TNGQS 359 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: 293 Number of extensions: 14 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: 362 Length adjustment: 30 Effective length of query: 341 Effective length of database: 332 Effective search space: 113212 Effective search space used: 113212 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 17 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