Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate CCNA_01670 CCNA_01670 sulfate transport ATP-binding protein cysA
Query= TCDB::Q97UF2 (371 letters) >FitnessBrowser__Caulo:CCNA_01670 Length = 339 Score = 181 bits (460), Expect = 2e-50 Identities = 113/315 (35%), Positives = 170/315 (53%), Gaps = 18/315 (5%) Query: 3 TIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTSG 62 TI + ++ K F + A++ V + I G +LGPSG GKTT LR IAGLE P +G Sbjct: 2 TIAIRSVEKQFGR----YPALNKVDLEIADGELLALLGPSGSGKTTLLRTIAGLEFPDAG 57 Query: 63 YIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDK---- 118 + FD + V+ S R + VFQ +AL+ +MTV NIAF L + K KDK Sbjct: 58 QVLFDGQDVT-----YASAAARRVGFVFQQYALFKHMTVAKNIAFGLDVRK-GKDKPSKA 111 Query: 119 -IENKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQI 177 I +V+E+ + + L G+ RYP +LSGGQ QR A++RAL P VLLLDEPF LDA + Sbjct: 112 EIARRVEELLKLVELEGLGGRYPSQLSGGQRQRVALSRALAVQPSVLLLDEPFGALDATV 171 Query: 178 RESARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATD 237 R+S R +R++ +TT+ V+HD + +A++ ++ NG+ QIGTP ++++ P T Sbjct: 172 RKSLRRELRRVHDATGVTTIFVTHDQEEALELADRVAILNNGRIEQIGTPDQVHDAPETA 231 Query: 238 LIARLTGEINLIQAKIIENNAIIANLKVPLNNMELKGQSNIVIGLRPDDLTLSDTLLDKY 297 + GE N ++ L VP + ++ + V RP D L + + Sbjct: 232 FVCGFVGEANRFDGQVSGGRFKAGALTVPASALKDGAATAYV---RPHDFALDEAGFEVL 288 Query: 298 IDMGIVKVKLVSYGA 312 I+ V+ L + A Sbjct: 289 IERAQVQGALTAVTA 303 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: 233 Number of extensions: 11 Number of successful extensions: 4 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: 339 Length adjustment: 29 Effective length of query: 342 Effective length of database: 310 Effective search space: 106020 Effective search space used: 106020 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