Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate Echvi_1022 Echvi_1022 ABC-type spermidine/putrescine transport systems, ATPase components
Query= TCDB::Q97UF2 (371 letters) >FitnessBrowser__Cola:Echvi_1022 Length = 345 Score = 151 bits (382), Expect = 2e-41 Identities = 85/259 (32%), Positives = 144/259 (55%), Gaps = 12/259 (4%) Query: 1 MTTIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPT 60 M+ +++ +SK F + T+ AV ++ + I+ G ++G +G GKTT L+LIAGLE P Sbjct: 1 MSLLQLHGISKKFPQ--TKQFAVKDIHMEIEEGSVQAIVGENGSGKTTLLKLIAGLEHPD 58 Query: 61 SGYIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIE 120 G I F + + + + + + +R + ++FQ +AL+P MT+ +N+ L + Sbjct: 59 KGEIVFSGQTIVNGKSALPA-NQREVGVIFQEYALFPQMTLLENVREALH------QESR 111 Query: 121 NKVKEVSEELGLSGV---LNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQI 177 N + + L L+G+ + YP +LS GQ QR A+ARAL PK+LLLD+PF +LD + Sbjct: 112 NARQIAMDSLALAGLEDSFSAYPHQLSSGQRQRAALARALASRPKLLLLDDPFRSLDTRF 171 Query: 178 RESARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATD 237 + +R I + +T ++ SH D ++A+ ++ G Q+GTP EIY+ PA Sbjct: 172 KNEISEDIRDIVKATGITAIVASHHAKDALSLADSIAILHKGILQQVGTPVEIYKKPANA 231 Query: 238 LIARLTGEINLIQAKIIEN 256 +A G+ N + A E+ Sbjct: 232 YVANFFGKRNELLATPTED 250 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: 286 Number of extensions: 13 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: 345 Length adjustment: 29 Effective length of query: 342 Effective length of database: 316 Effective search space: 108072 Effective search space used: 108072 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