Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate Pf6N2E2_3975 Taurine transport ATP-binding protein TauB
Query= reanno::acidovorax_3H11:Ac3H11_2560 (259 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3975 Length = 286 Score = 186 bits (473), Expect = 4e-52 Identities = 103/219 (47%), Positives = 137/219 (62%), Gaps = 3/219 (1%) Query: 4 VSIQAVSRVFETAKGQRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSG 63 +S+ VS + T + + +A V FEV D +LGPSGCGKSTLL+ + G G Sbjct: 21 LSVDNVSLEYRTPQ-RVVRATHQVSFEVDPADRFVLLGPSGCGKSTLLKAIGGFIAPCEG 79 Query: 64 RVLLDGAPVEGPGAERGMVFQSYT-LFPWLTIEQNIRFGLRERG-MPEAQQKERAAYFIA 121 + L G V PG +R +VFQ + L PW T++QN+ F L G + + +ERA +++ Sbjct: 80 EIRLQGQTVNAPGPDRIVVFQEFDQLPPWKTVKQNVMFALLASGTLKRREAEERALHYLD 139 Query: 122 KVGLRGFEQHFPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQELLLGI 181 KVGL F +P LSGGM+ R AIARALA PKILLMDEPF ALD TR MQE LL + Sbjct: 140 KVGLAAFADAYPHTLSGGMKARVAIARALAMQPKILLMDEPFAALDALTRRKMQEELLLL 199 Query: 182 WEAERKTVLFVTHDIDEAIFMANRVAVFSARPGRIKTEL 220 WE R T+LFVTH I+EA+ + NR+ + S PGR++ E+ Sbjct: 200 WEEVRFTLLFVTHSIEEALVVGNRILLLSPHPGRVRAEV 238 Lambda K H 0.322 0.136 0.394 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: 200 Number of extensions: 8 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: 259 Length of database: 286 Length adjustment: 25 Effective length of query: 234 Effective length of database: 261 Effective search space: 61074 Effective search space used: 61074 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 47 (22.7 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