Align NatC, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate BWI76_RS05985 BWI76_RS05985 branched-chain amino acid ABC transporter permease
Query= TCDB::Q8YY08 (377 letters) >FitnessBrowser__Koxy:BWI76_RS05985 Length = 349 Score = 86.3 bits (212), Expect = 1e-21 Identities = 62/199 (31%), Positives = 99/199 (49%), Gaps = 6/199 (3%) Query: 184 GVGIILGLLA--TAIYISGVITLYNYIPKAGLMLVSLLVLAFVFWRLEYLVRSPWGRVLK 241 G G I+ +LA +G I L + + L+ L + LV S +GR++K Sbjct: 144 GFGFIIKILAINNPQITNGAIGLNDIPQQPHLLFWCGLFALLATGMILQLVWSKYGRMMK 203 Query: 242 AIREDEEIPKAMGKNVFWYKLQSLMLGGAIAGIAGAFFAWQISAIYPDNFQPQLTFDSWI 301 A+R+DE+ AMG N F K + GI G A ++ I P F LTF I Sbjct: 204 AVRDDEDAAIAMGVNTFRIKTCAFATSAFFEGIGGGLLASLLTTISPGLFDFMLTFQLLI 263 Query: 302 MVILGGAGNNIGSILGAVIYFAYDAITREVLPKIIPLDEARLGAF---RIMCIGLILMVL 358 +++LGG G+ G++LG V+ R L + + LGA+ R++ L+L+++ Sbjct: 264 IIVLGGLGSTTGALLGTVLVVGSGEWLR-FLDQPLQFFGHDLGAYPGLRMVVFSLLLLII 322 Query: 359 MIWRPQGILGKKEELTLGK 377 M++ +G+LGKKE +GK Sbjct: 323 MLFAREGLLGKKEIWQVGK 341 Score = 55.5 bits (132), Expect = 2e-12 Identities = 47/173 (27%), Positives = 77/173 (44%), Gaps = 34/173 (19%) Query: 3 EYLIFLAISTATFALFSLGLNLQWGFTGLINFGHIAFMTLGAYTTVLLSLKG---VPLFI 59 +Y+I + + F + ++ NL G TG ++ F+ +GAY T LL L + +F Sbjct: 34 DYIIRVISTIFVFMILAVSYNLINGVTGQLSLEPNGFVAVGAYVTALLILSSDSKLDMFE 93 Query: 60 SA-----------------IVGAIFAALLGLVIGFATLRLREDYLAIVTIGTGELIR-LV 101 A ++ + AA L + + R+R DYLAIVT+G G +I+ L Sbjct: 94 MAAPSPWILVLHAGFLPALLISGLCAAALAVCLALPVFRVRGDYLAIVTLGFGFIIKILA 153 Query: 102 VNNQDLPVGDTWVSGAFGVQSYPIPLSTEPNLFFRLLMIGILTLLFAVTVFSL 154 +NN + +GA G+ P +P+L F G+ LL + L Sbjct: 154 INNPQI------TNGAIGLNDIP----QQPHLLF---WCGLFALLATGMILQL 193 Lambda K H 0.328 0.145 0.441 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: 385 Number of extensions: 21 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 377 Length of database: 349 Length adjustment: 29 Effective length of query: 348 Effective length of database: 320 Effective search space: 111360 Effective search space used: 111360 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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