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 H281DRAFT_04452 H281DRAFT_04452 amino acid/amide ABC transporter membrane protein 2, HAAT family (TC 3.A.1.4.-)
Query= TCDB::Q8YY08 (377 letters) >FitnessBrowser__Burk376:H281DRAFT_04452 Length = 438 Score = 66.2 bits (160), Expect = 2e-15 Identities = 55/167 (32%), Positives = 81/167 (48%), Gaps = 20/167 (11%) Query: 5 LIFLAISTATFALFSLGLNLQWGFTGLINFGHIAFMTLGAYTTV-LLSLKGVPLFISAIV 63 L++LA TAT +F+L NL G TGL++FGH A+ LGA + + G PL + +V Sbjct: 51 LVYLA-QTATMIVFALSYNLLLGETGLLSFGHAAYSGLGALIAAQVFNRIGAPLALLPLV 109 Query: 64 GAIFAALLGLVIGFATLRLREDYLAIVTIGTGELIRLVVNNQDLPVGDTWVSGAFGVQSY 123 G AA G ++GF + R A++T+G GEL+ LP W G GV Sbjct: 110 GGAGAASCGALLGFISTRRAGTAFAMITLGIGELVAAAA--WTLP---DWFGGEAGV--- 161 Query: 124 PIPLSTEPNLFFRLLMIGILTL---LFAVTVFSLWRWIRNAQKLQLT 167 I ++ P M+G T A T+ +LW + +A L+ Sbjct: 162 AIDRASGP-------MLGAFTFGPAREAYTLIALWCLLASAAMFALS 201 Score = 36.2 bits (82), Expect = 2e-06 Identities = 30/138 (21%), Positives = 56/138 (40%), Gaps = 12/138 (8%) Query: 231 LVRSPWGRVLKAIREDEEIPKAMGKNVFWYKLQSLMLGGAIAGIAGAFFAWQISAIYPDN 290 L R+ + R+ A+R++ A+G + +++ AGIAG + + D+ Sbjct: 200 LSRTSFMRLANAVRDNPARAAAIGCYPRRVRYGVVVMSAFFAGIAGTLALINVELVSTDS 259 Query: 291 FQPQLTFDSWIMVILGGAGNNIGSILGAVIYFAYDAITREVLPKIIPLDEARLGAFRIMC 350 + I ++GG G G + GAV+ + V R F Sbjct: 260 VSMVRSGSVLIATVIGGTGVFFGPVAGAVVLTFFSVAVASV---------TRAWLF---Y 307 Query: 351 IGLILMVLMIWRPQGILG 368 +GL +V+++ P G+ G Sbjct: 308 LGLFFIVIVVAAPDGLAG 325 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: 446 Number of extensions: 26 Number of successful extensions: 3 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: 438 Length adjustment: 31 Effective length of query: 346 Effective length of database: 407 Effective search space: 140822 Effective search space used: 140822 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: 50 (23.9 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