Align NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate SMc02120 SMc02120 general L-amino acid transport permease ABC transporter protein
Query= TCDB::Q8YPM7 (381 letters) >FitnessBrowser__Smeli:SMc02120 Length = 384 Score = 243 bits (621), Expect = 5e-69 Identities = 152/383 (39%), Positives = 220/383 (57%), Gaps = 35/383 (9%) Query: 4 LTWLRKNLFSTWYNSLLTVICSALSLWLVQGIIVWATTKAQWAVIQVNLRLFLVGRFPQT 63 ++WLRKNLF+T ++ LT+I + WLV I W A W+ + L Q Sbjct: 27 VSWLRKNLFATPKDTALTIISLLILAWLVPPAIQWLFIDAAWSGGGRGVCATLSQGGSQP 86 Query: 64 EYWRVWIVLAIASTLGAVTAGIFFNQQKLT--WRKVGLFAFIVGLLLILFTLDLSSRLWL 121 E W A + + A A F + L WR +VG+L +L Sbjct: 87 EGWSG----ACWAFVNAKFAQFLFGRYPLDERWRPA-----LVGILFVL----------- 126 Query: 122 LLTAVLLIPGFLLGSRLTNLVAPWLSLIWLLSFPII--LWLIGGGFGLRPVSSNLWNGLL 179 LL+P + L A L+ L++ PI+ + L GG FGL V + LW GL+ Sbjct: 127 -----LLVPMLIPRIPYKGLNA----LLLLVALPILSAILLPGGWFGLTYVETPLWGGLM 177 Query: 180 LTLLMAAISIVLSFPIGVLLALGRTSNLPVVRWFSILYIEIVRGVPLIGILFLAQVMLPL 239 +TL+++ + I +S P+G+LLALGR SN+PV++ ++IE++RGVPLI +LF+A VMLPL Sbjct: 178 VTLVLSFVGIAVSLPLGILLALGRRSNMPVIKMLCTVFIEVIRGVPLITVLFMASVMLPL 237 Query: 240 FFAADVRLDRVLRAIAGLVLFSAAYMAENVRGGLQAVSRGQVEAAKALGLNTFFVVLLIV 299 F V D+ LRA+ G+ LF++AYMAE VRGGLQA+ +GQ E A +LGL+ + + IV Sbjct: 238 FLPQGVTFDKFLRALIGVSLFASAYMAEVVRGGLQAIPKGQYEGADSLGLSFWQKMGFIV 297 Query: 300 LPQALRAVIPALVGQFIGLFKDTSLLSLVGLVELTGIARSILAQPQFIGRYAEV--YLFI 357 LPQAL+ VIP +V FIGLFKDTSL+S++G+ +L GI R + + + +F Sbjct: 298 LPQALKLVIPGIVNTFIGLFKDTSLVSIIGMFDLLGIVRLNFSDTNWATAVTPLTGLIFA 357 Query: 358 GLIYWLFCYSMSLASRRLERQLN 380 G ++WLFC+ MS S +ER L+ Sbjct: 358 GFVFWLFCFGMSRYSGFMERLLD 380 Lambda K H 0.332 0.145 0.452 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: 521 Number of extensions: 26 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: 381 Length of database: 384 Length adjustment: 30 Effective length of query: 351 Effective length of database: 354 Effective search space: 124254 Effective search space used: 124254 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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