Align NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate PfGW456L13_1700 Glutamate Aspartate transport system permease protein GltK (TC 3.A.1.3.4)
Query= TCDB::Q8YPM7 (381 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1700 Length = 365 Score = 249 bits (635), Expect = 1e-70 Identities = 144/379 (37%), Positives = 222/379 (58%), Gaps = 40/379 (10%) Query: 4 LTWLRKNLFSTWYNSLLTVICSALSLWLVQGIIVWATTKAQWAVIQVNLRLFLVGRFPQT 63 + W+R N+FS+W N+LLT+ L +V I+ QWA++ N Sbjct: 20 MAWMRANMFSSWLNTLLTLFAFYLIYLVVPPIL-------QWAILDAN------------ 60 Query: 64 EYWRVWIVLAIASTLGAVTAGIFFNQQKLTWRKVGLFAFIVGLLLILFTLDLSSRLWLLL 123 W+ + A +F Q + G F + ++ + +DL+ +WL + Sbjct: 61 -----WVGTSQADCTKEGACWVFIQQ------RFGQFMYGYYPPVLRWRVDLT--VWLAI 107 Query: 124 TAVLLIPGFLLGSRLTNLVAPWLSLIWLLSFPIILWLI--GGGFGLRPVSSNLWNGLLLT 181 V P F+ SR + LS +L+ +PII W + GG GL V+++ W GL+LT Sbjct: 108 VGVA--PLFI--SRFHHKAVYGLS--FLVLYPIIAWCLLHGGVLGLDAVATSQWGGLMLT 161 Query: 182 LLMAAISIVLSFPIGVLLALGRTSNLPVVRWFSILYIEIVRGVPLIGILFLAQVMLPLFF 241 L++A + I + P+G++LALGR SN+P +R + +IE RGVPLI +LF++ VMLPLF Sbjct: 162 LVIATVGIAGALPLGIVLALGRRSNMPAIRVVCVTFIEFWRGVPLITVLFMSSVMLPLFL 221 Query: 242 AADVRLDRVLRAIAGLVLFSAAYMAENVRGGLQAVSRGQVEAAKALGLNTFFVVLLIVLP 301 + D++LRA+ G++LF +AY+AE VRGGLQA+ +GQ EAA A+GL + + L++LP Sbjct: 222 PEGMNFDKLLRALIGVILFQSAYVAEVVRGGLQAIPKGQYEAAAAMGLGYWRSMGLVILP 281 Query: 302 QALRAVIPALVGQFIGLFKDTSLLSLVGLVELTGIARSILAQPQFIGRYAEVYLFIGLIY 361 QAL+ VIP +V FI LFKDTSL+ ++GL +L + A P+++G E Y+F L++ Sbjct: 282 QALKLVIPGIVNTFIALFKDTSLVIIIGLFDLLNSVKQAAADPKWLGMATEGYVFAALVF 341 Query: 362 WLFCYSMSLASRRLERQLN 380 W+FC+ MS S LER+L+ Sbjct: 342 WIFCFGMSRYSMHLERKLD 360 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: 489 Number of extensions: 23 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: 381 Length of database: 365 Length adjustment: 30 Effective length of query: 351 Effective length of database: 335 Effective search space: 117585 Effective search space used: 117585 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