Align NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate AO353_04605 AO353_04605 amino acid ABC transporter permease
Query= TCDB::Q8YPM7 (381 letters) >FitnessBrowser__pseudo3_N2E3:AO353_04605 Length = 365 Score = 245 bits (626), Expect = 1e-69 Identities = 146/379 (38%), Positives = 220/379 (58%), Gaps = 40/379 (10%) Query: 4 LTWLRKNLFSTWYNSLLTVICSALSLWLVQGIIVWATTKAQWAVIQVNLRLFLVGRFPQT 63 L W+R+++FS+W N+LLT+ L +V I+ WA A W R T Sbjct: 20 LAWMREHMFSSWINTLLTLFAFYLIYLVVPPILHWAILDANWVGTT---------RADCT 70 Query: 64 EYWRVWIVLAIASTLGAVTAGIFFNQQKLTWRKVGLFAFIVGLLLILFTLDLSSRLWLLL 123 + W+ I G G + +L WR +DL+ +WL + Sbjct: 71 KEGACWVF--IQQRFGQFMYGYY--PPELRWR-----------------VDLT--VWLAV 107 Query: 124 TAVLLIPGFLLGSRLTNLVAPWLSLIWLLSFPIILWLI--GGGFGLRPVSSNLWNGLLLT 181 V P F+ SR LS +L+ +PI+ +++ G GL V+++ W GL+LT Sbjct: 108 IGVA--PLFI--SRFPRKAVYGLS--FLVLYPIVAYILLHGDILGLTNVATSQWGGLMLT 161 Query: 182 LLMAAISIVLSFPIGVLLALGRTSNLPVVRWFSILYIEIVRGVPLIGILFLAQVMLPLFF 241 L++A + IV + P+G++LALGR SNLP +R + +IE RGVPLI +LF++ VMLPLF Sbjct: 162 LVIATVGIVGALPLGIMLALGRRSNLPAIRVVCVTFIEFWRGVPLITVLFMSSVMLPLFL 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: 492 Number of extensions: 22 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