Align NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate GFF2244 HP15_2194 amino acid ABC transporter, permease protein
Query= TCDB::Q8YPM7 (381 letters) >FitnessBrowser__Marino:GFF2244 Length = 362 Score = 245 bits (625), Expect = 2e-69 Identities = 141/392 (35%), Positives = 210/392 (53%), Gaps = 70/392 (17%) Query: 6 WLRKNLFSTWYNSLLTVICSALSLWLVQGIIVWATTKAQ---------------WAVIQV 50 W+R+NLFS W+N++LT+ + L + V ++ W A W I Sbjct: 19 WMRENLFSGWFNTVLTLGVAYLLVTSVGPLLNWFFLDANFVGSDPSACTGAGACWLFISQ 78 Query: 51 NLRLFLVGRFPQTEYWRVWIVLAIASTLGAVTAGIFFNQQKLTWRKVGLFAFIVGLLLIL 110 L F+ G +P WRV ++ Sbjct: 79 RLNFFIYGFYPDELQWRVDVMF-------------------------------------- 100 Query: 111 FTLDLSSRLWLLLTAVLLIPGFLLGSRLTNLVAPWLSLIWLLSFPIILWLI--GGGFGLR 168 LL AV +P F+ R WL L + PI+ + + GG FGL Sbjct: 101 -----------LLLAVSFVPQFI--ERFPG--RKWLGLFGIFGLPIVGYFLIPGGSFGLE 145 Query: 169 PVSSNLWNGLLLTLLMAAISIVLSFPIGVLLALGRTSNLPVVRWFSILYIEIVRGVPLIG 228 V S+ W GL+LTL++A I I+ S PIG+LLALGR S++P++R +++IE+ R VPLI Sbjct: 146 EVQSSKWGGLMLTLILAYIGIIASLPIGILLALGRRSDMPIIRGICVVFIEVWRAVPLIT 205 Query: 229 ILFLAQVMLPLFFAADVRLDRVLRAIAGLVLFSAAYMAENVRGGLQAVSRGQVEAAKALG 288 +LF+A VMLPLF V +++ RA+ G+ L+ +AYMAE +RGGLQA+ RGQ EAA ALG Sbjct: 206 VLFMASVMLPLFLPEGVNFEKLARALIGITLWQSAYMAEVIRGGLQAIPRGQYEAADALG 265 Query: 289 LNTFFVVLLIVLPQALRAVIPALVGQFIGLFKDTSLLSLVGLVELTGIARSILAQPQFIG 348 L + + L++LPQAL+ VIP +V FI LFKDT+L+ ++GL ++ G +S + P + Sbjct: 266 LGYWRKMGLVILPQALKMVIPGIVNTFISLFKDTTLVLIIGLFDILGTVQSTVTDPAWQN 325 Query: 349 RYAEVYLFIGLIYWLFCYSMSLASRRLERQLN 380 E Y+F+ +W+FC+ +S S+ LER+L+ Sbjct: 326 VAIEGYVFVAFCFWVFCFGISRYSQNLERKLD 357 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: 502 Number of extensions: 25 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: 362 Length adjustment: 30 Effective length of query: 351 Effective length of database: 332 Effective search space: 116532 Effective search space used: 116532 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: 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