Align Basic amino acid uptake transporter, BgtAB (characterized)
to candidate WP_083710231.1 BW971_RS16650 ABC transporter permease subunit
Query= TCDB::Q8YSA2 (501 letters) >NCBI__GCF_900156495.1:WP_083710231.1 Length = 589 Score = 195 bits (496), Expect = 3e-54 Identities = 151/475 (31%), Positives = 239/475 (50%), Gaps = 47/475 (9%) Query: 51 GNLQGFSIDLMNAIASAANLKVNFQSLPFDGIIPALQSRTVDAAISSITITAERAETVAF 110 G+ GF +L+ AIA+ L++ F F G++ + + D SSIT T ER +TV F Sbjct: 94 GSFTGFDNELLKAIAAKLKLRIQFSGTEFSGLLSQVANNRFDVGSSSITTTDERRKTVDF 153 Query: 111 SRPYFKAGLAIAIRSSNEDITGFDSL-KNKKIAVQIGTTGAGKAKSIPGAQIRSFDSAPL 169 + Y G + + I GF +L K+ +I V GT ++ + F Sbjct: 154 TNGY-DFGYFSLVAPAGGSIKGFANLSKSTRIGVVQGTVQDDYVQNTLHLEAVKFPDYAT 212 Query: 170 ALQELLNNNVDAVINDAPVTLYAINTGNLQGIKVVEKLLT-EEYYGIATAQNSPYLA-LI 227 A L + +DA + + AI G+ G + E + + A +N P L + Sbjct: 213 AYANLKSGQIDAWVAPSQQAEGAIRPGD--GTTIAENTFSVNNFVAWAVGKNKPKLTEAL 270 Query: 228 NDGLNRVLADGSYSQIYQKWFKVE-------------PPSLPDKSLY--ENQTNTHKSG- 271 N GL+ ++ADG+Y+++Y W E P LPD + EN+ K+ Sbjct: 271 NSGLDAIIADGTYAKLYTDWVPRELPKGWKPGSKAAPAPRLPDIAAIARENEAKAPKTDN 330 Query: 272 ----------------SINLILQFLPTLLQGALV-TIQLTILSTVLGLICGTLIALTRLS 314 S +L + LP LL+ L T+ L+++S VLG I G ++A+ +S Sbjct: 331 AAKPKSTLQQLGTTFFSWDLYAKALPDLLKTGLPNTLILSVVSGVLGTILGMVLAVAGIS 390 Query: 315 QFTPARLFARAYVDFFRGTPLLVQIFMIYFGIPALAQQLGFTFNFDRWVAGVIALSVNAA 374 + R AR Y D FRG P +V I ++ GI + + L T N W+ G +AL++ AA Sbjct: 391 RSRWLRWPARIYTDIFRGLPAVVVILVVGLGIGPVVKNL--TGNNPYWL-GAVALALLAA 447 Query: 375 AYIAEIVRAGIQSIETGQTEAAKSLGLNPWLTMRLVIFPQAFRRMLPPLGNEFISLLKDT 434 AYI EI R+GIQS++ GQ EA++++G + +MRLV+ PQ RR+LP L N+FISL+KD+ Sbjct: 448 AYIGEIFRSGIQSVDDGQLEASRAIGFSYRQSMRLVVVPQGVRRVLPALMNQFISLIKDS 507 Query: 435 SLVAVIGF----EELFRKGQLIVADNYRAFEIYAAVAIVYLCLTLLASQVLSRLE 485 SLV +G ELF G+ + A + AA ++YL LT+ + +++ ++ Sbjct: 508 SLVYFLGLLASQRELFAVGRDLNAQTGNLSPLVAA-GLIYLVLTIPLTHLVNYID 561 Lambda K H 0.323 0.137 0.394 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: 662 Number of extensions: 40 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: 501 Length of database: 589 Length adjustment: 35 Effective length of query: 466 Effective length of database: 554 Effective search space: 258164 Effective search space used: 258164 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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