Align Basic amino acid uptake transporter, BgtAB (characterized)
to candidate WP_089136315.1 CES79_RS03445 ABC transporter permease subunit
Query= TCDB::Q8YSA2 (501 letters) >NCBI__GCF_002217945.1:WP_089136315.1 Length = 479 Score = 244 bits (624), Expect = 4e-69 Identities = 165/486 (33%), Positives = 254/486 (52%), Gaps = 35/486 (7%) Query: 15 LICLFLT-GCSGNLSQGKTL-RIATEPAFPPFEFTAQGGNLQGFSIDLMNAIASAANLKV 72 LI +F+T G ++ T ++AT+ FPPFEF G IDL++AIA KV Sbjct: 15 LIAMFITFGLGATPAKATTTYQVATDSTFPPFEFANSHNKYVGIDIDLLHAIAKDQGFKV 74 Query: 73 NFQSLPFDGIIPALQSRTVDAAISSITITAERAETVAFSRPYFKAGLAIAIRSSNEDITG 132 N + F+ + ++QS D I+ ++IT ER T FS+PYF +G+ +A + N IT Sbjct: 75 NIKPTSFNSAVQSVQSGQADGVIAGMSITKEREATFDFSKPYFMSGVVMAAKP-NGKITK 133 Query: 133 FDSLKNKKIAVQIGTTGAGKAKSIP---GAQIRSFDSAPLALQELLNNNVDAVINDAPVT 189 L+ K++AV+ GT+GA A+SI G +I +FD + Q++L N A D+PV Sbjct: 134 LSQLRGKRVAVKTGTSGAQYAQSIHKKYGFRIVTFDESNDMYQDVLTGNSAACFEDSPVM 193 Query: 190 LYAINTGNLQGIKVVEKLLTEEYYGIATAQ--NSPYLALINDGLNRVLADGSYSQIYQKW 247 YA+ G +K+ K YG A + N L + N+GL + ++G Y++I + + Sbjct: 194 KYAVRQGTK--LKIYTKPTLNGPYGFAVKKGHNKKLLRMFNNGLADLKSNGEYARITRHY 251 Query: 248 FKVEPPSLPDKSLYENQTNTHKSGSINLILQFLPTLLQGALVTIQLTILSTVLGLICGTL 307 + S T + L+ Q LL G T+ LT+++ + G + Sbjct: 252 LGAKGSS----------DTTSDRTFLGLLKQNKGALLNGFEQTVWLTVVAIFFATLFGVI 301 Query: 308 IALTRLSQFTPARLF---ARAYVDFFRGTPLLVQIFMIYFGIPALAQQLGFTFNFDRWVA 364 + L + P + F + + FRG PLLV IY GIP+L +VA Sbjct: 302 VGLLGV---VPNKFFNGLSTTLIYIFRGLPLLVLALFIYTGIPSLTGS-----KIPAFVA 353 Query: 365 GVIALSVNAAAYIAEIVRAGIQSIETGQTEAAKSLGLNPWLTMRLVIFPQAFRRMLPPLG 424 G I L N AYIA V+ GI +++ GQ EAA+SLGL +MR +I PQ R M+P Sbjct: 354 GTITLMFNEGAYIAAFVKGGINAVDDGQMEAARSLGLPFGKSMRRIILPQGIRIMIPSFI 413 Query: 425 NEFISLLKDTSLVAVIGFEELFRKGQLIVADNYRAFEIYAAVAIVYL----CLTLLASQV 480 N+FI LKDTS++++IG EL + G++I+A N F+++ +AI+YL LT L++ V Sbjct: 414 NQFIITLKDTSILSIIGIIELTQTGKIIIARNLEGFKVWTIIAIIYLIVITLLTWLSNWV 473 Query: 481 LSRLEM 486 R+ + Sbjct: 474 ERRIRL 479 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: 562 Number of extensions: 34 Number of successful extensions: 5 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: 479 Length adjustment: 34 Effective length of query: 467 Effective length of database: 445 Effective search space: 207815 Effective search space used: 207815 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