Align Basic amino acid uptake transporter, BgtAB (characterized)
to candidate WP_049778262.1 MVAN_RS23625 glutamine ABC transporter permease
Query= TCDB::Q8YSA2 (501 letters) >NCBI__GCF_000015305.1:WP_049778262.1 Length = 468 Score = 295 bits (756), Expect = 2e-84 Identities = 176/471 (37%), Positives = 256/471 (54%), Gaps = 25/471 (5%) Query: 20 LTGCSGNLSQGKTLRIATEPAFPPFEFTAQGGNLQGFSIDLMNAIASAANLKVNFQSLPF 79 L G + +Q + IAT+ F PFEF GG L G +DL+ IA V+ + L F Sbjct: 13 LLGAATASAQEQNYVIATDTTFAPFEFQDAGGELVGIDMDLIREIAKDQGFTVDIRPLGF 72 Query: 80 DGIIPALQSRTVDAAISSITITAERAETVAFSRPYFKAGLAIAIRSSNEDITGFDSLKNK 139 D + A+Q+ I+ ++IT ER FS PYF++G+ +A+ SN+ I ++ L+ + Sbjct: 73 DAALQAVQANQAAGVIAGMSITDERKAVFDFSDPYFESGVQMAVLDSNDTIASYEDLRGQ 132 Query: 140 KIAVQIGTTGAGKAKSIP---GAQIRSFDSAPLALQELLNNNVDAVINDAPVTLYAINTG 196 ++AV+ GT GA A+SI G QI SF + +E+ N AV D PV LY I G Sbjct: 133 RVAVKNGTEGAEFAESIKDKYGFQIVSFADSASMFEEVKTGNSVAVFEDYPVLLYGIQQG 192 Query: 197 NLQGIKVVEKLLTEEYYGIAT--AQNSPYLALINDGLNRVLADGSYSQIYQKWFKVEPPS 254 N G K V YG A +N+ L N+GL + G Y I + + E Sbjct: 193 N--GFKTVTPKEQGSNYGFAVNKGRNAELLTKFNEGLKNLKESGRYDAIIESYLGEEAAE 250 Query: 255 LPDKSLYENQTNTHKSGSINLILQFLPTLLQGALVTIQLTILSTVLGLICGTLIALTRLS 314 D S + L+ P L++G +T+ LT++S + L+ G + L R+S Sbjct: 251 T-DNSFF------------GLLKSTFPILMEGLRLTLILTVVSIAIALVLGVMFGLFRVS 297 Query: 315 QFTPARLFARAYVDFFRGTPLLVQIFMIYFGIPALAQQLGFTFNFDRWVAGVIALSVNAA 374 + R YVD FRGTPLLVQ F IYFG+P+ F AG+I LS+NA Sbjct: 298 RSIWLRAIGTTYVDIFRGTPLLVQAFFIYFGVPS-----ALDFRMTALTAGIITLSLNAG 352 Query: 375 AYIAEIVRAGIQSIETGQTEAAKSLGLNPWLTMRLVIFPQAFRRMLPPLGNEFISLLKDT 434 AY+ EIVR GIQS++ GQ EAA+SLG+ TMR VI PQA R M+P N+F+ LKDT Sbjct: 353 AYMTEIVRGGIQSVDKGQMEAARSLGIGYLPTMRKVILPQAIRTMIPSYVNQFVITLKDT 412 Query: 435 SLVAVIGFEELFRKGQLIVADNYRAFEIYAAVAIVYLCLTLLASQVLSRLE 485 S+++VIG EL + G+LI+A NY++F ++ + ++Y + + +++ RLE Sbjct: 413 SILSVIGIAELTQTGRLIIARNYQSFTMWLIIGVIYFIVIMALTKLSDRLE 463 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: 517 Number of extensions: 22 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: 468 Length adjustment: 34 Effective length of query: 467 Effective length of database: 434 Effective search space: 202678 Effective search space used: 202678 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