Align Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale)
to candidate H281DRAFT_02405 H281DRAFT_02405 amino acid/amide ABC transporter substrate-binding protein, HAAT family
Query= uniprot:G8ALJ3 (366 letters) >FitnessBrowser__Burk376:H281DRAFT_02405 Length = 382 Score = 216 bits (550), Expect = 8e-61 Identities = 131/366 (35%), Positives = 201/366 (54%), Gaps = 8/366 (2%) Query: 8 LVAVAATAMTASVAKAD-IAVATAGPITGQYATFGEQMKKGIEQAVADINAAGGVLGQK- 65 LVA + A TA+ D + + AGP+TG A +G+ + GI AV DINA V+G K Sbjct: 13 LVAAMSLAGTANAQSTDDVKIGFAGPMTGAQAHYGKDFQNGITLAVEDINATKPVIGGKP 72 Query: 66 --LKLEVGDDACDPKQAVAVANQLAKAGVKFVAGHFCSGSSIPASQVYAEEGVLQISPAS 123 L+ DD DP+ VA +L G+K + GHF SG++IPAS++YA G+ +I+ A Sbjct: 73 VRFVLDSADDQADPRTGTTVAQKLVDDGIKGMLGHFNSGTTIPASRIYANAGIPEIAMA- 131 Query: 124 TNPKLTEQNLKNVFRVCGRDDQQGQIAGKYLLENYKGKNVAILHDKSAYGKGLADETQKA 183 T P+ T+Q K FR+ D QQG +AG + ++ K + I+ D++AYG+GLAD+ +KA Sbjct: 132 TAPEYTQQGFKTTFRMMTSDTQQGSVAGTFAVKTLGVKKIVIVDDRTAYGQGLADQFEKA 191 Query: 184 LNAGGQKEKIYEAYTAGEKDYSALVSKLKQEAVDVVYVGGYHTEAGLLARQMKDQGLNAP 243 A G E D+ ++++KLK D++Y GG ++A + +QMK G+ AP Sbjct: 192 AKAAGGTIVDREYTNDKAVDFKSILTKLKAANPDLIYYGGADSQAAPMVKQMKALGIKAP 251 Query: 244 IVSGDALVTNEYWAITGPAGENTMMTFGPDP-REMPEAKEAVEKFRKAGYEP-EGYTLYT 301 ++ G+ + T + I G A T+ + P EMP K+ V K++K E + Y+ Y Sbjct: 252 LMGGEMVHTPTFIQIAGDAANGTVASLAGLPLEEMPGGKDYVAKYKKRFNEDVQTYSPYA 311 Query: 302 YAALQIWAEAAKQANSTDSAKIADVLRKNSYNTVI-GKIGFDAKGDVTSPAYVWYRWNNG 360 Y A K+ANSTD AK VL K S V + +DAKGD+ + Y+ +G Sbjct: 312 YDGAMAMFAAMKKANSTDPAKYLPVLAKTSMPAVTSSNLSYDAKGDLKNGGITLYKVVDG 371 Query: 361 QYAQVK 366 ++ ++ Sbjct: 372 KWTTLQ 377 Lambda K H 0.312 0.129 0.366 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: 332 Number of extensions: 17 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 366 Length of database: 382 Length adjustment: 30 Effective length of query: 336 Effective length of database: 352 Effective search space: 118272 Effective search space used: 118272 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (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