Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate H281DRAFT_04061 H281DRAFT_04061 amino acid/amide ABC transporter membrane protein 2, HAAT family
Query= uniprot:A0A165KER0 (358 letters) >FitnessBrowser__Burk376:H281DRAFT_04061 Length = 389 Score = 448 bits (1152), Expect = e-130 Identities = 227/353 (64%), Positives = 276/353 (78%), Gaps = 3/353 (0%) Query: 1 MKNTKTNWIIGAVALLVLPLILQSFG-NAWVRIADLALLYVLLALGLNIVVGYAGLLDLG 59 + T T II A ++ P+I+ + G N WVR+ D A+LYV+LALGLN+VVG+AGLLDLG Sbjct: 19 LAKTLTVGIITAFFVIAAPMIIGTAGGNYWVRVLDFAMLYVMLALGLNVVVGFAGLLDLG 78 Query: 60 YVAFYAVGAYLFALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAP 119 Y+AFYAVGAY AL++SPHL F A + PNGLH I++P A +AAFFG +LGAP Sbjct: 79 YIAFYAVGAYTAALLSSPHLTSQFEWIAHLAPNGLHVPFLIIVPCAMAVAAFFGVILGAP 138 Query: 120 TLKLRGDYLAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVF 179 TL+LRGDYLAIVTLGFGEI+RIFLNNLD PVN+TNGPKG+ IDSV + L + +F Sbjct: 139 TLRLRGDYLAIVTLGFGEIVRIFLNNLDRPVNITNGPKGITGIDSVHLGDFSLAQTHSLF 198 Query: 180 GFDINSVTLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLL 239 GF SV YYYLF++ ++ + +C RLQ SRIGRAW AIREDEIAAKAMGINTRN+KLL Sbjct: 199 GFQFPSVYSYYYLFVLAALLVIWVCTRLQHSRIGRAWAAIREDEIAAKAMGINTRNVKLL 258 Query: 240 AFGMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSA 299 AF MGASFGG+SGAMFGAFQGFVSPESF+L ES++++A VVLGG+GHIPGVILGAVLL+ Sbjct: 259 AFAMGASFGGLSGAMFGAFQGFVSPESFTLPESIVVLACVVLGGMGHIPGVILGAVLLAV 318 Query: 300 LPEVLRYVAGPLQAMTDGR--LDSAILRQLLIALAMIIIMLLRPRGLWPSPEH 350 LPE LR GPLQ M G +D+ ++RQL+ ALAM++IML R GLWPSP+H Sbjct: 319 LPEFLRSTMGPLQHMLFGHEIVDTEVIRQLVYALAMVLIMLYRSEGLWPSPKH 371 Lambda K H 0.328 0.144 0.430 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: 449 Number of extensions: 16 Number of successful extensions: 3 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: 358 Length of database: 389 Length adjustment: 30 Effective length of query: 328 Effective length of database: 359 Effective search space: 117752 Effective search space used: 117752 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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