Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 1 (characterized)
to candidate AZOBR_RS08660 AZOBR_RS08660 ABC transporter permease
Query= reanno::Smeli:SMc02119 (397 letters) >FitnessBrowser__azobra:AZOBR_RS08660 Length = 399 Score = 384 bits (985), Expect = e-111 Identities = 194/379 (51%), Positives = 264/379 (69%) Query: 19 INDPQVRGIFYQAITIIILAALIYWIVDNTVDNLRRANIASGYDFVRSRAGFDVGQSLIS 78 ++DP VR +FYQ + + I+ A+ ++++ NT+DNL + +IA+G+ F+ A F +G+SLI Sbjct: 21 LSDPTVRAVFYQVLVVGIVIAVGWFLIHNTLDNLSKRSIATGFGFLDREASFGIGESLID 80 Query: 79 FTSDSTYGRALLVGFINTLLVAITGIITATIIGFIVGIGRLSHNWIIAKLSLAYVEVFRN 138 + +YGRA LVG +NTL V+I G++ AT++G ++G+ RLS NW+IAKL+ YVE+ RN Sbjct: 81 YHPRDSYGRAFLVGVLNTLKVSIIGVVLATVLGTLIGVARLSSNWLIAKLASTYVEIVRN 140 Query: 139 IPPLLVIFFWYSGVLSILPQARDALALPFDIFLSNRGVAFPRPIAEEGAEYTLLAFVIAV 198 IPPLL +FFWY+ V +P R AL +FLS RG+ P P A+ A IAV Sbjct: 141 IPPLLQLFFWYALVSESMPPVRQALNPIPGVFLSQRGLFVPVPSADPVWGTMGFALAIAV 200 Query: 199 AASVFFARYARKRQLATGERLPVLWTVLGLIIGLPLVTFLVTGAPITFDIPVAGKFNLTG 258 +F R+A+ RQ TG+ P+ L L+IGLPL+ ++ GAP D+P FN G Sbjct: 201 IGVIFLRRWAKARQERTGQPFPIGTASLSLLIGLPLIAYIAGGAPTALDVPKLQGFNFVG 260 Query: 259 GSVVGPEFMSLFLALSFYTAAFIAEIVRAGIRGVSKGQTEAAHALGIRPALTTRLVVVPQ 318 G V+ PEF ++ + L YTAAFIAE+VR+GI V+ GQTEAA ALGI T RLVV+PQ Sbjct: 261 GVVLTPEFFAILVGLVVYTAAFIAEVVRSGILAVNWGQTEAARALGIDSGKTLRLVVLPQ 320 Query: 319 AMRIIIPPLTSQYLNLTKNSSLAVAIGYADLVAVGGTILNQTGQSIEIVSIWLIVYLSLS 378 A+R+I+PPLTSQYLNLTKNSSLA+AIGY DLV++ T LNQTGQ+IE V++ + YL +S Sbjct: 321 ALRVIVPPLTSQYLNLTKNSSLALAIGYPDLVSIANTTLNQTGQAIEGVAMIMGTYLVIS 380 Query: 379 LATSLFMNWYNARMALVER 397 L S+FMNWYN R+ALVER Sbjct: 381 LGISIFMNWYNKRIALVER 399 Lambda K H 0.327 0.141 0.412 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: 465 Number of extensions: 13 Number of successful extensions: 2 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: 397 Length of database: 399 Length adjustment: 31 Effective length of query: 366 Effective length of database: 368 Effective search space: 134688 Effective search space used: 134688 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