Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate AZOBR_RS08660 AZOBR_RS08660 ABC transporter permease
Query= uniprot:Q31RP0 (377 letters) >FitnessBrowser__azobra:AZOBR_RS08660 Length = 399 Score = 271 bits (694), Expect = 2e-77 Identities = 158/365 (43%), Positives = 230/365 (63%), Gaps = 16/365 (4%) Query: 22 WQLLVLLVVGLGAIWLVDNLVYNLSQRGLSLSFDWLDQSAGFNIGESAIAYRTADSYARA 81 +Q+LV+ +V +L+ N + NLS+R ++ F +LD+ A F IGES I Y DSY RA Sbjct: 31 YQVLVVGIVIAVGWFLIHNTLDNLSKRSIATGFGFLDREASFGIGESLIDYHPRDSYGRA 90 Query: 82 LVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVRNTPLLLQLIVW 141 +VG++N+L+V IG++L TV+GTL GVA S NWL+ +L+ YV +VRN P LLQL W Sbjct: 91 FLVGVLNTLKVSIIGVVLATVLGTLIGVARLSSNWLIAKLASTYVEIVRNIPPLLQLFFW 150 Query: 142 YFPILLSLPAAQQPWHWLGSLYLSKQGIYLPWPQ------TPGWLVVILAIALVLFVSWL 195 Y + S+P +Q + + ++LS++G+++P P T G+ + I I ++ W Sbjct: 151 YALVSESMPPVRQALNPIPGVFLSQRGLFVPVPSADPVWGTMGFALAIAVIGVIFLRRWA 210 Query: 196 AQRQ-RSPRDWRWLYGAIAVVTVLMLL--------TQLSWPQQLQPGQIRGGLRLSLEFT 246 RQ R+ + + +++++ L L+ T L P+ LQ GG+ L+ EF Sbjct: 211 KARQERTGQPFPIGTASLSLLIGLPLIAYIAGGAPTALDVPK-LQGFNFVGGVVLTPEFF 269 Query: 247 ALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQIVVPQALRVIVPSL 306 A+L+GLV YT AFI E++R GIL+V GQ EAA ALG+ +TL +V+PQALRVIVP L Sbjct: 270 AILVGLVVYTAAFIAEVVRSGILAVNWGQTEAARALGIDSGKTLRLVVLPQALRVIVPPL 329 Query: 307 NSQYVGFAKNSSLAIAVGYPDLYATAQTTLNQTGRPVEVFLILMLTYLAINAVISAGMNG 366 SQY+ KNSSLA+A+GYPDL + A TTLNQTG+ +E ++M TYL I+ IS MN Sbjct: 330 TSQYLNLTKNSSLALAIGYPDLVSIANTTLNQTGQAIEGVAMIMGTYLVISLGISIFMNW 389 Query: 367 LQQRL 371 +R+ Sbjct: 390 YNKRI 394 Lambda K H 0.326 0.140 0.445 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: 406 Number of extensions: 15 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: 377 Length of database: 399 Length adjustment: 30 Effective length of query: 347 Effective length of database: 369 Effective search space: 128043 Effective search space used: 128043 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