Align D-serine/D-alanine/glycine transporter (characterized, see rationale)
to candidate GFF4342 PS417_22235 aromatic amino acid transporter
Query= uniprot:A0A0C4YRF7 (472 letters) >FitnessBrowser__WCS417:GFF4342 Length = 473 Score = 397 bits (1019), Expect = e-115 Identities = 193/455 (42%), Positives = 294/455 (64%), Gaps = 14/455 (3%) Query: 18 DLHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFFIMRALGEL 77 +L RGLK+RHIQ+IA+GGAIG GLFLG+ + AGP ++L YAI G F IMR LGE+ Sbjct: 10 ELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAFMIMRQLGEM 69 Query: 78 LLYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWFPDVPQWI 137 ++ PV+GSF+ +A ++ G FAGF +GW+ W ++++ GM+E+TAV YVHYW+P++P W+ Sbjct: 70 IVEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYVHYWWPEIPTWV 129 Query: 138 PALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFGVTPLGPTASFS 197 A A ++ L+N V VFGE EFWFA+IKVV IV MI +G ++ G GP AS + Sbjct: 130 SAAAFFVLINLINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGTG--GPQASVT 187 Query: 198 NLWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNGVVWRILI 257 NLW HGGF P G G+V+ + I+MF++ G+E++G TA EA P V+P A N V++RILI Sbjct: 188 NLWEHGGFFPHGVGGLVMAMAIIMFSFGGLEMLGFTAAEADKPRTVIPKAINQVIYRILI 247 Query: 258 FYVGALIIMMALVPWNELKPGV---------SPFVYVFERIGVPGAAAIVNLVVITAAAS 308 FY+GAL+++++L PW+ L + SPFV VF +G AA I+N VV+TAA S Sbjct: 248 FYIGALVVLLSLTPWDSLLATLNASGDAYSGSPFVQVFSMLGSDTAAHILNFVVLTAALS 307 Query: 309 SCNSGIFSTGRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLLNYIVPEQV 368 NSG + RML +A+ G AP+A ++ + VP +I SAA+ + VL+NY++P+ Sbjct: 308 VYNSGTYCNSRMLLGMAEQGDAPKALAKIDKRGVPVRSILASAAITLVAVLMNYLIPQHA 367 Query: 369 FVWVTSISLVGSLWTWSIIMIAHLGYRKAI-AAGRVKAVAFRMPGAPYANWLVVAFMIAV 427 + S+ + + W++I +H +R+ + G+V F+ PY N++ +AF++ + Sbjct: 368 LELLMSLVVATLVINWAMISFSHFKFRQHMNRTGQVP--LFKALWYPYGNYVCLAFVVFI 425 Query: 428 AVLLSLDPGTRVALYVAPVWFALLGIGYRFTKSRA 462 V++ + PG +V+++ PVW + + Y R+ Sbjct: 426 LVIMLMIPGIQVSVFAIPVWVMFMAVCYGIKNKRS 460 Lambda K H 0.328 0.142 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: 684 Number of extensions: 35 Number of successful extensions: 4 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: 472 Length of database: 473 Length adjustment: 33 Effective length of query: 439 Effective length of database: 440 Effective search space: 193160 Effective search space used: 193160 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 (21.8 bits) S2: 51 (24.3 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