Align D-serine/D-alanine/glycine transporter (characterized, see rationale)
to candidate PP_0927 PP_0927 aromatic amino acid transport protein
Query= uniprot:A0A0C4YRF7 (472 letters) >FitnessBrowser__Putida:PP_0927 Length = 453 Score = 412 bits (1059), Expect = e-119 Identities = 200/443 (45%), Positives = 295/443 (66%), Gaps = 3/443 (0%) Query: 19 LHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFFIMRALGELL 78 L RGLK+RHIQ+IA+GGAIG GLFLG + I +AGP ++L YAI G+ F IMR LGE++ Sbjct: 10 LQRGLKNRHIQLIALGGAIGTGLFLGIAQTIQLAGPSVLLGYAIAGLMAFLIMRQLGEMV 69 Query: 79 LYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWFPDVPQWIP 138 + PV+GSF+ +A ++ FAGF +GW+YW ++V+ GMAE+TAV +YV YW+PD P W Sbjct: 70 VEEPVAGSFSHFAHQYWSEFAGFVSGWNYWVVYVLVGMAELTAVGIYVQYWWPDFPTWAT 129 Query: 139 ALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFGVTPLGPTASFSN 198 A V+ L+N V V+GE+EFWFAL+KVV IV+MI G ++ G GP AS +N Sbjct: 130 AAIFFVVINLINLTQVKVYGEMEFWFALVKVVAIVSMIGFGAWLL--GSGHGGPDASVAN 187 Query: 199 LWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNGVVWRILIF 258 LW +GGF P G G+V+ L ++MF++ G+EL+G+TA EA NP + +P ATN VV+RILIF Sbjct: 188 LWQYGGFFPNGVTGLVMALAVIMFSFGGLELVGITAAEADNPRESIPKATNQVVYRILIF 247 Query: 259 YVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVNLVVITAAASSCNSGIFSTG 318 Y+GAL ++++L PW ++ G SPFV +F + A I+N+VV+TAA S NS +++ Sbjct: 248 YIGALAVLLSLYPWQKVVQGGSPFVMIFHELDSDLVATILNIVVLTAALSVYNSCVYANS 307 Query: 319 RMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLLNYIVPEQVFVWVTSISLV 378 RML+ LA G APR +VS VP A+ SA G+ VL+NY++P F + ++++ Sbjct: 308 RMLFGLASQGDAPRQLLKVSRSGVPLTALAVSAFATGLCVLINYLMPGGAFGLLMALAVS 367 Query: 379 GSLWTWSIIMIAHLGYRKAIAAGRVKAVAFRMPGAPYANWLVVAFMIAVAVLLSLDPGTR 438 + W+ I I HL +RKA A + ++ G P N+L +AF++ + V++ L P R Sbjct: 368 ALVINWASISITHLKFRKAKLAAGITPF-YKSLGHPLTNYLCLAFIVLILVVMYLTPPIR 426 Query: 439 VALYVAPVWFALLGIGYRFTKSR 461 +++ + P W A+L + ++ K+R Sbjct: 427 ISVMLIPAWIAVLWVAFKLKKAR 449 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: 716 Number of extensions: 38 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: 453 Length adjustment: 33 Effective length of query: 439 Effective length of database: 420 Effective search space: 184380 Effective search space used: 184380 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