Align D-serine/D-alanine/glycine transporter (characterized, see rationale)
to candidate AO353_05965 AO353_05965 aromatic amino acid transporter
Query= uniprot:A0A0C4YRF7 (472 letters) >FitnessBrowser__pseudo3_N2E3:AO353_05965 Length = 466 Score = 410 bits (1053), Expect = e-119 Identities = 201/452 (44%), Positives = 297/452 (65%), Gaps = 12/452 (2%) Query: 19 LHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFFIMRALGELL 78 L RGLK+RHIQ+IA+GGAIG GLFLG+ + AGP ++L YAI G F IMR LGE++ Sbjct: 11 LKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAFLIMRQLGEMI 70 Query: 79 LYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWFPDVPQWIP 138 + PV+GSF+ +A + G FAGF +GW+YW ++V+ GMAE+TAV YV +W+P+VP W+ Sbjct: 71 VEEPVAGSFSHFAHNYWGSFAGFLSGWNYWVLYVLVGMAELTAVGKYVQFWWPEVPTWVS 130 Query: 139 ALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFGVTPLGPTASFSN 198 A ++ L+N + V VFGE+EFWFA+IKVV I+ MI +G ++ G GP AS SN Sbjct: 131 AAVFFVLVNLINTMNVKVFGEMEFWFAIIKVVAIIGMIALGCYMLVSGTG--GPQASVSN 188 Query: 199 LWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNGVVWRILIF 258 LW+HGGF P GT G+++ + +MF++ G+EL+G+TA EA P KV+P A N VV+R+LIF Sbjct: 189 LWSHGGFFPNGTNGLLMAMAFIMFSFGGLELVGITAAEASEPRKVIPKAINQVVYRVLIF 248 Query: 259 YVGALIIMMALVPWNELKPGV---------SPFVYVFERIGVPGAAAIVNLVVITAAASS 309 YVGAL ++++L PW++L + SPFV +F IG AA I+N VV+TAA S Sbjct: 249 YVGALTVLLSLYPWDQLLQTLGASGDAYSGSPFVQIFALIGSNTAAQILNFVVLTAALSV 308 Query: 310 CNSGIFSTGRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLLNYIVPEQVF 369 NSG++ RMLY LA+ G AP++ +++ + VP A+ SA + + V++NY+ P + Sbjct: 309 YNSGVYCNSRMLYGLAEQGDAPKSLMKLNKQGVPLRALGISALITMLCVVVNYVAPNEAL 368 Query: 370 VWVTSISLVGSLWTWSIIMIAHLGYRKAIAAGRVKAVAFRMPGAPYANWLVVAFMIAVAV 429 + ++ + + W++I + HL +RKA+ R F+ +PY N+L +AFM + Sbjct: 369 ELLFALVVASLMINWAMISLTHLKFRKAMGQ-RGIVPGFKAFWSPYTNYLCLAFMAMIIY 427 Query: 430 LLSLDPGTRVALYVAPVWFALLGIGYRFTKSR 461 ++ L PG R ++Y PVW +L + YR +R Sbjct: 428 VMLLIPGVRASVYAIPVWVLILFVFYRIRVAR 459 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: 743 Number of extensions: 40 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: 466 Length adjustment: 33 Effective length of query: 439 Effective length of database: 433 Effective search space: 190087 Effective search space used: 190087 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