Align D-serine/D-alanine/glycine transporter (characterized, see rationale)
to candidate RR42_RS33495 RR42_RS33495 aromatic amino acid transporter
Query= uniprot:A0A0C4YRF7 (472 letters) >FitnessBrowser__Cup4G11:RR42_RS33495 Length = 465 Score = 412 bits (1060), Expect = e-120 Identities = 195/448 (43%), Positives = 297/448 (66%), Gaps = 5/448 (1%) Query: 19 LHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFFIMRALGELL 78 L RGLK+RHIQ+IA+GGAIG GLFLG + I +AGP ++L YA+ G+ FFIMR LGE++ Sbjct: 13 LKRGLKNRHIQLIALGGAIGTGLFLGIAQTIKMAGPSVLLGYAVAGIIAFFIMRQLGEMV 72 Query: 79 LYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWFPDVPQWIP 138 + PV+GSF+ +A ++ G FAGF +GW+YW ++++ MAE++AV +YV YW+P +P W Sbjct: 73 VDEPVAGSFSHFANKYCGSFAGFMSGWNYWVLYILVSMAELSAVGIYVQYWWPHIPTWAS 132 Query: 139 ALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFGVTPLGPTASFSN 198 AL ++ +N +V FGE+EFWF+++KV+ IV MIV G ++ G GP AS SN Sbjct: 133 ALGFFLLINAINLTSVKSFGEMEFWFSIVKVLAIVGMIVFGGYLLASGTA--GPQASVSN 190 Query: 199 LWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNGVVWRILIF 258 LW HGGF P G G+V+ + ++MF++ G+EL+G+TA EA PEK +P ATN V++RILIF Sbjct: 191 LWQHGGFFPNGISGLVMAMAVIMFSFGGLELVGITAAEADEPEKTIPKATNQVIYRILIF 250 Query: 259 YVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVNLVVITAAASSCNSGIFSTG 318 YVGAL ++++L PW ++ G SPFV +F + A ++N VV+TAA S NSG++ Sbjct: 251 YVGALGVLLSLYPWEKVVTGGSPFVLIFHAMNSDIVATVLNAVVLTAALSVYNSGVYCNS 310 Query: 319 RMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLLNYIVPEQVFVWVTSISLV 378 RML+ LA+ G AP+A +V+ + +P A+ SA V++NY +P + F + + + Sbjct: 311 RMLFGLAKQGNAPKALLKVNKRGIPLAALGVSALATAACVVINYFMPGEAFELLMGLVVS 370 Query: 379 GSLWTWSIIMIAHLGYRK-AIAAGRVKAVAFRMPGAPYANWLVVAFMIAVAVLLSLDPGT 437 + W++I I HL +R+ AAG + F+ G P N++ +AF+ + ++ L PG Sbjct: 371 ALIINWAMISIIHLKFRRDKRAAG--QETRFKSLGYPLTNYVCLAFLAGILYVMYLTPGL 428 Query: 438 RVALYVAPVWFALLGIGYRFTKSRALLE 465 R+++Y+ P W A+LG+ YR + + E Sbjct: 429 RISVYLIPAWLAVLGLSYRLRQKQKRAE 456 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: 711 Number of extensions: 33 Number of successful extensions: 3 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: 465 Length adjustment: 33 Effective length of query: 439 Effective length of database: 432 Effective search space: 189648 Effective search space used: 189648 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