Align D-serine/D-alanine/glycine transporter (characterized, see rationale)
to candidate BWI76_RS08745 BWI76_RS08745 proline-specific permease
Query= uniprot:A0A0C4YRF7 (472 letters) >FitnessBrowser__Koxy:BWI76_RS08745 Length = 459 Score = 426 bits (1095), Expect = e-124 Identities = 205/433 (47%), Positives = 292/433 (67%) Query: 19 LHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFFIMRALGELL 78 L RGL RHI+ IA+G AIG GLF G+ AI AGP ++L+Y IGG A+F +MRALGE+ Sbjct: 9 LLRGLNARHIRFIALGSAIGTGLFYGSASAIKAAGPAVLLAYLIGGAAVFIVMRALGEMA 68 Query: 79 LYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWFPDVPQWIP 138 + PVSGSF++YA +++GP AGF TGW+Y F V+ +A++TA +Y+ W+PDVP+WI Sbjct: 69 VRNPVSGSFSSYARQYLGPLAGFITGWTYTFEMVIVALADVTAFGIYMGLWYPDVPRWIW 128 Query: 139 ALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFGVTPLGPTASFSN 198 L+ + + +N +V VFGE+EFW +LIKVV I+AMIV G +IIFFG P N Sbjct: 129 VLSIIFFIGAMNLCSVRVFGEMEFWLSLIKVVAIIAMIVAGGSIIFFGFGNAFPATGLEN 188 Query: 199 LWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNGVVWRILIF 258 LW+HGGF P G G++ +L IVMFA+ GVE+IGVTA EA+NP+KV+P A N + RI++F Sbjct: 189 LWSHGGFAPNGWEGIIASLGIVMFAFGGVEIIGVTAAEAKNPQKVIPQAINTIPLRIVLF 248 Query: 259 YVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVNLVVITAAASSCNSGIFSTG 318 YV L I+MA+ PWN SPFV +F+ +G+P AA I+N++VI+A+ S+ NS IF G Sbjct: 249 YVCTLAILMAIFPWNSFGERGSPFVLIFDGLGIPAAATILNIIVISASISAINSDIFGAG 308 Query: 319 RMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLLNYIVPEQVFVWVTSISLV 378 RM+Y +A+ G AP++F R++S VP + + + V+LNY++PEQVFV + S++ Sbjct: 309 RMMYGMAKEGLAPKSFQRIASNGVPWMTVVVMGVALLAAVVLNYLMPEQVFVLIASLAAF 368 Query: 379 GSLWTWSIIMIAHLGYRKAIAAGRVKAVAFRMPGAPYANWLVVAFMIAVAVLLSLDPGTR 438 ++W W +I++AH R+ ++A +AF +P P A L + FM V +L + TR Sbjct: 369 ATVWVWVMILLAHFAMRRGLSAEERGNIAFPVPLWPVAPLLTLLFMGLVIAVLGMVEETR 428 Query: 439 VALYVAPVWFALL 451 +AL VW LL Sbjct: 429 IALIAGLVWLGLL 441 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: 759 Number of extensions: 43 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: 459 Length adjustment: 33 Effective length of query: 439 Effective length of database: 426 Effective search space: 187014 Effective search space used: 187014 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