Align D-serine/D-alanine/glycine transporter (characterized, see rationale)
to candidate BWI76_RS06245 BWI76_RS06245 proline-specific permease ProY
Query= uniprot:A0A0C4YRF7 (472 letters) >FitnessBrowser__Koxy:BWI76_RS06245 Length = 456 Score = 420 bits (1079), Expect = e-122 Identities = 192/443 (43%), Positives = 296/443 (66%) Query: 19 LHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFFIMRALGELL 78 L RGL RHI+ +A+G AIG GLF G+ AI +AGP ++L+Y IGGVA + IMRALGE+ Sbjct: 7 LKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGPSVLLAYIIGGVAAYIIMRALGEMS 66 Query: 79 LYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWFPDVPQWIP 138 ++ P + SF+ YA++++GP AG+ TGW+Y F ++ +A++TA +Y+ WFP VP W+ Sbjct: 67 VHNPAASSFSRYAQDYLGPLAGYITGWTYCFEILIVAIADVTAFGIYMGVWFPAVPHWVW 126 Query: 139 ALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFGVTPLGPTASFSN 198 L+ + ++ VN ++V VFGELEFWF+ KV TI+ MI+ G II +G+ G N Sbjct: 127 VLSVVLIICAVNLMSVKVFGELEFWFSFFKVATIIIMILAGFGIIIWGIGNGGQPTGIHN 186 Query: 199 LWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNGVVWRILIF 258 LW++GGF G LG+V++LQ+VMFAY G+E+IG+TAGEA++PEK +P A N V RIL+F Sbjct: 187 LWSNGGFFSNGWLGMVMSLQMVMFAYGGIEIIGITAGEAKDPEKSIPRAINSVPMRILVF 246 Query: 259 YVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVNLVVITAAASSCNSGIFSTG 318 YVG L ++M++ PWN++ SPFV F+ +G+ AA+I+N VV+TA+ S+ NS +F G Sbjct: 247 YVGTLFVIMSIYPWNQVGTNGSPFVLTFQHLGITFAASILNFVVLTASLSAINSDVFGVG 306 Query: 319 RMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLLNYIVPEQVFVWVTSISLV 378 RML+ +A+ G AP+ F + S + VP + + + V LNYI+PE VF+ + S++ Sbjct: 307 RMLHGMAEQGSAPKMFAKTSRRGVPWVTVMVMTIALLFAVYLNYIMPENVFLVIASLATF 366 Query: 379 GSLWTWSIIMIAHLGYRKAIAAGRVKAVAFRMPGAPYANWLVVAFMIAVAVLLSLDPGTR 438 ++W W +I+++ + +R+ + KA+ F++PG + + F++ + L+ P TR Sbjct: 367 ATVWVWIMILLSQIAFRRRLPPEEAKALKFKVPGGVTTTVIGLLFLVFIIGLIGYHPDTR 426 Query: 439 VALYVAPVWFALLGIGYRFTKSR 461 ++LYV W LL IG++F R Sbjct: 427 ISLYVGFAWIILLLIGWQFKTRR 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: 747 Number of extensions: 42 Number of successful extensions: 1 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: 456 Length adjustment: 33 Effective length of query: 439 Effective length of database: 423 Effective search space: 185697 Effective search space used: 185697 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