Align D-serine/D-alanine/glycine transporter (characterized, see rationale)
to candidate 14540 b0402 predicted cryptic proline transporter (NCBI)
Query= uniprot:A0A0C4YRF7 (472 letters) >FitnessBrowser__Keio:14540 Length = 457 Score = 417 bits (1072), Expect = e-121 Identities = 192/447 (42%), Positives = 296/447 (66%) Query: 13 VHEEKDLHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFFIMR 72 + + L RGL RHI+ +A+G AIG GLF G+ AI +AGP ++L+Y IGG+A + IMR Sbjct: 1 MESKNKLKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGPSVLLAYIIGGIAAYIIMR 60 Query: 73 ALGELLLYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWFPD 132 ALGE+ ++ P + SF+ YA+E +GP AG+ TGW+Y F ++ +A++TA +Y+ WFP Sbjct: 61 ALGEMSVHNPAASSFSRYAQENLGPLAGYITGWTYCFEILIVAIADVTAFGIYMGVWFPT 120 Query: 133 VPQWIPALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFGVTPLGP 192 VP WI L+ + ++ VN ++V VFGELEFWF+ KV TI+ MIV G II +G+ G Sbjct: 121 VPHWIWVLSVVLIICAVNLMSVKVFGELEFWFSFFKVATIIIMIVAGFGIIIWGIGNGGQ 180 Query: 193 TASFSNLWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNGVV 252 NLW++GGF G LG+V++LQ+VMFAY G+E+IG+TAGEA++PEK +P A N V Sbjct: 181 PTGIHNLWSNGGFFSNGWLGMVMSLQMVMFAYGGIEIIGITAGEAKDPEKSIPRAINSVP 240 Query: 253 WRILIFYVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVNLVVITAAASSCNS 312 RIL+FYVG L ++M++ PWN++ SPFV F+ +G+ AA+I+N VV+TA+ S+ NS Sbjct: 241 MRILVFYVGTLFVIMSIYPWNQVGTAGSPFVLTFQHMGITFAASILNFVVLTASLSAINS 300 Query: 313 GIFSTGRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLLNYIVPEQVFVWV 372 +F GRML+ +A+ G AP+ F + S + +P + + + V LNYI+PE VF+ + Sbjct: 301 DVFGVGRMLHGMAEQGSAPKIFSKTSRRGIPWVTVLVMTTALLFAVYLNYIMPENVFLVI 360 Query: 373 TSISLVGSLWTWSIIMIAHLGYRKAIAAGRVKAVAFRMPGAPYANWLVVAFMIAVAVLLS 432 S++ ++W W +I+++ + +R+ + VKA+ F++PG + F++ + L+ Sbjct: 361 ASLATFATVWVWIMILLSQIAFRRRLPPEEVKALKFKVPGGVATTIGGLIFLLFIIGLIG 420 Query: 433 LDPGTRVALYVAPVWFALLGIGYRFTK 459 P TR++LYV W +L IG+ F + Sbjct: 421 YHPDTRISLYVGFAWIVVLLIGWMFKR 447 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: 740 Number of extensions: 44 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: 457 Length adjustment: 33 Effective length of query: 439 Effective length of database: 424 Effective search space: 186136 Effective search space used: 186136 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