Align D-serine/D-alanine/glycine transporter (characterized, see rationale)
to candidate Pf1N1B4_1580 Histidine transport protein (permease)
Query= uniprot:A0A0C4YRF7 (472 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1580 Length = 469 Score = 427 bits (1099), Expect = e-124 Identities = 201/441 (45%), Positives = 299/441 (67%), Gaps = 2/441 (0%) Query: 17 KDLHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFFIMRALGE 76 K L RGL RHI+ +A+G AIG GLF G+ AI +AGP ++L+Y IGG A+F +MRALGE Sbjct: 6 KGLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMRALGE 65 Query: 77 LLLYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWFPDVPQW 136 + ++ PV+GSF YA ++GP AGF GW+Y F V+ GMA++TA +Y+ +WFP+V +W Sbjct: 66 MAVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFPEVDRW 125 Query: 137 IPALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFGVT--PLGPTA 194 I L ++V+ +N V VFGE+EFW +L+KV IVAMI+ G I+ FG++ P Sbjct: 126 IWVLGIVSVVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAPGAQAT 185 Query: 195 SFSNLWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNGVVWR 254 SNLW+HGGFMP G G++ + +VMFA+ G+E+IGVTAGEA++P++VLP A N V R Sbjct: 186 DISNLWSHGGFMPNGVGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQRVLPRAINAVPLR 245 Query: 255 ILIFYVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVNLVVITAAASSCNSGI 314 IL+FYV ++++M++ PW ++ SPFV +F+ +G+ AA I+N+VVI+AA S+ NS I Sbjct: 246 ILLFYVLTMLVLMSIFPWQQIGSQGSPFVQIFDNLGISSAATILNIVVISAAVSAINSDI 305 Query: 315 FSTGRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLLNYIVPEQVFVWVTS 374 F GRM+Y LAQ G AP+ F R+S VP + + ++ + +GVLLNY++PE VF+ + S Sbjct: 306 FGAGRMMYGLAQQGHAPKGFARLSRNGVPWLTVVVMSSALLLGVLLNYLIPENVFLLIAS 365 Query: 375 ISLVGSLWTWSIIMIAHLGYRKAIAAGRVKAVAFRMPGAPYANWLVVAFMIAVAVLLSLD 434 ++ ++W W +I+ + R++++A +V + F +P PYA +AFM+ + +L Sbjct: 366 VATFATVWVWLMILFTQVAMRRSMSAEQVAQLKFPVPFWPYAPMAAIAFMLFIFGVLGYF 425 Query: 435 PGTRVALYVAPVWFALLGIGY 455 P T+ AL V VW LL + Y Sbjct: 426 PDTQAALIVGVVWIVLLVLAY 446 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: 762 Number of extensions: 45 Number of successful extensions: 2 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: 469 Length adjustment: 33 Effective length of query: 439 Effective length of database: 436 Effective search space: 191404 Effective search space used: 191404 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