Align histidine permease (characterized)
to candidate PfGW456L13_4790 D-serine/D-alanine/glycine transporter
Query= reanno::pseudo3_N2E3:AO353_12275 (468 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4790 Length = 473 Score = 511 bits (1315), Expect = e-149 Identities = 244/445 (54%), Positives = 326/445 (73%), Gaps = 2/445 (0%) Query: 8 LKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMRALGEMA 67 LKR L RHIR MALG+ IG GLF GSA AI+MAGPA++L+Y+IGG A+ ++MRALGEMA Sbjct: 18 LKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRALGEMA 77 Query: 68 VHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFPEVSRWIW 127 VHNPVAGSF +YA YLGP+AGF+ GW Y F ++ +A++TA +YMG WFP+V RWIW Sbjct: 78 VHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGIWFPDVPRWIW 137 Query: 128 VLGVVSIVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAPGQVTDIS 187 L + +G +NL VK FGE EFW +L+K+ I+AM+LGG GI+ FG G IS Sbjct: 138 ALAALISMGSINLIAVKAFGEFEFWFALIKIVTIIAMVLGGIGIIAFGFGN-DGVALGIS 196 Query: 188 NLWTQGGFMPNGMGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQHVLPRAINAVPLRILL 247 NLWT GGFMPNG+ G++ S +VMFA+ G+E+IG+TAGEAK+PQ +P AI +V RILL Sbjct: 197 NLWTHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGSVFWRILL 256 Query: 248 FYVLTMLVLMSIFPWQQIGSQGSPFVQIFDKLGISSAATILNIVVITAAISAINSDIFGA 307 FYV + V++SI+PW +IG+QGSPFV F++LGI +AA I+N VVITAA+S+ N IF Sbjct: 257 FYVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGGIFST 316 Query: 308 GRMMFGLAQQGHAPKGFAHLSRNGVPWMTVVVMSVALLLGVLLNYLIPENVFLLIASIAT 367 GRM++ LAQ G AP GFA S NGVP +++ ALLLGVLLNYL+PE VF+ + +IAT Sbjct: 317 GRMLYSLAQNGQAPAGFAKTSNNGVPRRALLLSIGALLLGVLLNYLVPEKVFVWVTAIAT 376 Query: 368 FATVWVWLMILFTQVAMRRSMTAEQVAQLKFPVPFWPYAPMAAIAFMLFVFGVLGYFPDT 427 F +W W+MIL Q+ R+ ++A + A LK+ + +P + A+AF++ V G++ YFPDT Sbjct: 377 FGAIWTWVMILLAQLKFRKGLSASEAAGLKYRMWLYPVSSYLALAFLVLVVGLMAYFPDT 436 Query: 428 QAALIVGVVWIVLL-VLAYLMWVKP 451 + AL VG ++VLL VL Y+ ++P Sbjct: 437 RVALYVGPAFLVLLTVLFYVFKLQP 461 Lambda K H 0.329 0.142 0.441 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: 799 Number of extensions: 41 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: 468 Length of database: 473 Length adjustment: 33 Effective length of query: 435 Effective length of database: 440 Effective search space: 191400 Effective search space used: 191400 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