Align histidine permease (characterized)
to candidate GFF1065 PS417_05405 D-alanine/D-serine/glycine permease
Query= reanno::pseudo3_N2E3:AO353_12275 (468 letters) >FitnessBrowser__WCS417:GFF1065 Length = 472 Score = 506 bits (1303), Expect = e-148 Identities = 247/453 (54%), Positives = 328/453 (72%), Gaps = 5/453 (1%) 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+ RWIW Sbjct: 78 VHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGVWFPDTPRWIW 137 Query: 128 VLGVVSIVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAPGQVTDIS 187 L + +G +NL VK FGE EFW +L+K+ I+AM++GG GI+ FG G IS Sbjct: 138 ALAALISMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGN-DGVALGIS 196 Query: 188 NLWTQGGFMPNGMGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQHVLPRAINAVPLRILL 247 NLW GGFMPNG+ G++ S +VMFA+ G+E+IG+TAGEAK+PQ +P AI +V RILL Sbjct: 197 NLWAHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPSAIGSVFWRILL 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 FA S NGVP +++ ALLLGVLLNYL+PE VF+ + SIAT Sbjct: 317 GRMLYSLAQNGQAPATFAKTSSNGVPRKALLLSIFALLLGVLLNYLVPEKVFVWVTSIAT 376 Query: 368 FATVWVWLMILFTQVAMRRSMTAEQVAQLKFPVPFWPYAPMAAIAFMLFVFGVLGYFPDT 427 F +W WLMIL Q+ R+S++ + A LK+ + +P + A+AF+L V G++ YFPDT Sbjct: 377 FGAIWTWLMILLAQLKFRKSLSPAEQAGLKYRMWLYPVSSYLALAFLLLVVGLMAYFPDT 436 Query: 428 QAALIVGVVWIVLL-VLAYLMWVKP---AAGQA 456 + AL VG V++VLL VL Y+ ++P A G+A Sbjct: 437 RIALYVGPVFLVLLTVLFYVFKLQPTQVAQGEA 469 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: 793 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: 472 Length adjustment: 33 Effective length of query: 435 Effective length of database: 439 Effective search space: 190965 Effective search space used: 190965 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