Align HutX aka HISX, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate PfGW456L13_1920 Histidine transporter, periplasmic histidine-binding protein
Query= TCDB::Q9KKE3 (346 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1920 Length = 337 Score = 306 bits (785), Expect = 4e-88 Identities = 145/328 (44%), Positives = 208/328 (63%), Gaps = 2/328 (0%) Query: 18 MLAASASGANASYCGDGKTVTFAGIDWESGAFITEVMKTILSKGYDCQVDSIPGNSVTLE 77 +LA S AS + F I WESG+ ITE+++ I+ KGY D++PG++V+LE Sbjct: 12 LLALSLLSHPASATEKAAPIHFGDITWESGSLITEILRLIVEKGYGYPTDTLPGSTVSLE 71 Query: 78 QATANNDVQIFAEEWLGRSDVWNKAVEEKKVIAVGKTFVGASEGWFVPDYVVHGDPARNI 137 A A ND+Q+ EEW GRS W KA E KV +G T GA+EGW+VP+YV+ GDP R I Sbjct: 72 AALAKNDIQVIGEEWAGRSPAWVKAAAEGKVFGLGDTVKGATEGWWVPEYVIKGDPERGI 131 Query: 138 EAKAPDLKSVSQLTDPKIAEIFADPEEPSKGRFLNCPSGWTCEGVSTAKLEAYKLGETYV 197 + AP+LKSV+ L K ++F DPE+PS+GRFLN P+GWT E V++ KL+AY L +YV Sbjct: 132 KPLAPELKSVADLA--KYKDVFRDPEDPSRGRFLNSPTGWTSEIVNSQKLKAYDLTASYV 189 Query: 198 NFRPGTGTALDAAITSAYLQGEPIFFYYWSPTAILGKFKLIQLEEPAYNEACWKELSSAN 257 NFR G+G ALDA + S+ +G+P+ FYYWSPT +LG+FKL++L+EP ++ WK L+ AN Sbjct: 190 NFRTGSGAALDAEVASSIRRGKPVLFYYWSPTPLLGRFKLVKLDEPPFDAEAWKTLADAN 249 Query: 258 GKRDEGCAFPSVDVAYGVNSTFASEAPEIVEILEKATFPLDEVNASLAYMADNKVDATAA 317 +G +A GV++ F ++ P++V EK P+D +N +L M++ + Sbjct: 250 NPNPKGTRSMPASLAIGVSAPFKAQYPDLVTFFEKVDLPIDLLNQTLGQMSEKRQKPREV 309 Query: 318 AAEFLKTKGDIWSKWVSDEARGKIEAGL 345 A FL+ + +W WV E K+ A L Sbjct: 310 AEAFLREQPQVWKGWVPGEVATKVSASL 337 Lambda K H 0.314 0.130 0.391 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: 337 Number of extensions: 12 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: 346 Length of database: 337 Length adjustment: 29 Effective length of query: 317 Effective length of database: 308 Effective search space: 97636 Effective search space used: 97636 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 49 (23.5 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