Align HutX aka HISX, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate Pf1N1B4_4296 Histidine transporter, periplasmic histidine-binding protein
Query= TCDB::Q9KKE3 (346 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4296 Length = 338 Score = 310 bits (795), Expect = 3e-89 Identities = 144/310 (46%), Positives = 205/310 (66%), Gaps = 2/310 (0%) Query: 37 VTFAGIDWESGAFITEVMKTILSKGYDCQVDSIPGNSVTLEQATANNDVQIFAEEWLGRS 96 + FA ++WESG+ IT++++ I+ KGY D++PG ++TLE A ANND+Q+ EEW GRS Sbjct: 31 IHFADLNWESGSLITDILRIIVEKGYGLPTDTLPGTTITLETALANNDIQVIGEEWAGRS 90 Query: 97 DVWNKAVEEKKVIAVGKTFVGASEGWFVPDYVVHGDPARNIEAKAPDLKSVSQLTDPKIA 156 VW KA E KV A+G T GA+EGW+VP+YV+ GDPA+ I+ APDL+S+S L P+ Sbjct: 91 PVWVKAEAEGKVAALGDTVKGATEGWWVPEYVIKGDPAKGIKPMAPDLRSISDL--PRYK 148 Query: 157 EIFADPEEPSKGRFLNCPSGWTCEGVSTAKLEAYKLGETYVNFRPGTGTALDAAITSAYL 216 ++F DPE P KGRFLN P GWT E V+ KL+AY L ++YVNFR G+G ALDA I+S+ Sbjct: 149 DVFKDPETPGKGRFLNSPIGWTSEVVNKQKLKAYGLDDSYVNFRSGSGAALDAEISSSIR 208 Query: 217 QGEPIFFYYWSPTAILGKFKLIQLEEPAYNEACWKELSSANGKRDEGCAFPSVDVAYGVN 276 +G+P+ FYYWSPT +LG+FKLIQL+EP ++ WK L+ A+ + ++ GV+ Sbjct: 209 RGKPVLFYYWSPTPLLGRFKLIQLQEPPFDAEAWKTLTDADNPNPKPTRSLPSKLSIGVS 268 Query: 277 STFASEAPEIVEILEKATFPLDEVNASLAYMADNKVDATAAAAEFLKTKGDIWSKWVSDE 336 + F + P+I E K P++ +N +LA M++ AA F+K D+W WV + Sbjct: 269 TPFQKQYPQIAEFFTKVDLPIEALNMALADMSEKHTPPRQAAEAFMKAHPDVWRAWVPKD 328 Query: 337 ARGKIEAGLK 346 K+ A LK Sbjct: 329 VADKVSAALK 338 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: 332 Number of extensions: 14 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: 338 Length adjustment: 29 Effective length of query: 317 Effective length of database: 309 Effective search space: 97953 Effective search space used: 97953 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