Align HutX aka HISX, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate AO353_21435 AO353_21435 ABC transporter substrate-binding protein
Query= TCDB::Q9KKE3 (346 letters) >FitnessBrowser__pseudo3_N2E3:AO353_21435 Length = 337 Score = 306 bits (784), Expect = 5e-88 Identities = 141/309 (45%), Positives = 204/309 (66%), Gaps = 2/309 (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 ++G T GA+EGW+VP+YV+ GDPA+ I+ APDL+SVS L P+ Sbjct: 91 PVWVKAEAEGKVASIGDTVKGATEGWWVPEYVIKGDPAKGIKPLAPDLRSVSDL--PRYK 148 Query: 157 EIFADPEEPSKGRFLNCPSGWTCEGVSTAKLEAYKLGETYVNFRPGTGTALDAAITSAYL 216 ++F+DPE P KGRFLN P GWT E V+ KL+AY L ++YVNFR G+G ALDA ITS+ Sbjct: 149 DVFSDPESPGKGRFLNSPIGWTSEVVNKQKLKAYGLTDSYVNFRSGSGAALDAEITSSIR 208 Query: 217 QGEPIFFYYWSPTAILGKFKLIQLEEPAYNEACWKELSSANGKRDEGCAFPSVDVAYGVN 276 +G+P+ FYYWSPT +LG+FKLIQLEEP ++ WK L+ A+ + ++ GV+ Sbjct: 209 RGKPVLFYYWSPTPLLGRFKLIQLEEPPFDAEAWKTLTDADNPNPKPTRSLPSKLSIGVS 268 Query: 277 STFASEAPEIVEILEKATFPLDEVNASLAYMADNKVDATAAAAEFLKTKGDIWSKWVSDE 336 + F + P++ E K P+ +N +LA +++ AA F+K ++W W+ + Sbjct: 269 APFQKQYPQVTEFFSKVDLPIGPLNKALAEISEKHTAPRQAAEAFMKAHPEVWRAWLPKD 328 Query: 337 ARGKIEAGL 345 K+ A L Sbjct: 329 VADKVSASL 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: 324 Number of extensions: 15 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