Align HutX aka HISX, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate SMc02378 SMc02378 periplasmic binding transmembrane protein
Query= TCDB::Q9KKE3 (346 letters) >FitnessBrowser__Smeli:SMc02378 Length = 332 Score = 175 bits (443), Expect = 2e-48 Identities = 118/343 (34%), Positives = 177/343 (51%), Gaps = 26/343 (7%) Query: 11 TFAAAGLMLAASASGANASYCGDGKTVTFAGIDWESGAFITEVMKTILSKGYDCQVDSIP 70 T AAGL+ SA A+A+ CGD VT A ++W+S + V K IL++GY C + + Sbjct: 8 TCLAAGLLGLGSA--ASAAECGD---VTIANMNWQSAEVLASVDKFILTEGYGCSAELVV 62 Query: 71 GNSV-TLEQATANNDVQIFAEEWLGR-SDVWNKAVEEKKVIAVGKTFV-GASEGWFVPDY 127 G++V T+ + I E W+ DV N+ ++E K++ GA +GW+VP Y Sbjct: 63 GDTVPTITSMIEKGEPDIAPEGWVDLLPDVVNRGLQEGKLVGAAVALSDGAVQGWWVPKY 122 Query: 128 VVHGDPARNIEAKAPDLKSVSQLTDPKIAEIFADPEEPSKGRFLNCPSGWTCEGVSTAKL 187 +V +P D+K++ + K E+F DPE+PSKG N P GW V+T Sbjct: 123 IVDANP---------DIKTIDDVLKHK--ELFPDPEDPSKGAIFNGPQGWGGTVVTTQLY 171 Query: 188 EAY---KLGETYVNFRPGTGTALDAAITSAYLQGEPIFFYYWSPTAILGKFKLIQLEEPA 244 +AY G T V+ G+ LD +I AY + + YYW+PTA+LGK+++++LE Sbjct: 172 KAYGAEAAGFTLVD--TGSAAGLDGSIAKAYERKQGWAGYYWAPTALLGKYEMVKLEHGV 229 Query: 245 YNE-ACWKELSSANGKRD-EGCAFPSVDVAYGVNSTFASEAPEIVEILEKATFPLDEVNA 302 N+ A WK ++ D + +P V V FA A +E L + D VN Sbjct: 230 PNDMAEWKRCNTVADCPDPKKNDWPKDKVQTLVTKEFADRAGPAMEYLNTRAWTNDTVNK 289 Query: 303 SLAYMADNKVDATAAAAEFLKTKGDIWSKWVSDEARGKIEAGL 345 +A+M DN+ A FL+ D+W+KWVS E KI+A L Sbjct: 290 LMAWMTDNQASGEEGAKHFLEENPDLWTKWVSPEVAEKIKAAL 332 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: 354 Number of extensions: 18 Number of successful extensions: 5 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: 332 Length adjustment: 28 Effective length of query: 318 Effective length of database: 304 Effective search space: 96672 Effective search space used: 96672 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