Align HutX aka HISX, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate SM_b21572 SM_b21572 amino acid uptake ABC transporter substrate-binding protein precursor
Query= TCDB::Q9KKE3 (346 letters) >FitnessBrowser__Smeli:SM_b21572 Length = 333 Score = 171 bits (432), Expect = 3e-47 Identities = 116/349 (33%), Positives = 180/349 (51%), Gaps = 27/349 (7%) Query: 8 MRLTFAAAGLMLA--ASASGANASYCGDGKTVTFAGIDWESGAFITEVMKTILSKGYDCQ 65 M+ A+ LML A AS ++A+ CG TVT A ++W+S ++ + K IL++GY C Sbjct: 1 MKKLLASTCLMLGLIAGASTSSAAECG---TVTIASMNWQSAEVLSNLDKFILNEGYGCS 57 Query: 66 VDSIPGNSV-TLEQATANNDVQIFAEEWLGR-SDVWNKAVEEKKVIAVGKTFV-GASEGW 122 + G++V T+ I E W+ DV K ++ ++I VG G +GW Sbjct: 58 AEITIGDTVPTITSMAEKGQPDIAPEAWIDLLPDVVKKGQDDGRIITVGSPLPDGGVQGW 117 Query: 123 FVPDYVVHGDPARNIEAKAPDLKSVSQLTDPKIAEIFADPEEPSKGRFLNCPSGWTCEGV 182 ++P Y+ P D+K++ K E+F E+PSKG LN P GW V Sbjct: 118 WIPQYLADAHP---------DIKTIGDAL--KHPELFPASEDPSKGAILNGPQGWGGTVV 166 Query: 183 STAKLEAY---KLGETYVNFRPGTGTALDAAITSAYLQGEPIFFYYWSPTAILGKFKLIQ 239 +T A+ K G T V+ G+ LD AI AY + E + YYWSPTA+LGK+K+++ Sbjct: 167 TTQLFSAFDGEKAGFTLVD--TGSAAGLDGAIAKAYERKEGLLTYYWSPTALLGKYKMVK 224 Query: 240 LEEPAYNEAC-WKELSSANGKRD-EGCAFPSVDVAYGVNSTFASEA-PEIVEILEKATFP 296 L+ ++A WK ++ D + A+P + V F+ PE+++ L K ++ Sbjct: 225 LDPGVPHDAAEWKRCNTVADCPDPKPNAWPVDTIVTLVAKPFSERVGPEVMDYLTKRSWS 284 Query: 297 LDEVNASLAYMADNKVDATAAAAEFLKTKGDIWSKWVSDEARGKIEAGL 345 + V+ +A+M DN+ A FL+ D+WSKWVS EA KI+A L Sbjct: 285 NETVSQLMAWMTDNQASGEEGAKRFLEENEDMWSKWVSPEAAEKIKAAL 333 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: 344 Number of extensions: 20 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: 333 Length adjustment: 28 Effective length of query: 318 Effective length of database: 305 Effective search space: 96990 Effective search space used: 96990 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