Align HutX aka HISX, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate GFF2248 PGA1_c22800 glycine betaine-binding protein
Query= TCDB::Q9KKE3 (346 letters) >FitnessBrowser__Phaeo:GFF2248 Length = 323 Score = 151 bits (382), Expect = 2e-41 Identities = 100/330 (30%), Positives = 162/330 (49%), Gaps = 24/330 (7%) Query: 20 AASASGANASYCGDGKTVTFAGIDWESGAFITEVMKTILSKGYDCQVDSIP-GNSVTLEQ 78 A +AS A A CG+ V+ DW S +T V K ++ +GY C V ++P ++ L Sbjct: 15 AITASAAQADDCGE---VSIMQGDWGSAQIVTAVAKFLMEEGYGCDVTAMPLSSNPALAS 71 Query: 79 ATANNDVQIFAEEWLGRSDVWNKAVEEKKVIAVGKTFV-GASEGWFVPDYVVHGDPARNI 137 + + I E W + + V+ +I V + G EG+FVP+Y+V Sbjct: 72 VSETGEPDILTEIWTNGAPAYQGLVDSGAIIPVTEVLSDGGVEGFFVPNYLVE------- 124 Query: 138 EAKAPDLKSVSQLTDPKIAEIFADPEEPSKGRFLNCPSGWTCEGVSTAKLEAYKLGETYV 197 + P+L ++ + A+PE RF NCP GWTC VST ++A L + + Sbjct: 125 --EHPELATIEGIA--------ANPELVGN-RFHNCPEGWTCLNVSTNLMKAGGLIDAGI 173 Query: 198 -NFRPGTGTALDAAITSAYLQGEPIFFYYWSPTAILGKFKLIQLEEPAYNEACWKELSSA 256 NF G+G L A+I +AY EP F +YW+PT++LGK+ + ++ ++ +A Sbjct: 174 ENFVHGSGETLAASIAAAYENKEPWFGFYWAPTSVLGKYPMTLVDMGPHDPEKHACNITA 233 Query: 257 NGKRDEGCAFPSVDVAYGVNSTFASEAPEIVEILEKATFPLDEVNASLAYMADNKVDATA 316 AFP +V ++ F +E EI E++ +F ++ +LA++ DN Sbjct: 234 ECDTPAMSAFPRSEVVTVLSKEFMAENAEISELMTNLSFTNAQMGETLAWVEDNNASYDE 293 Query: 317 AAAEFLKTKGDIWSKWVSDEARGKIEAGLK 346 A FL T D+W W++D AR K+ A L+ Sbjct: 294 GAVHFLTTYKDVWGAWLNDAARDKLSALLQ 323 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: 285 Number of extensions: 12 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 346 Length of database: 323 Length adjustment: 28 Effective length of query: 318 Effective length of database: 295 Effective search space: 93810 Effective search space used: 93810 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