Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate 8500289 DvMF_1045 glycine betaine/L-proline ABC transporter, ATPase subunit (RefSeq)
Query= TCDB::Q9KKE1 (275 letters) >FitnessBrowser__Miya:8500289 Length = 397 Score = 303 bits (775), Expect = 5e-87 Identities = 160/264 (60%), Positives = 195/264 (73%) Query: 1 MADIEIRNVYKIFGHDAKKALTMVEDGLDKADILSRSGCTVGLNDVSLKIGAGKIFVIMG 60 MA IEIR++ KIFG +KAL MV G K +I R+ VG+N + + G+I V+MG Sbjct: 1 MAKIEIRDLTKIFGPVPEKALAMVRAGKPKDEIYKRTKHAVGVNRATFDVDEGEIVVVMG 60 Query: 61 LSGSGKSTLVRHINRLIEPTSGEVLFDGDNILDLGAKALRAFRMRRVSMVFQSFALMPHR 120 LSGSGKSTLVR +NRLIEPT G V DG ++ L K LRA R R MVFQ+FAL PHR Sbjct: 61 LSGSGKSTLVRCLNRLIEPTDGTVRIDGTDVTTLSVKDLRALRQRTFGMVFQNFALFPHR 120 Query: 121 TVLQNVVYGQRVRGVSKDDAREIGMKWIDTVGLSGYDAKFPHQLSGGMKQRVGLARALAA 180 TVL+N YG V G +K R+ + + VGL+G++A P QLSGGM+QRVGLARALA Sbjct: 121 TVLENAEYGLEVMGAAKATRRDKAAEALARVGLAGWEAARPGQLSGGMQQRVGLARALAL 180 Query: 181 DTDVILMDEAFSALDPLIRGDMQDQLLQLQRNLAKTIVFITHDLDEALRIGSEIAILRDG 240 D D++LMDEAFSALDPLIR DMQD+LL+LQ ++ KTIVFI+HDLDEAL+IG I ++RDG Sbjct: 181 DPDILLMDEAFSALDPLIRRDMQDELLRLQDDVRKTIVFISHDLDEALKIGDRIVLMRDG 240 Query: 241 QVVQVGTPNDILDNPANDYVARFV 264 VVQVGTP DIL +PA+DYVARFV Sbjct: 241 AVVQVGTPEDILTSPADDYVARFV 264 Lambda K H 0.323 0.139 0.397 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: 379 Number of extensions: 15 Number of successful extensions: 1 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: 275 Length of database: 397 Length adjustment: 28 Effective length of query: 247 Effective length of database: 369 Effective search space: 91143 Effective search space used: 91143 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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