Align ABC transporter for L-Histidine, permease component 1 (characterized)
to candidate 8500595 DvMF_1343 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= reanno::acidovorax_3H11:Ac3H11_2554 (222 letters) >FitnessBrowser__Miya:8500595 Length = 337 Score = 147 bits (372), Expect = 2e-40 Identities = 79/212 (37%), Positives = 138/212 (65%), Gaps = 16/212 (7%) Query: 15 LLAGALVTVEITAASLLLGCVMGLLVGIGRLNPKRRVVYALCTAYVAAIRGTPLLVQLFI 74 LL G +T+E++ +++ G V+G++ G+ R++ + + T Y+ IRG+PLLVQ+F+ Sbjct: 127 LLEGLWITLEVSVLAIIGGIVIGVVTGLCRISINPMLRWGAIT-YIEIIRGSPLLVQIFL 185 Query: 75 LFFGLPQFGILLPAFV------------CGVIGLGIYSGAYVSEVVRGAIQSIDKGQMEA 122 +F + G L+ A + GV+ L +++GAYV+E+VR IQS+ +GQMEA Sbjct: 186 WYFVV---GTLINALLEHVGLGGISPLWYGVMALALFTGAYVAEIVRAGIQSVHRGQMEA 242 Query: 123 ARSIGMSSGLAMRTVVLPQAVVRMIPPLGNEFIALIKNSALVSLLTIHDLMHEGQKIISV 182 ARS+GM+ AMR V+LPQA R++PPL +FI+LIK+S+L+ ++ I +L +++++ Sbjct: 243 ARSLGMNYAQAMRKVILPQAFRRIMPPLAGQFISLIKDSSLLGVIAIRELTKATREVVTT 302 Query: 183 SYRSLEVYLAIAVVYFILTGATTLVLRRIELR 214 S + E+++ AV+Y +LT +L ++ +E R Sbjct: 303 SLQPFELWIVCAVLYLVLTFTLSLFVQYLERR 334 Lambda K H 0.328 0.143 0.412 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: 207 Number of extensions: 12 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: 222 Length of database: 337 Length adjustment: 25 Effective length of query: 197 Effective length of database: 312 Effective search space: 61464 Effective search space used: 61464 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 47 (22.7 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