Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate 3610344 Dshi_3725 inner-membrane translocator (RefSeq)
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >FitnessBrowser__Dino:3610344 Length = 294 Score = 153 bits (387), Expect = 4e-42 Identities = 97/292 (33%), Positives = 163/292 (55%), Gaps = 16/292 (5%) Query: 7 QLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSLGIT-WV 65 Q++NGL+LG L+A+G T+++G++ +IN +HGE Y +GA+ AL A+ + G+ WV Sbjct: 12 QMLNGLALGVSVILVALGLTIIFGLLDVINMSHGEFYAVGAYGAL----ALAAFGVNYWV 67 Query: 66 PLALLVMLVASMLFTAVYGWTVERIAYRPLRSSP--RLAPLISAIGMSIFLQNYVQILQG 123 +A++ +++ + G ER R + ++ L+ G+ + ++ ++I+ G Sbjct: 68 LMAMVPLMMIPL------GIVTERYLIRRVYDGADRHVSTLLLTFGLGLIAEDVLKIIFG 121 Query: 124 ARSKPLQPILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRACEQD 183 ++ + LPG LM + + RL I I+ A++ ++ RT LG RA D Sbjct: 122 PNTQRPENPLPGATDLM--GIFIPTYRLFLIAISAAVILAVAFVVYRTRLGAIVRAASFD 179 Query: 184 KKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTAAVLGG 243 + MA LGV V V S F G ALA +AG+++ IY V +G + AFT ++GG Sbjct: 180 RNMAASLGVRVGWVYSGAFAFGVALAGLAGVLLAPIYSVFPT-MGRDFILIAFTVVIVGG 238 Query: 244 IGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGLLGR 295 +GS+ GA++ G+V+ I+A S + W + F ++VLVL+FRP GL GR Sbjct: 239 MGSIWGAVVAGIVLTQIQAISSLVISPVWSEPIVFGVMVLVLMFRPQGLFGR 290 Lambda K H 0.329 0.144 0.425 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: 312 Number of extensions: 17 Number of successful extensions: 3 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: 301 Length of database: 294 Length adjustment: 26 Effective length of query: 275 Effective length of database: 268 Effective search space: 73700 Effective search space used: 73700 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: 48 (23.1 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