Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate RR42_RS00195 RR42_RS00195 ABC transporter permease
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >FitnessBrowser__Cup4G11:RR42_RS00195 Length = 309 Score = 184 bits (467), Expect = 2e-51 Identities = 101/305 (33%), Positives = 175/305 (57%), Gaps = 10/305 (3%) Query: 6 QQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSLGITWV 65 Q + NGL LG IY ++A+G+T+ +G++ +I F+HG+ M+GAF L + L I Sbjct: 6 QYVFNGLMLGMIYAMVAVGFTLFFGVLDVIKFSHGDTLMVGAFAGLAASTGVLMLDIQSP 65 Query: 66 PLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQIL--QG 123 + LL +++ ++ T + G + + PLR + L L++ + + ++ V++ G Sbjct: 66 WIRLLAVVLCAICVTGLLGAAIAKFLILPLRKAAPLNTLLATLMLGTVMRESVRLFYPDG 125 Query: 124 ARSKPLQPILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRACEQD 183 + KP +LP ++ G++S+ L + IA++ G LITRT G A RA QD Sbjct: 126 SNPKPFPALLP-TASIELGSLSLRADNLILLATGIAIIVGVHLLITRTRFGMAIRAVAQD 184 Query: 184 KKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTAAVLGG 243 + A L+G+N + V+ LTF +G+ +AA+AG+M L Y I+F +G L GV F AA+LGG Sbjct: 185 GETARLMGINFEAVVLLTFALGSGMAALAGVMNGLYYNEINFNVGLLLGVIGFAAAILGG 244 Query: 244 IGSLPGAMLGGVVIGLIEAFWSGYM-------GSEWKDVATFTILVLVLIFRPTGLLGRP 296 +G++ GA+LGG + ++ S + S +KDV F ++++++ ++PTGL+ Sbjct: 245 LGNIYGAILGGFLFAALQVLGSATLPALIPDIPSAYKDVFAFAVVIVLMAWKPTGLIAEK 304 Query: 297 EIEKV 301 E+V Sbjct: 305 SSERV 309 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: 297 Number of extensions: 17 Number of successful extensions: 4 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: 309 Length adjustment: 27 Effective length of query: 274 Effective length of database: 282 Effective search space: 77268 Effective search space used: 77268 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