Align ABC transporter permease (characterized, see rationale)
to candidate AZOBR_RS25470 AZOBR_RS25470 ABC transporter permease
Query= uniprot:A0A165KC95 (309 letters) >FitnessBrowser__azobra:AZOBR_RS25470 Length = 297 Score = 183 bits (464), Expect = 5e-51 Identities = 111/303 (36%), Positives = 174/303 (57%), Gaps = 20/303 (6%) Query: 3 ILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMP 62 ++ QQI+NG+V+GS YAL ALG+T+++G++ ++N AHG V M GA T G+ Sbjct: 1 LVAQQIVNGIVVGSTYALFALGFTLIFGVLHVLNLAHGAVFMWGAFT-----GLFAVTAL 55 Query: 63 GAPGWVILLLATIIACVVAATLNFVIEKVAYRPLR--SSPRLAPLITAIGMSILLQTLAM 120 G P L A +A + A L+ +++ VA+RPLR SP A +I+++G++ +L + A Sbjct: 56 GLP----LPAAFAVAMLAAGLLSVLVDAVAFRPLRRRGSPEFAAIISSLGVAQILMSAAQ 111 Query: 121 IIWKPNYKPYPT-MLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRA 179 I + +P P +++ G ++ QI+I+G AV +A+L+ + T+ GR +RA Sbjct: 112 IASNTQVQRFPFGTFPIVFYQVFGLRVSLQQIVIVGSVAVLVAALLAFLFATSFGRQIRA 171 Query: 180 TAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAA 239 A + R ASL+GV P V + TF + LA AG++ + + MG L+ F Sbjct: 172 VAISERTASLLGVNPGAVHALTFFLCGALAGAAGVIIGIAFNSVHFLMGEPYLLRGFVVI 231 Query: 240 VFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSG 299 V GG+G++AGAVVGG+L G+I+ TL+ L S +D F +L +IL LRPSG Sbjct: 232 VLGGLGSVAGAVVGGLLFGMIQ--------TLSVAFLSSALSDAILFGLLFVILLLRPSG 283 Query: 300 LLG 302 G Sbjct: 284 FFG 286 Lambda K H 0.327 0.142 0.419 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: 187 Number of extensions: 9 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: 309 Length of database: 297 Length adjustment: 27 Effective length of query: 282 Effective length of database: 270 Effective search space: 76140 Effective search space used: 76140 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 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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