Align ABC transporter permease (characterized, see rationale)
to candidate 17518 b3457 leucine/isoleucine/valine transporter subunit (NCBI)
Query= uniprot:A0A165KC95 (309 letters) >FitnessBrowser__Keio:17518 Length = 308 Score = 244 bits (624), Expect = 1e-69 Identities = 135/305 (44%), Positives = 197/305 (64%), Gaps = 19/305 (6%) Query: 5 LQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIG--MMQGAMP 62 LQQ+ NG+ LGS YALIA+GYTMVYGII +INFAHGEV MIG+ S+ I MM G Sbjct: 9 LQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMMGI-- 66 Query: 63 GAPGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAMII 122 GW+++ + A V+A+ + IE+VAYRP+R+S RL LI+AIGMSI LQ + Sbjct: 67 -DTGWLLVAAGFVGAIVIASAYGWSIERVAYRPVRNSKRLIALISAIGMSIFLQNYVSLT 125 Query: 123 WKPNYKPYPTMLPSSPFEIG-----GAFITPTQILILGVTAVALASLVYLVNHTNLGRAM 177 P++ + + +G A IT Q +I VT +A+ +L + ++ +GRA Sbjct: 126 EGSRDVALPSLF-NGQWVVGHSENFSASITTMQAVIWIVTFLAMLALTIFIRYSRMGRAC 184 Query: 178 RATAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFT 237 RA AE+ ++ASL+G+ D VI+ TF+IGA +AA+AG++ YG +GF+ G+KAFT Sbjct: 185 RACAEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMAGMKAFT 244 Query: 238 AAVFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRP 297 AAV GGIG++ GA++GG++LG+ EA+ S Y+ T Y D+ +F +LI++L + P Sbjct: 245 AAVLGGIGSIPGAMIGGLILGIAEALSSAYLST--------EYKDVVSFALLILVLLVMP 296 Query: 298 SGLLG 302 +G+LG Sbjct: 297 TGILG 301 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: 248 Number of extensions: 10 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: 308 Length adjustment: 27 Effective length of query: 282 Effective length of database: 281 Effective search space: 79242 Effective search space used: 79242 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 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