Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Dsui_2059 Dsui_2059 ABC-type branched-chain amino acid transport system, permease component
Query= uniprot:Q1MCU1 (463 letters) >FitnessBrowser__PS:Dsui_2059 Length = 287 Score = 160 bits (404), Expect = 7e-44 Identities = 112/308 (36%), Positives = 163/308 (52%), Gaps = 44/308 (14%) Query: 144 IYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYFGLSFWVLLPLSGIFAALWG 203 ++ +LA + + + GLL L AF VGAY ALL+ + SF +L GI L Sbjct: 20 VHALLALSIWLTLS-CGLLSLANAAFMGVGAYVSALLTLHLEWSFGSVLLAGGIAPTLVA 78 Query: 204 VILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTDVTKGTFGISSIPKATLFGIPFDATA 263 +I+G PVLRL G YLA+ TLAFGE++R+ ++N ++T G G++ IP AT Sbjct: 79 LIIGAPVLRLSGVYLAMATLAFGEVVRITVLN-LEITGGPEGLNGIPLAT---------- 127 Query: 264 GGFAKLFHLPISSAYYKIFLFYLILALCMLTAYVTIRLRRMPIGRAWEALREDEIACRSL 323 + +H+ LILA+ + Y RLRR +GRA+EA++EDE+A R + Sbjct: 128 ----EGWHIA------------LILAVAV---YGLARLRRSKVGRAFEAIKEDEVAARLM 168 Query: 324 GINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFVFLESAVILAIVVLGGMGSLTG 383 GIN KL AF+ GA AG AG+ A F+SP + F + IL + VLGG SL G Sbjct: 169 GINVDRYKLLAFSLGAFIAGVAGALNAHFTFFISPREYGFENAVDILTMAVLGGTSSLIG 228 Query: 384 IAIAAIVMVGGTELLREMSFLKLIFGPDFTPELYRMLIFGLAMVVVMLFKPRGFVGSREP 443 + + ++ ELLR + + +R L+ G +V+V+LF P+G SR Sbjct: 229 PMLGSSILTLLPELLRSL-------------QDFRSLVNGAVLVLVVLFLPKGLWESRRI 275 Query: 444 TAFLRERK 451 AF + K Sbjct: 276 RAFFKRLK 283 Lambda K H 0.330 0.145 0.432 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: 357 Number of extensions: 15 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: 463 Length of database: 287 Length adjustment: 29 Effective length of query: 434 Effective length of database: 258 Effective search space: 111972 Effective search space used: 111972 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: 49 (23.5 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