Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate AZOBR_RS08240 AZOBR_RS08240 ABC transporter permease
Query= uniprot:Q1MCU1 (463 letters) >FitnessBrowser__azobra:AZOBR_RS08240 Length = 505 Score = 380 bits (976), Expect = e-110 Identities = 213/401 (53%), Positives = 268/401 (66%), Gaps = 31/401 (7%) Query: 58 LLAIFVAVAAIGRFAMVVFIRPNIDRRKLSKA-REGELD-ISTEKSFFHRHFLKIALIAL 115 L I +A A+ V+ IR R KLS+A R+ +D I+ + R IA++ Sbjct: 102 LRVILIAGGAVIAIRAVLAIRTG--RSKLSQAERDKRMDHIAAQVQHASRWLGPIAVVVA 159 Query: 116 LLYPMVVVAIKGPQGSLTYVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAY 175 L +P +A + + + GI +L Y+ML WGLNIVVGLAGLLDLGYVAFYAVGAY Sbjct: 160 LAFPFTPLADR-------QLLDIGILLLTYIMLGWGLNIVVGLAGLLDLGYVAFYAVGAY 212 Query: 176 SYALLSSYFGLSFWVLLPLSGIFAALWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLIN 235 SYALL+ YFG SFWV LPL+G AA+ GV+LGFPVLRLRGDY AIVTL FGEIIR++LIN Sbjct: 213 SYALLAHYFGFSFWVCLPLAGFLAAMSGVLLGFPVLRLRGDYFAIVTLGFGEIIRIILIN 272 Query: 236 WTDVTKGTFGISSIPKATLFGI------PFDATAGGFAKLFHLPISSAYYKIFLFYLILA 289 W T G GIS IP+ + FGI P + TA F ++F L S + IFL+YLIL Sbjct: 273 WYQFTGGPNGISGIPRPSFFGIADFTRTPAEGTA-AFHEMFGLEFSPLHRIIFLYYLILV 331 Query: 290 LCMLTAYVTIRLRRMPIGRAWEALREDEIACRSLGINTVTTKLTAFATGAMFAGFAGSFF 349 L ++ T+R+R++P+GRAWEALRED+IAC SLGIN KL AFA AMF GFAGSFF Sbjct: 332 LALVVNLFTMRVRKLPLGRAWEALREDDIACASLGINRTNMKLAAFAIAAMFGGFAGSFF 391 Query: 350 AARQGFVSPESFVFLESAVILAIVVLGGMGSLTGIAIAAIVMVGGTELLREMSFLKLIFG 409 A RQGF+SPESF F+ESA+ILAIVVLGGMGS G+ +AA +++G E RE++ Sbjct: 392 ATRQGFISPESFTFIESAIILAIVVLGGMGSQIGVVVAAFLVIGLPEAFRELAD------ 445 Query: 410 PDFTPELYRMLIFGLAMVVVMLFKPRGFVGSREPTAFLRER 450 YRML FG+ MV++ML++PRG + R+PT L R Sbjct: 446 -------YRMLAFGMGMVLIMLWRPRGLLAHRDPTILLHGR 479 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: 754 Number of extensions: 49 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: 505 Length adjustment: 34 Effective length of query: 429 Effective length of database: 471 Effective search space: 202059 Effective search space used: 202059 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: 52 (24.6 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