Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate HSERO_RS00890 HSERO_RS00890 ABC transporter ATP-binding protein
Query= uniprot:Q1MCU1 (463 letters) >FitnessBrowser__HerbieS:HSERO_RS00890 Length = 404 Score = 254 bits (650), Expect = 3e-72 Identities = 155/366 (42%), Positives = 214/366 (58%), Gaps = 48/366 (13%) Query: 113 IALLLYPMVVVAIKGPQGSLTYVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAV 172 + LLL M+V Q ++V + +L Y+MLA GLN+VVG AGLLDLGY+AFYA+ Sbjct: 19 LLLLLALMIVFPFVAQQFGNSWVRIMDVALL-YIMLALGLNVVVGFAGLLDLGYIAFYAI 77 Query: 173 GAYSYALLSS--------------------------------YFGLSFWVLLPLSGIFAA 200 GAYS LL+S LS W+++P+S AA Sbjct: 78 GAYSAGLLASPQFAAVIESFVNTYPSVGNFLVWLCGPEIVQNGIHLSLWLIVPISAFLAA 137 Query: 201 LWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINW---TDVTKGTFGISSIPKATLFGI 257 L+G +LG P L+LRGDYLAIVTL FGEIIR+ + N ++T G GI+ I +FG+ Sbjct: 138 LFGALLGAPTLKLRGDYLAIVTLGFGEIIRIFMNNLNAPVNITNGPQGINLIDPIKVFGV 197 Query: 258 PF--DATAGGFAKLF--HLPISSAYYKIFLFYLILALCMLTAYVTIRLRRMPIGRAWEAL 313 + +G K+F +P +AYY +L L LC+ + ++RL+ +GRAW A+ Sbjct: 198 SLAGEPGSGSMVKVFGMSMPSVNAYY-----FLFLLLCIGVIFFSVRLQDSRLGRAWVAI 252 Query: 314 REDEIACRSLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFVFLESAVILAIV 373 REDEIA +++GINT KL AFA GA F G AG+ F A QGFVSPESF ES +LA+V Sbjct: 253 REDEIAAKAMGINTRNVKLLAFAMGASFGGVAGAMFGAFQGFVSPESFSLTESIAVLAMV 312 Query: 374 VLGGMGSLTGIAIAAIVMVGGTELLREM--SFLKLIFGPDF-TPELYRMLIFGLAMVVVM 430 VLGG+G + G+ + +++ E+LR + IFG + E+ R L++GLAMVV+M Sbjct: 313 VLGGIGHIPGVVLGGVILAALPEVLRHVVEPVQMAIFGKVWIDAEVLRQLLYGLAMVVIM 372 Query: 431 LFKPRG 436 L +P G Sbjct: 373 LTRPAG 378 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: 583 Number of extensions: 37 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 463 Length of database: 404 Length adjustment: 32 Effective length of query: 431 Effective length of database: 372 Effective search space: 160332 Effective search space used: 160332 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: 51 (24.3 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