Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate 206139 DVU0714 branched-chain amino acid ABC transporter, permease protein
Query= uniprot:Q1MCU1 (463 letters) >MicrobesOnline__882:206139 Length = 317 Score = 197 bits (502), Expect = 3e-55 Identities = 114/300 (38%), Positives = 173/300 (57%), Gaps = 33/300 (11%) Query: 140 IQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYFGLSFWVLLPLSGIFA 199 + I +Y +LA LN+++G AGL +G+ AFYAVGAY+ A+L++ + + +P++G+ A Sbjct: 31 VSIGLYAVLALSLNLILGQAGLFHMGHAAFYAVGAYTAAILNTVYHVPVLWTMPVAGLLA 90 Query: 200 ALWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWT-DVTKGTFGISSIPKATLFGIP 258 AL+ +++ P++ LRGDYL IVT+ EI+R+ LIN +T G GI I + LFG Sbjct: 91 ALFALVVARPIIHLRGDYLLIVTIGIVEIVRIALINNVFGITGGANGIFGISRPMLFGYK 150 Query: 259 FDATAGGFAKLFHLPISSAYYKIFLFYLILALCMLTAYVTIRLRRMPIGRAWEALREDEI 318 I +YLI ++ + RL GRA ++ED++ Sbjct: 151 ISK------------------PIQFYYLIWTWVAISILLFRRLECSRFGRALNYIKEDDV 192 Query: 319 ACRSLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFVFLESAVILAIVVLGGM 378 A G++T KL AF GA++AG G+F+AA+ +SPESF F ES V+ AIV+LGG Sbjct: 193 AAEGSGVDTAYYKLAAFVLGALWAGMTGTFYAAKMTIISPESFSFWESVVLFAIVILGG- 251 Query: 379 GSLTGIAIAAIVMVGGTELLREMSFLKLIFGPDFTPELYRMLIFGLAMVVVMLFKPRGFV 438 GS G+ + A +++G EL R+ + RMLIFGLAMVV+M+F+P+G + Sbjct: 252 GSNRGVLLGAFLLIGLPELFRDFASA-------------RMLIFGLAMVVMMIFRPQGML 298 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: 457 Number of extensions: 33 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: 463 Length of database: 317 Length adjustment: 30 Effective length of query: 433 Effective length of database: 287 Effective search space: 124271 Effective search space used: 124271 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: 50 (23.9 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