Align PP1069, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate SMa2197 SMa2197 ABC transporter permease
Query= TCDB::Q88NY4 (223 letters) >FitnessBrowser__Smeli:SMa2197 Length = 304 Score = 109 bits (272), Expect = 7e-29 Identities = 70/220 (31%), Positives = 127/220 (57%), Gaps = 20/220 (9%) Query: 15 LWEGMVMTLKLMVMGVIGGIVLGTILALMRLSSSKLLSNLAGAYVNYFRSIPLLLVITWF 74 LW G+ +T+ L V+ ++ G+VLGTI A+M ++ + ++S +A AY+ +FR P+L+ + ++ Sbjct: 67 LW-GLSLTVWLTVVTMVIGVVLGTIFAIMAMADNVVISTVANAYIWFFRGTPVLVQLIFW 125 Query: 75 Y----------LAVPFVLRWIT-GEDTPVGAFTSCVVAFMMFEAAYFCEIVRAGVQSISK 123 Y + VPF W++ +T + T+ V+ + E AY EI+R+G+ S+ Sbjct: 126 YNLGALFPQLSVGVPFTSLWVSVPTNTLISPVTAAVLGLGLNEGAYMSEIIRSGLMSVDP 185 Query: 124 GQMGAAQALGMNYAQTMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYTVGLVDFLNSAR 183 GQ AA++LGM +T+ I+LPQA + P Q+I + + +SLV + L D L SA+ Sbjct: 186 GQRQAAKSLGMTNGKTLWRILLPQAMPVIIPPTGNQTIGMLKTSSLVSVISLADLLYSAQ 245 Query: 184 SNGDIIGRSHEF--LIFAGVVYFLISFSASWLVKRLQKRI 221 + I R+ + L+ +++L +A+ ++ +Q RI Sbjct: 246 T---IYSRNFQTIPLLIVACIWYL---AATTILSAVQVRI 279 Lambda K H 0.330 0.141 0.417 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: 157 Number of extensions: 8 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: 223 Length of database: 304 Length adjustment: 24 Effective length of query: 199 Effective length of database: 280 Effective search space: 55720 Effective search space used: 55720 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 (21.9 bits) S2: 47 (22.7 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