Align PP1069, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate GFF355 PS417_01810 ABC transporter permease
Query= TCDB::Q88NY4 (223 letters) >FitnessBrowser__WCS417:GFF355 Length = 319 Score = 124 bits (311), Expect = 2e-33 Identities = 78/210 (37%), Positives = 117/210 (55%), Gaps = 9/210 (4%) Query: 13 PALWEGMVMTLKLMVMGVIGGIVLGTILALMRLSSSKLLSNLAGAYVNYFRSIPLLLVIT 72 P +W G+ TL L V+ I G+++G L RLSS+ L +L+ YV R PLL+ I Sbjct: 116 PLMW-GLWTTLWLSVVSGILGLIIGLATGLCRLSSNPTLRDLSTIYVELVRGTPLLVQIF 174 Query: 73 WFYLAVPFVLRWITGEDTPVGAFTSCVVAFMMFEAAYFCEIVRAGVQSISKGQMGAAQAL 132 FY + VL + + + A +F AY EIVRAGVQSI++GQ AA++L Sbjct: 175 IFYFFIGTVLN--------LSREFAGIAALSLFTGAYVAEIVRAGVQSITRGQNEAARSL 226 Query: 133 GMNYAQTMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYTVGLVDFLNSARSNGDIIGRS 192 G++ +Q+MR ++LPQAF+++ P L Q I L +DTSLV + + + L S R Sbjct: 227 GLSASQSMRHVVLPQAFKRVLPPLAGQFISLVKDTSLVSVIAITELLKSGREVITTSFSP 286 Query: 193 HEFLIFAGVVYFLISFSASWLVKRLQKRIS 222 E L +Y LI+ S + RL++R++ Sbjct: 287 FEILFCVAGLYLLINLPLSKMASRLERRLA 316 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: 177 Number of extensions: 8 Number of successful extensions: 3 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: 223 Length of database: 319 Length adjustment: 25 Effective length of query: 198 Effective length of database: 294 Effective search space: 58212 Effective search space used: 58212 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