Align PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate 3606889 Dshi_0319 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= TCDB::Q88NY3 (248 letters) >FitnessBrowser__Dino:3606889 Length = 411 Score = 88.6 bits (218), Expect = 2e-22 Identities = 50/128 (39%), Positives = 74/128 (57%), Gaps = 1/128 (0%) Query: 111 LISVVICLGLFTAARVCEQVRTGIQALPKGQEAAARAMGFSLPQIYNNVLLPQAYRIIIP 170 LI++ L L+T A + E VR GI A+ KGQ AA A+G +I + ++LPQA R+IIP Sbjct: 279 LIALWFALALYTGAFIAENVRAGILAVSKGQTEAAAALGMRPNRIMSLIILPQALRVIIP 338 Query: 171 PLTSEFLNVFKNSSVASLIGLMELLAQT-KQTAEFSANLFEAFTLATLIYFTLNMGLMLL 229 P+ S++LN+ KNSS+A+ IG M+L T + FE L L Y +++ + L Sbjct: 339 PVISQYLNLTKNSSLAAAIGYMDLTGTLGGVTLNQTGRSFECVLLLMLFYLLISLSISAL 398 Query: 230 MRMVEKKV 237 M + V Sbjct: 399 MNLYNNAV 406 Score = 50.8 bits (120), Expect = 4e-11 Identities = 26/77 (33%), Positives = 45/77 (58%) Query: 18 SETYLDWYITGLGWTIAIAITAWIIALLLGSLLGVMRTVPNRLVSGIATAYVELFRNVPL 77 ++T++ GL T+ +A I A + G L GV+R N LV+ + + YVE+FRN+P+ Sbjct: 87 TDTHMRAAFVGLLNTLLVAFLGCITATIFGVLAGVLRLSKNWLVAKVMSVYVEIFRNIPV 146 Query: 78 LVQLFIWYFLVPDLLPE 94 L+ + I ++ LP+ Sbjct: 147 LIWIVIISAVMSQALPQ 163 Lambda K H 0.325 0.139 0.425 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: 228 Number of extensions: 10 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 248 Length of database: 411 Length adjustment: 27 Effective length of query: 221 Effective length of database: 384 Effective search space: 84864 Effective search space used: 84864 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 48 (23.1 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