Align PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate GFF139 Psest_0139 ABC-type histidine transport system, ATPase component
Query= TCDB::Q88NY5 (256 letters) >FitnessBrowser__psRCH2:GFF139 Length = 257 Score = 222 bits (566), Expect = 5e-63 Identities = 121/242 (50%), Positives = 167/242 (69%), Gaps = 14/242 (5%) Query: 14 ISIKNVNKWYGDFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKCVNALEPFQKGDIVVD 73 + I+N++K YGD +VL S + G+V+ + G SGSGKST ++C+N LE +G+I+V Sbjct: 8 LEIRNLHKRYGDLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHEGEILVA 67 Query: 74 GTSI------------ADPKTNLPKLRSRVGMVFQHFELFPHLTITENLTIAQRKVLGRS 121 G + AD K L ++RS +G VFQ+F L+PH+TI +N+ A R+VLG+S Sbjct: 68 GEQLKLKRDKQGDLVAADGK-QLNRIRSELGFVFQNFNLWPHMTILDNIIEAPRRVLGQS 126 Query: 122 EAEATKKGLALLDRVGLSAHAKKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDP 181 +AEAT+ ALL +VG++ +P QLSGGQQQR AIAR LAM P V+LFDEPTSALDP Sbjct: 127 KAEATEVAEALLAKVGIADKRHVYPNQLSGGQQQRAAIARTLAMQPKVILFDEPTSALDP 186 Query: 182 EMVSEVLDVMVQLAQEGMTMMCVTHEMGFARKVANRVIFMDKGSIIEDCTKEEFFGD-QS 240 EMV EVL V+ LA+EG TM+ VTHEM FA++V++ V+F+ +G + E T E+ F + QS Sbjct: 187 EMVQEVLAVIRSLAEEGRTMLLVTHEMNFAKQVSSEVVFLHQGLVEEQGTPEQVFDNPQS 246 Query: 241 AR 242 AR Sbjct: 247 AR 248 Lambda K H 0.319 0.134 0.383 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: 176 Number of extensions: 3 Number of successful extensions: 2 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: 256 Length of database: 257 Length adjustment: 24 Effective length of query: 232 Effective length of database: 233 Effective search space: 54056 Effective search space used: 54056 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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