Align PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate WP_011372556.1 SUDEN_RS04860 sulfate/molybdate ABC transporter ATP-binding protein
Query= TCDB::Q88NY5 (256 letters) >NCBI__GCF_000012965.1:WP_011372556.1 Length = 290 Score = 124 bits (311), Expect = 2e-33 Identities = 79/228 (34%), Positives = 128/228 (56%), Gaps = 11/228 (4%) Query: 16 IKNVNKWYGDFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKCVNALEPFQKGDIVVDGT 75 IK +N G+ + D +++ GE + + G SGSGK+TL++ + LE + G I VD Sbjct: 7 IKPLNTADGEINLAVD--KKIEDGEFLTLFGKSGSGKTTLLRIIAGLEVPESGYIKVDNE 64 Query: 76 SIADPKT--NLPKLRSRVGMVFQHFELFPHLTITENLTIAQRKVLGRSEAEATKKGLALL 133 D K N+P R VG VFQ + LFP++++ +NL A + + KK +L Sbjct: 65 VWFDSKRGINIPPQRRNVGFVFQDYALFPNMSVEDNLKFALQ------DKNKFKKVDDIL 118 Query: 134 DRVGLSAHAKKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVSEVLDVMVQ 193 + + +K P LSGGQ+QRVA+ARAL +P ++L DEP SALD M ++ D + Sbjct: 119 KIMEIQNLSKMKPQHLSGGQKQRVAVARALMREPKILLLDEPLSALDSTMRQKLQDELFF 178 Query: 194 LAQE-GMTMMCVTHEMGFARKVANRVIFMDKGSIIEDCTKEEFFGDQS 240 + Q+ G+ + V+H++G ++++RV + G I D + E F +Q+ Sbjct: 179 IHQKFGIISLLVSHDIGEIFRLSSRVFKISSGEITHDGSPSEVFANQN 226 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: 149 Number of extensions: 9 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: 256 Length of database: 290 Length adjustment: 25 Effective length of query: 231 Effective length of database: 265 Effective search space: 61215 Effective search space used: 61215 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 Apr 09 2024. 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