Align Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale)
to candidate 202786 SO3692 ABC transporter, ATP-binding protein (NCBI ptt file)
Query= uniprot:Q88GX0 (260 letters) >FitnessBrowser__MR1:202786 Length = 246 Score = 149 bits (375), Expect = 7e-41 Identities = 81/199 (40%), Positives = 122/199 (61%), Gaps = 3/199 (1%) Query: 34 HVLRDIDLQVREGERIVLCGPSGSGKSTLIRCINRLEVAQQGSIQVDGIDLA-ATTREAA 92 H LRD +L+V EGE + + GPSGSGK+T + LE G +DGI+++ + ++A Sbjct: 19 HALRDFNLEVSEGEFVAVTGPSGSGKTTFLNIAGLLEGFTHGDYFLDGINVSNLSDNKSA 78 Query: 93 QVRSD-IGMVFQHFNLFPHMSVLDNCLLAPTSVRGLSRKDAEERARMYLSKVGIESQAHK 151 VR++ IG +FQ FNL P +++ +N + P RG S K+ R L +VG+ ++ Sbjct: 79 AVRNEKIGFIFQGFNLIPDLNLAEN-IEVPLRYRGFSAKERNRRVEQALEQVGLAARMKH 137 Query: 152 YPSQLSGGQQQRVAIARALCMKPRIMLFDEPTSALDPEMVAEVLDVLVQLAGTGMTMLCV 211 P+QLSGGQQQRVAIARAL +PR +L DEPT LD M +V+++L + G T++ V Sbjct: 138 LPTQLSGGQQQRVAIARALAGEPRFLLADEPTGNLDSLMARQVMELLENINQAGTTIIMV 197 Query: 212 THEMGFARQVAERVLFLEG 230 TH+ AR+ + ++G Sbjct: 198 THDPELARRAQRNIQIVDG 216 Lambda K H 0.322 0.137 0.395 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: 141 Number of extensions: 7 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: 260 Length of database: 246 Length adjustment: 24 Effective length of query: 236 Effective length of database: 222 Effective search space: 52392 Effective search space used: 52392 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 (21.9 bits) S2: 46 (22.3 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