Align Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale)
to candidate N515DRAFT_1821 N515DRAFT_1821 putative ABC transport system ATP-binding protein
Query= uniprot:Q88GX0 (260 letters) >FitnessBrowser__Dyella79:N515DRAFT_1821 Length = 238 Score = 149 bits (377), Expect = 4e-41 Identities = 85/222 (38%), Positives = 135/222 (60%), Gaps = 4/222 (1%) Query: 34 HVLRDIDLQVREGERIVLCGPSGSGKSTLIRCINRLEVAQQGSIQVDGIDLAATTREA-A 92 + LRD ++ V+EGE + + GPSGSGK+T + LE G +DG++++ A + Sbjct: 19 YALRDFNIDVKEGEFVAVTGPSGSGKTTFLTIAGLLETFTGGEYHLDGVEVSNLNDNARS 78 Query: 93 QVRSD-IGMVFQHFNLFPHMSVLDNCLLAPTSVRGLSRKDAEERARMYLSKVGIESQAHK 151 ++R++ IG +FQ FNL P ++V DN + P RG+ + ++R L +VG+ S+A Sbjct: 79 KIRNEKIGFIFQAFNLIPDLNVYDN-VEVPLRYRGMKALERKQRIMDALERVGLASRAKH 137 Query: 152 YPSQLSGGQQQRVAIARALCMKPRIMLFDEPTSALDPEMVAEVLDVLVQLAGTGMTMLCV 211 YP++LSGGQQQRVAIARAL PR++L DEPT LD +M V+++L ++ G T++ V Sbjct: 138 YPAELSGGQQQRVAIARALAGSPRLLLADEPTGNLDTQMARGVMELLEEIHREGATIVMV 197 Query: 212 THEMGFARQVAERVLFLEGGQIIEDSPPQVFFNQPRTERAKA 253 TH+ A + A+R + + GQ+++ + F Q A A Sbjct: 198 THDPELATR-AQRNVHVIDGQVVDLAEDPRFHQQQARAGAPA 238 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: 164 Number of extensions: 6 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: 238 Length adjustment: 24 Effective length of query: 236 Effective length of database: 214 Effective search space: 50504 Effective search space used: 50504 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