Align ABC transporter (characterized, see rationale)
to candidate 209225 DVU0291 ABC transporter, ATP-binding protein
Query= uniprot:A0A166QFW2 (381 letters) >MicrobesOnline__882:209225 Length = 354 Score = 178 bits (451), Expect = 2e-49 Identities = 115/318 (36%), Positives = 167/318 (52%), Gaps = 18/318 (5%) Query: 4 LKLDNVNKQLGGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLLID 63 L ++ + + L G +L DV+L AAGE V VGPSG GK+TLLR IAGLD+ G + Sbjct: 3 LAVEGLGRTLAGREVLHDVNLTAAAGEVVCLVGPSGVGKTTLLRCIAGLDAPDEGTI--- 59 Query: 64 GRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQILQL 123 RV + GV +VFQ Y L+PH+SV++N++FG + +L+ERV + +L Sbjct: 60 --RVTPPQGHGGGVVLVFQDYLLFPHLSVFENVAFGPRARGVRGAALKERVHTMLRAFRL 117 Query: 124 DK-----LLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIAR 178 D + R P +LS GQRQRVA+ RA+ +P +LL DEP +NLD LR +M + Sbjct: 118 DTDDLAHMASRYPAQLSAGQRQRVALARALVCDPAVLLLDEPFANLDRGLRGEMAAFVRD 177 Query: 179 LHDRLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPR 238 + R G + VTHD EA + D++ V+ GG + Q+ P ++Y PA A FLG Sbjct: 178 VVRRFGVATVTVTHDLEEAFAIGDRLGVMLGGTLAQLAPPLDVYRHPADEATARFLGP-- 235 Query: 239 MNFLSARLQTPGETSLVDTLVWGITSLPFDSSNLAAGTPLSLGIRP---EHVSLKAADGT 295 ++ +T T +DT T+ L P +L +RP L +A T Sbjct: 236 ---VTVLDETTRRTLGIDTPPAAATACADTMQGLRLYRPEALAVRPWADGPAVLVSARFT 292 Query: 296 AGVVVTAVEYLGSETYVH 313 V+ ++ G E VH Sbjct: 293 GQVMQLLLDVEGQELLVH 310 Lambda K H 0.320 0.137 0.394 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: 313 Number of extensions: 21 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: 381 Length of database: 354 Length adjustment: 30 Effective length of query: 351 Effective length of database: 324 Effective search space: 113724 Effective search space used: 113724 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: 49 (23.5 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