Align ABC transporter related (characterized, see rationale)
to candidate 207830 DVU2343 amino acid ABC transporter, ATP-binding protein
Query= uniprot:B2TBJ9 (263 letters) >MicrobesOnline__882:207830 Length = 242 Score = 229 bits (585), Expect = 3e-65 Identities = 119/242 (49%), Positives = 165/242 (68%), Gaps = 11/242 (4%) Query: 13 NIHKSFGDHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPDDGSVSLAGEEL 72 ++HK +G+ HVL+GI+ +G+V+ I G SGSGKS+F+RCLN LE G + L G+ + Sbjct: 8 DVHKWYGEFHVLRGITQKVEKGEVLVICGPSGSGKSSFIRCLNRLEPIQKGQILLEGKSI 67 Query: 73 KMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGPMRVQKRSRAESV 132 K V+ +R+++G+VFQ FNL+ H++VL+N+ P++V+K RA++ Sbjct: 68 HDKDV-----------DVNDLRTEVGIVFQQFNLYPHLSVLKNVTLAPIKVRKMPRAKAE 116 Query: 133 EEAEALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEPTSALDPELVGE 192 A LL +VG+ ++ G YP LSGGQQQRVAIARALAM PKVMLFDEPTSALDPE++ E Sbjct: 117 AVAMELLERVGIHDQAGKYPVELSGGQQQRVAIARALAMQPKVMLFDEPTSALDPEMINE 176 Query: 193 VLRVMRSLAEEGRTMLVVTHEMGFARHVSNRVMFLHQGQVEADGTPDEVFVECKSDRFRQ 252 VL M+ LA EG TML VTHEMGFAR V++RV+F+ G V + PD F + +R + Sbjct: 177 VLNCMKDLAREGMTMLCVTHEMGFAREVADRVIFMDGGNVVEEAPPDIFFSNPQHERTKA 236 Query: 253 FV 254 F+ Sbjct: 237 FL 238 Lambda K H 0.318 0.133 0.377 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: 185 Number of extensions: 8 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: 263 Length of database: 242 Length adjustment: 24 Effective length of query: 239 Effective length of database: 218 Effective search space: 52102 Effective search space used: 52102 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 (21.7 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