Align ABC transporter for L-Lysine, ATPase component (characterized)
to candidate CCNA_01670 CCNA_01670 sulfate transport ATP-binding protein cysA
Query= reanno::pseudo5_N2C3_1:AO356_09895 (257 letters) >FitnessBrowser__Caulo:CCNA_01670 Length = 339 Score = 144 bits (362), Expect = 3e-39 Identities = 87/244 (35%), Positives = 137/244 (56%), Gaps = 19/244 (7%) Query: 8 LEIRNLHKRYGQLEVLKGVSLTARDGDVISILGSSGSGKSTFLRCINLLENPNQGQILVA 67 + IR++ K++G+ L V L DG+++++LG SGSGK+T LR I LE P+ GQ+L Sbjct: 3 IAIRSVEKQFGRYPALNKVDLEIADGELLALLGPSGSGKTTLLRTIAGLEFPDAGQVLFD 62 Query: 68 GEELKLKAAKNGELVAADGKQINRLRSEIGFVFQNFNLWPHMSVLDNI---IEAPRRVLG 124 G+++ +A +GFVFQ + L+ HM+V NI ++ + Sbjct: 63 GQDVTYASAA---------------ARRVGFVFQQYALFKHMTVAKNIAFGLDVRKGKDK 107 Query: 125 QSKAEAVEVAEALLAKVGIADKRHAYPAELSGGQQQRAAIARTLAMQPKVILFDEPTSAL 184 SKAE E LL V + YP++LSGGQ+QR A++R LA+QP V+L DEP AL Sbjct: 108 PSKAEIARRVEELLKLVELEGLGGRYPSQLSGGQRQRVALSRALAVQPSVLLLDEPFGAL 167 Query: 185 DPEMVQEVLSVIRALAE-EGRTMLLVTHEMGFARQVSSEVVFLHQGLVEEQGSPQQVFEN 243 D + + + +R + + G T + VTH+ A +++ V L+ G +E+ G+P QV + Sbjct: 168 DATVRKSLRRELRRVHDATGVTTIFVTHDQEEALELADRVAILNNGRIEQIGTPDQVHDA 227 Query: 244 PLSA 247 P +A Sbjct: 228 PETA 231 Lambda K H 0.317 0.132 0.363 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: 169 Number of extensions: 12 Number of successful extensions: 4 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: 257 Length of database: 339 Length adjustment: 26 Effective length of query: 231 Effective length of database: 313 Effective search space: 72303 Effective search space used: 72303 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 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