Align Arginine transport ATP-binding protein ArtM (characterized)
to candidate CCNA_01670 CCNA_01670 sulfate transport ATP-binding protein cysA
Query= SwissProt::P54537 (240 letters) >FitnessBrowser__Caulo:CCNA_01670 Length = 339 Score = 154 bits (389), Expect = 2e-42 Identities = 87/233 (37%), Positives = 139/233 (59%), Gaps = 10/233 (4%) Query: 2 IKVEKLSKSFGKHEVLKNISTTIAEGEVVAVIGPSGSGKSTFLRCLNLLEKPNGGTITIK 61 I + + K FG++ L + IA+GE++A++GPSGSGK+T LR + LE P+ G + Sbjct: 3 IAIRSVEKQFGRYPALNKVDLEIADGELLALLGPSGSGKTTLLRTIAGLEFPDAGQVLFD 62 Query: 62 DTEITKPKTNTLKVRENIGMVFQHFHLFPHKTVLENIMYAPVNVKK----ESKQAAQEKA 117 ++T +V G VFQ + LF H TV +NI + ++V+K SK + Sbjct: 63 GQDVTYASAAARRV----GFVFQQYALFKHMTVAKNIAFG-LDVRKGKDKPSKAEIARRV 117 Query: 118 EDLLRKVGLFEKRNDYPNRLSGGQKQRVAIARALAMNPDIMLFDEPTSALDPEMVKEVLQ 177 E+LL+ V L YP++LSGGQ+QRVA++RALA+ P ++L DEP ALD + K + + Sbjct: 118 EELLKLVELEGLGGRYPSQLSGGQRQRVALSRALAVQPSVLLLDEPFGALDATVRKSLRR 177 Query: 178 VMKELVE-TGMTMVIVTHEMGFAKEVADRVLFMDQGMIVEDGNPKEFFMSPKS 229 ++ + + TG+T + VTH+ A E+ADRV ++ G I + G P + +P++ Sbjct: 178 ELRRVHDATGVTTIFVTHDQEEALELADRVAILNNGRIEQIGTPDQVHDAPET 230 Lambda K H 0.317 0.134 0.368 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: 171 Number of extensions: 7 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: 240 Length of database: 339 Length adjustment: 26 Effective length of query: 214 Effective length of database: 313 Effective search space: 66982 Effective search space used: 66982 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 (21.6 bits) S2: 47 (22.7 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