Align ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale)
to candidate Synpcc7942_0249 Synpcc7942_0249 ATPase
Query= uniprot:A0A1N7U8S3 (276 letters) >FitnessBrowser__SynE:Synpcc7942_0249 Length = 261 Score = 212 bits (540), Expect = 6e-60 Identities = 123/264 (46%), Positives = 171/264 (64%), Gaps = 18/264 (6%) Query: 19 QPVTAAIK-----LQVEGIHKRYG-EHEVLKGVSLNARQGDVISLIGASGSGKSTMLRCI 72 +PVTA + EG+ K YG + + L GVSL ++G+V+ ++G SGSGKST LR + Sbjct: 9 EPVTAIASAPETMIYAEGVEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTL 68 Query: 73 NFLEQPDAGVITLDGISIEMRQGRAGTRAPHQDQLQNLRTRLAMVFQHFNLWSHMTVLEN 132 N LE G I ++G + + + + +R + MVFQ FNL+ H+TVL+N Sbjct: 69 NALESHQRGEIWIEGHRL----------SHDRRDIATIRQEVGMVFQQFNLFPHLTVLQN 118 Query: 133 ITMAPRRVLDVSAAEAEKRARMYLDKVGLPSRVADQYPAFLSGGQQQRVAIARALAMEPE 192 + +AP +V A+AE AR L++V + + AD+YP LSGGQQQRVAIARALAM+P Sbjct: 119 LMLAPVQVRRWPVAQAEATARQLLERVRIAEQ-ADKYPGQLSGGQQQRVAIARALAMQPR 177 Query: 193 IILFDEPTSALDPELVGEVLKVIQTLAEEGRTMLMVTHEMGFARQVSSQVLFLHQGR-VE 251 I+LFDEPTSALDPE+V EVL V++ LA EG TML+ THE+GFAR+V+ +V+ + G+ VE Sbjct: 178 ILLFDEPTSALDPEMVREVLDVMRDLASEGMTMLVATHEVGFAREVADRVVLMADGQIVE 237 Query: 252 EHGDARILDQPNSERLQQFLSNRL 275 E R P S+R +QFL+ L Sbjct: 238 EAPPDRFFTAPQSDRAKQFLAQIL 261 Lambda K H 0.319 0.133 0.372 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: 232 Number of extensions: 14 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: 276 Length of database: 261 Length adjustment: 25 Effective length of query: 251 Effective length of database: 236 Effective search space: 59236 Effective search space used: 59236 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: 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