Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Synpcc7942_0513 Synpcc7942_0513 ATPase
Query= uniprot:Q1MCU3 (247 letters) >FitnessBrowser__SynE:Synpcc7942_0513 Length = 250 Score = 122 bits (305), Expect = 9e-33 Identities = 79/236 (33%), Positives = 127/236 (53%), Gaps = 7/236 (2%) Query: 12 LQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVFE 71 +++ V YG + V + V +GE+V L+G NGAGK+T G + G V + Sbjct: 11 IRLENVRKSYGKRLIVNRVSLSVAQGEVVGLLGPNGAGKTTTFYMTTGLERPDEGHVWLD 70 Query: 72 GRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNL--KHFAEDVEKIFTL 129 ++TR+P + ARL I + IF +TV+ENL + + + + VE++ + Sbjct: 71 ETELTRLPMTQRARLGIGYLAQEASIFRHLTVVENLLLVLQQTGIRGREQRQRVEELLSE 130 Query: 130 FPRLKERHAQRGGTLSGGEQQMLSIGRALMA---RPKLLLLDEPSLGLAPLIVKGIFEAI 186 F K H Q G +SGGE++ I RAL PK LLLDEP G+ P+ V + E I Sbjct: 131 FRLEKVAHTQ-GIRVSGGERRRTEIARALAVGSQGPKFLLLDEPFAGIDPIAVAEVQEII 189 Query: 187 RKLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAYL 242 +L A+ + + + + N L+++ RAY++ +G++ +GS +EL +NP VR YL Sbjct: 190 ARL-RAQQMGILITDHNVRETLKITDRAYILRDGEILAAGSAEELASNPLVRQYYL 244 Lambda K H 0.320 0.137 0.387 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: 144 Number of extensions: 5 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: 247 Length of database: 250 Length adjustment: 24 Effective length of query: 223 Effective length of database: 226 Effective search space: 50398 Effective search space used: 50398 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: 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