Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate Synpcc7942_0815 Synpcc7942_0815 ATPase
Query= uniprot:A0A165KC78 (242 letters) >FitnessBrowser__SynE:Synpcc7942_0815 Length = 243 Score = 195 bits (495), Expect = 8e-55 Identities = 102/221 (46%), Positives = 148/221 (66%), Gaps = 3/221 (1%) Query: 22 IQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIEYLGKSIKGKGAWDL 81 + V+GV+ +V GEL++L+G NGAGK+T K + G + + G+I + G+ I + + Sbjct: 20 LDIVQGVNLQVAAGELLTLLGPNGAGKSTLAKTLLGLVPVRSGSIRFRGQEISRLSSEAI 79 Query: 82 VKEGLVMVPEGRGVFARMTITENLQMGAY-IRKDKAGILADIEKMFTIFPRLRERKDQLA 140 V+ G+ VP+ R VFA +T+ ENL+MG + IR A I +++ +FP L R+ Q A Sbjct: 80 VRLGIGYVPQVRNVFASLTVAENLEMGLFQIRPQHRP--AAIARIYDLFPTLATRRSQRA 137 Query: 141 GTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIFEVVRDVYALGVTIVLVEQ 200 GT+SGGE+Q+LAMGRAL ++P +L+LDEPS LSP+MV +FE +R + G TI+LVEQ Sbjct: 138 GTLSGGERQLLAMGRALAAEPTLLVLDEPSAALSPLMVATVFEQIRAINNSGTTIILVEQ 197 Query: 201 NASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAYLG 241 N RAL +ADRG ++ESG TGP +LL+DP + YLG Sbjct: 198 NTRRALQLADRGCILESGRDRQTGPAAELLDDPLLGELYLG 238 Lambda K H 0.317 0.136 0.373 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: 160 Number of extensions: 7 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: 242 Length of database: 243 Length adjustment: 23 Effective length of query: 219 Effective length of database: 220 Effective search space: 48180 Effective search space used: 48180 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: 46 (22.3 bits)
This GapMind analysis is from Apr 09 2024. 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