Align Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale)
to candidate Synpcc7942_1414 Synpcc7942_1414 ATPase
Query= uniprot:Q88GX0 (260 letters) >FitnessBrowser__SynE:Synpcc7942_1414 Length = 241 Score = 154 bits (390), Expect = 1e-42 Identities = 100/243 (41%), Positives = 142/243 (58%), Gaps = 13/243 (5%) Query: 18 PVLIRIEGLNKHYG----AFHVLRDIDLQVREGERIVLCGPSGSGKSTLIRCINRLEVAQ 73 P +I+ E ++K YG L +D QVR GE + G SGSGKST + I L+ Sbjct: 6 PPVIQFEHVSKIYGEGETTVRALDHVDFQVRAGEYCAIMGASGSGKSTAMNLIGCLDRPT 65 Query: 74 QGSIQVDGIDLAATTREA-AQVRS-DIGMVFQHFNLFPHMSVLDNCLLAPTSVRGLSRKD 131 G +DG D+A +A A VR+ IG VFQ F+L P +S ++N +L P G+S+++ Sbjct: 66 AGRYYLDGTDVADLDDDALAAVRNRKIGFVFQQFHLLPQLSAVENVML-PMIYAGISQQE 124 Query: 132 AEERARMYLSKVGIESQAHKYPSQLSGGQQQRVAIARALCMKPRIMLFDEPTSALDPEMV 191 +RA L++VG+ + P+QLSGGQQQRVAIARA+ +P ++L DEPT ALD + Sbjct: 125 RRDRAVAALTQVGLAQRLDNKPNQLSGGQQQRVAIARAIVNQPVLLLADEPTGALDSQTT 184 Query: 192 AEVLDVLVQLAGTGMTMLCVTHEMGFARQVAERVLFLEGGQIIEDSPPQVFFNQPRTERA 251 EVL++ QL G+T++ VTHE A + AERV++ GQI ++ N PR A Sbjct: 185 EEVLNIFDQLHQRGITIVIVTHEAEVADR-AERVIWFRDGQIQRETQ-----NPPRPVLA 238 Query: 252 KAF 254 F Sbjct: 239 ATF 241 Lambda K H 0.322 0.137 0.395 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: 166 Number of extensions: 9 Number of successful extensions: 3 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: 260 Length of database: 241 Length adjustment: 24 Effective length of query: 236 Effective length of database: 217 Effective search space: 51212 Effective search space used: 51212 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 (21.9 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