Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Synpcc7942_1893 Synpcc7942_1893 ATPase
Query= uniprot:Q1MCU3 (247 letters) >FitnessBrowser__SynE:Synpcc7942_1893 Length = 258 Score = 130 bits (326), Expect = 3e-35 Identities = 79/248 (31%), Positives = 137/248 (55%), Gaps = 17/248 (6%) Query: 11 LLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVF 70 LL+ G+ +G ++A+ V + V +G I LIG NGAGKSTL + +A G V F Sbjct: 7 LLEAEGLSKRFGGLQAVQDVRLQVAEGTITGLIGPNGAGKSTLFALLSNFLKADAGKVRF 66 Query: 71 EGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLKHF----------- 119 GR I ++ +++A+L + ++ + R R+TVLEN+ +G + F Sbjct: 67 RGRAIEKLQPYQLAQLGLVRTFQVARSLSRLTVLENMLLGGQQQRGEKFWQVWLHPQAIR 126 Query: 120 ---AEDVEKIFTLFP--RLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGL 174 E ++ F+L L + G+LSGG++++L + RALMA+P+L+LLDEP+ G+ Sbjct: 127 RQEQELRDRAFSLLSDVGLAAKAQDYAGSLSGGQRKLLEMARALMAQPQLVLLDEPAAGV 186 Query: 175 APLIVKGIFEAIRKLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLAN 234 P +++ I + I+ N+ +G++ ++E N + L R +V+ GK + G ++ + Sbjct: 187 NPALIEKICDHIQTWNQ-QGISFLIIEHNMDVIMSLCDRVWVLAEGKNLVDGPPAQIQQD 245 Query: 235 PEVRAAYL 242 +V AAYL Sbjct: 246 EQVLAAYL 253 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: 159 Number of extensions: 13 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: 247 Length of database: 258 Length adjustment: 24 Effective length of query: 223 Effective length of database: 234 Effective search space: 52182 Effective search space used: 52182 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