Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate Synpcc7942_0513 Synpcc7942_0513 ATPase
Query= uniprot:A0A165KC78 (242 letters) >FitnessBrowser__SynE:Synpcc7942_0513 Length = 250 Score = 111 bits (277), Expect = 2e-29 Identities = 74/243 (30%), Positives = 123/243 (50%), Gaps = 13/243 (5%) Query: 8 VLLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIE 67 V ++++ ++ +YG V V V +GE+V L+G NGAGKTTT TG ++G++ Sbjct: 9 VKIRLENVRKSYGKRLIVNRVSLSVAQGEVVGLLGPNGAGKTTTFYMTTGLERPDEGHVW 68 Query: 68 YLGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENL-----QMGAYIRKDKAGILADI 122 + + G+ + + +F +T+ ENL Q G R+ + + Sbjct: 69 LDETELTRLPMTQRARLGIGYLAQEASIFRHLTVVENLLLVLQQTGIRGREQRQRV---- 124 Query: 123 EKMFTIFPRLRERKDQLAGTMSGGEQQMLAMGRALM---SQPKVLLLDEPSMGLSPIMVD 179 E++ + F RL + +SGGE++ + RAL PK LLLDEP G+ PI V Sbjct: 125 EELLSEF-RLEKVAHTQGIRVSGGERRRTEIARALAVGSQGPKFLLLDEPFAGIDPIAVA 183 Query: 180 KIFEVVRDVYALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAY 239 ++ E++ + A + I++ + N L I DR Y++ G I G ++L ++P VR Y Sbjct: 184 EVQEIIARLRAQQMGILITDHNVRETLKITDRAYILRDGEILAAGSAEELASNPLVRQYY 243 Query: 240 LGE 242 LGE Sbjct: 244 LGE 246 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: 136 Number of extensions: 8 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: 250 Length adjustment: 24 Effective length of query: 218 Effective length of database: 226 Effective search space: 49268 Effective search space used: 49268 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 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