Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate CA265_RS04345 CA265_RS04345 lipoprotein-releasing system ATP-binding protein LolD
Query= uniprot:A0A165KC78 (242 letters) >FitnessBrowser__Pedo557:CA265_RS04345 Length = 216 Score = 95.5 bits (236), Expect = 7e-25 Identities = 72/220 (32%), Positives = 120/220 (54%), Gaps = 13/220 (5%) Query: 9 LLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIEY 68 +L+ G++ +YG +Q +KGV+FEV++GE+VS+IG +GAGK+T + I GTL D Sbjct: 1 MLKATGIRKSYGNLQILKGVNFEVQKGEIVSIIGPSGAGKSTLLH-ILGTLDKPDDGSVQ 59 Query: 69 LGKSIKGKGAWDLV----KEGLVMVPEGRGVFARMTITENLQMGAYIRK-DKAGILADIE 123 L ++ K DL+ + + V + + + EN+ + A+I K +K Sbjct: 60 LKGTVINKLNGDLLSTFRNQNIGFVFQFHHLLPEFSAIENICIPAFIAKTNKKQAETRAF 119 Query: 124 KMFTIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGL---SPIMVDK 180 ++ +F L++R +SGGEQQ +A+ RAL++ P ++L DEPS L + + + Sbjct: 120 ELLDLF-GLKDRAQHKPNQLSGGEQQRVAIARALINNPSIILADEPSGNLDSENAAGLHQ 178 Query: 181 IFEVVRDVYALGVTIVLVEQNASRALAIADRGYVMESGLI 220 +F +RD + T V+V N A +DR M+ GLI Sbjct: 179 LFVSLRDNF--HQTFVIVTHNEHLA-KTSDRVVSMKDGLI 215 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: 120 Number of extensions: 6 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: 216 Length adjustment: 23 Effective length of query: 219 Effective length of database: 193 Effective search space: 42267 Effective search space used: 42267 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