Align lacB: cytochrome c2 component of periplasmic glucoside 3-dehydrogenase (EC 1.1.99.13) (characterized)
to candidate CCNA_01268 CCNA_01268 cytochrome c
Query= reanno::Caulo:CCNA_01704 (120 letters) >FitnessBrowser__Caulo:CCNA_01268 Length = 168 Score = 69.3 bits (168), Expect = 2e-17 Identities = 44/110 (40%), Positives = 62/110 (56%), Gaps = 5/110 (4%) Query: 8 LAAVFAALASGAVAAPSGQQLFEQRCGMCHSLQQA-PGKMGPPLAGVVGRKAASFPGYTY 66 LAA+ A +G ++ +GQ F C CH++ + P GP L GV GRKA GY++ Sbjct: 51 LAALPAPYNTGDLS--NGQSKFAL-CRSCHTITEGGPDLTGPNLYGVFGRKAGVKEGYSF 107 Query: 67 SAALKGSGITWTADKLDAYSKAPTKVVPGTKM-LLGAPNDAERAAVIAYL 115 S A+K +G W A +LD + P +PGTKM G N+ +R +IAYL Sbjct: 108 SDAVKAAGFIWDAQQLDKWLADPRGFMPGTKMTFAGIKNEKDRIDLIAYL 157 Score = 21.9 bits (45), Expect = 0.004 Identities = 15/48 (31%), Positives = 21/48 (43%) Query: 68 AALKGSGITWTADKLDAYSKAPTKVVPGTKMLLGAPNDAERAAVIAYL 115 AA+ + +A D S + T AP DAE+AA +A L Sbjct: 7 AAVAALCVIVSACSKDGGSSSQAPADAPTPAAAPAPTDAEKAAALAAL 54 Lambda K H 0.317 0.129 0.377 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: 74 Number of extensions: 3 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 120 Length of database: 168 Length adjustment: 16 Effective length of query: 104 Effective length of database: 152 Effective search space: 15808 Effective search space used: 15808 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: 42 (20.8 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