Align (S)-citramalyl-CoA lyase (EC 4.1.3.25) (characterized)
to candidate HSERO_RS14045 HSERO_RS14045 aldolase
Query= BRENDA::Q9I562 (275 letters) >FitnessBrowser__HerbieS:HSERO_RS14045 Length = 277 Score = 201 bits (512), Expect = 1e-56 Identities = 129/275 (46%), Positives = 162/275 (58%), Gaps = 10/275 (3%) Query: 5 IVRSALFVPATRPERIPKALASGADRVIVDLEDAVEEGLKVEARANLRRFLV----DTPE 60 I S LFVPA RPER KAL SGAD VIVDLEDAV K AR L R+L + Sbjct: 2 IASSYLFVPANRPERYAKALDSGADAVIVDLEDAVARPYKEAARETLARWLAGPEGQASQ 61 Query: 61 ARVLVRINAAEHPGHADDLALCRDHAGVIGLLLPKVESAAQVRHAAVA--SGKPVWPIVE 118 AR+ VRINAA+ H DL L V G++LPK E AA V A A SG + ++E Sbjct: 62 ARLWVRINAADTVWHEQDL-LTFSALPVAGIVLPKAEDAAGVGAVAGALRSGSGLIALIE 120 Query: 119 SARGLAALGEIAAAAGVERLSFGSLDLALDLDLNSGSNAAEQILGHARYALLLQTRLAGL 178 SA GLAA+ +IAAA GV+RL+FGS+D LDL + G E+ L R ++L +RLAG+ Sbjct: 121 SAAGLAAMRQIAAAPGVQRLAFGSIDAQLDLGMQCGPE--EEELLSLRVEMVLASRLAGI 178 Query: 179 APPLDGVYPAIQNRAGLVEAVRFARDMGFGGLLCIHPSQVEPIHQTLMPSPAELEWARRV 238 A P+DGV + A LV V AR +GFG LCIHP QVE + + +PS EL WA V Sbjct: 179 AAPVDGVTAGFDDEALLVRGVERARRLGFGAKLCIHPRQVEVVRRGFLPSEQELAWAAEV 238 Query: 239 -AEAGASGAGVFVVDGEMVDAPVLGRARRLLERAG 272 A AS G + G M+D P++ +A + L + G Sbjct: 239 MAAVRASDGGAISLKGRMIDRPLILQAEKFLRQVG 273 Lambda K H 0.320 0.137 0.394 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: 186 Number of extensions: 9 Number of successful extensions: 5 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: 275 Length of database: 277 Length adjustment: 25 Effective length of query: 250 Effective length of database: 252 Effective search space: 63000 Effective search space used: 63000 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: 47 (22.7 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