Align cystathionine beta-synthase (EC 4.2.1.22) (characterized)
to candidate GFF810 HP15_789 cysteine synthase B
Query= BRENDA::P35520 (551 letters) >FitnessBrowser__Marino:GFF810 Length = 297 Score = 204 bits (519), Expect = 4e-57 Identities = 125/308 (40%), Positives = 184/308 (59%), Gaps = 23/308 (7%) Query: 78 PDILKKIGDTPMVRINKI-GKKFGLKCELLAKCEFFNAGGSVKDRISLRMIEDAERDGTL 136 P I +G TP+VR+ ++ G+ + +LAK E N GSVKDR ++ MI++AER G + Sbjct: 4 PTIEDYVGHTPLVRLQRLPGETSNV---ILAKLEGNNPAGSVKDRPAISMIQEAERRGDI 60 Query: 137 KPGDTIIEPTSGNTGIGLALAAAVRGYRCIIVMPEKMSSEKVDVLRALGAEIVRTPTNAR 196 KPGDT+IE TSGNTGI LA+AAA++GYR +++MP MS E+ +RA GAEIV T R Sbjct: 61 KPGDTLIEATSGNTGIALAMAAAIKGYRMVLIMPANMSEERRASMRAYGAEIV---TVTR 117 Query: 197 FDSPESHVGVAWRLKNEIPNSHILDQYRNASNPLAHYDTTADEILQQCDGKLDMLVASVG 256 + E+ +A +++ E +LDQ+ N NPLAHY TT EI +Q G++ V+S+G Sbjct: 118 EEGMETARDLALKMQAE-GKGTVLDQFSNQDNPLAHYRTTGPEIWEQTGGRVTHFVSSMG 176 Query: 257 TGGTITGIARKLKEKCPGCRIIGVDP-EGSILAEPEELNQTEQTTYEVEGIGYDFIPTVL 315 T GTI G++R LKE+ P RIIG+ P EG+ + + ++P + Sbjct: 177 TTGTIMGVSRYLKERNPDIRIIGLQPKEGASIPGIRRWPEA-------------YLPKIY 223 Query: 316 DRTVVDKWFKSNDEEAFTFARMLIAQEGLLCGGSAGSTVAVAVKAAQELQEGQRCVVILP 375 D VD+ EEA T R L ++EG+ CG S+G ++A A+K +Q++ E V I+ Sbjct: 224 DAARVDQVLDVGQEEAETTMRALASEEGIFCGVSSGGSIAAALKLSQQV-ENAIIVAIIC 282 Query: 376 DSVRNYMT 383 D Y++ Sbjct: 283 DRGDRYLS 290 Lambda K H 0.317 0.135 0.402 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: 403 Number of extensions: 21 Number of successful extensions: 4 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: 551 Length of database: 297 Length adjustment: 31 Effective length of query: 520 Effective length of database: 266 Effective search space: 138320 Effective search space used: 138320 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 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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