Align cysteine synthase (EC 2.5.1.47); cystathionine beta-synthase (EC 4.2.1.22) (characterized)
to candidate Dsui_2521 Dsui_2521 cysteine synthase A
Query= BRENDA::F9UT54 (303 letters) >FitnessBrowser__PS:Dsui_2521 Length = 328 Score = 194 bits (492), Expect = 3e-54 Identities = 121/303 (39%), Positives = 171/303 (56%), Gaps = 11/303 (3%) Query: 10 IGHTPLMALP-IEVPNHSHIYAKLEMFNPGGSIKDRLGAYLIEDGLQRGRVNAKTTIIEP 68 IG TPL+ L + + + AK+E NP S+K R+GA ++ D RG + ++EP Sbjct: 15 IGRTPLVRLNRVTDGAPATVLAKIEGRNPAYSVKCRIGAAMVWDAEIRGLLGPGKELVEP 74 Query: 69 TAGNTGIGLALATQAHHLRTILVVPEKFSMEKQVLMQALGAEIVHTPSEEGIKGAIRKAE 128 T+GNTGI LA + + L +PE S+E++ L+ A GA++V T +G+ GAI KAE Sbjct: 75 TSGNTGIALAFVAAVYGIPLTLTMPETMSLERRKLLAAYGAKLVLTEGTKGMGGAIAKAE 134 Query: 129 ALAATISNSYVPM-QFKNPANPAAYYHTLAPEILADMPAPITAFVAGAGSGGTFAGVAAY 187 +AA+ YV + QFKNPANPA + T PEI D + FV+G G+GGT GV+ Y Sbjct: 135 EIAASDPGKYVLLQQFKNPANPAIHESTTGPEIWIDTDDKVDIFVSGVGTGGTITGVSRY 194 Query: 188 LQAQDSATK-AVVVEPEGSIL-----NGGPAH--AHRTEGIGVEFIPPFFDQVRIDQTLT 239 + A +V VEP S + NG P H+ +GIG F+P D ID Sbjct: 195 FKKTRGAKLWSVAVEPSASPVLTQTRNGEPVKPGPHKIQGIGAGFVPQVLDLSLIDAIEQ 254 Query: 240 IADNDAFAQVRHLARDHGLLIGSSSGAALAASLQLATNLP-ANSHIVTIFPDSSERYLSQ 298 +++ +A A R LAR+ G++ G SSGAA+A + +LA A IV I PDS ERYLS Sbjct: 255 VSNEEAVAYARRLAREEGIISGISSGAAVAVASRLAQRRENAGKTIVVILPDSGERYLSS 314 Query: 299 KIY 301 ++ Sbjct: 315 VLF 317 Lambda K H 0.317 0.133 0.378 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: 263 Number of extensions: 20 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: 303 Length of database: 328 Length adjustment: 27 Effective length of query: 276 Effective length of database: 301 Effective search space: 83076 Effective search space used: 83076 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: 48 (23.1 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