Align cystathionine beta-synthase (EC 4.2.1.22) (characterized)
to candidate PP_3191 PP_3191 putative threonine ammonia-lyase / dehydratase
Query= BRENDA::P35520 (551 letters) >FitnessBrowser__Putida:PP_3191 Length = 350 Score = 70.9 bits (172), Expect = 8e-17 Identities = 88/306 (28%), Positives = 134/306 (43%), Gaps = 42/306 (13%) Query: 87 TPMVRINKIGKKFGLKCELLAKCEFFNAGGSVKDRIS---LRMIE-DAERDGTLKPGDTI 142 TP++ ++ G CE+L KCE GS K R + +R++ +A + G + Sbjct: 54 TPLLHSPRLSALTG--CEVLLKCEHLQHTGSFKFRGASNKMRLLPAEARKQG-------V 104 Query: 143 IEPTSGNTGIGLALAAAVRGYRCIIVMPEKMSSEKVDVLRALGAEIVRTPTNARFDSPES 202 I +SGN G LALA + G + S+ K + +RALGAE+V PT D + Sbjct: 105 IAASSGNHGQALALAGKMAGVPVKVYTTTGASAYKTEAMRALGAEVVCLPT----DPLSA 160 Query: 203 HVGVAWRLKNE-IPNSHILDQYRNASNPLAHYDTTADEILQQCDGKLDMLVASVGTGGTI 261 + A + K + +P + Y N +A T E+L+Q LD + +VG GG I Sbjct: 161 ELEAARQAKAQGVP---FVSPY-NDLQVIAGQGTIGMELLEQAP-DLDAVFVAVGGGGMI 215 Query: 262 TGIARKLKEKCPGCRIIGVDP-----------EGSI--LAEPEELNQTEQTTYEVEGIGY 308 +GI L+ PG IIG P G I L E L+ E I + Sbjct: 216 SGIGAALRVLKPGTEIIGCWPANDPTLQQSLKAGEIIELDACETLSDGTAGGVEPGSITF 275 Query: 309 DFIPTVLDRTVVDKWFKSNDEEAFTFARMLIAQEGLLCGGSAGSTVAVAVKAAQELQEGQ 368 +L TV+ +++E R + + E + G+A VA + A+ Q G+ Sbjct: 276 PLCQALLTDTVL-----VSEDEIRCAMRDIASSERWIIEGAAAVAVAGMQRLAERYQ-GK 329 Query: 369 RCVVIL 374 R VIL Sbjct: 330 RVAVIL 335 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: 415 Number of extensions: 13 Number of successful extensions: 3 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: 350 Length adjustment: 32 Effective length of query: 519 Effective length of database: 318 Effective search space: 165042 Effective search space used: 165042 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: 51 (24.3 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