Align Cystathionine beta-lyase PatB; CBL; Beta-cystathionase PatB; Cysteine lyase PatB; Cysteine-S-conjugate beta-lyase PatB; EC 4.4.1.13 (characterized)
to candidate GFF2543 PS417_12965 aminotransferase
Query= SwissProt::Q08432 (387 letters) >FitnessBrowser__WCS417:GFF2543 Length = 383 Score = 253 bits (646), Expect = 6e-72 Identities = 138/385 (35%), Positives = 211/385 (54%), Gaps = 10/385 (2%) Query: 2 NFDKREERLGTQSVKWDKTGELFGVTDALPMWVADMDFRAPEAITEALKERLDHGIFGYT 61 +FD R GT S KW + + D LPMW+ADMD AP A+ +AL R+D + GY+ Sbjct: 4 DFDTIHPRFGTGSTKWSRYPQ-----DVLPMWIADMDIAAPPAVLQALHARIDQQVLGYS 58 Query: 62 TPDQKTKDAVCGWMQNRHGWKVNPESITFSPGVVTALSMAVQAFTEPGDQVVVQPPVYTP 121 ++A+ + ++GW+V P+ + F PGV +MA+ AF +PG VV+Q P Y P Sbjct: 59 VAGPDVREAIIADLWAKYGWRVQPDELLFLPGVEPGFNMALHAFVQPGQPVVLQTPNYRP 118 Query: 122 FYHMVEKNGRHILHNPLLEKDGAYAIDFEDLETKLSDPSVTLFILCNPHNPSGRSWSRED 181 + P + +G Y + L+ L L NPHNP G+ + RE+ Sbjct: 119 IRLAPGHWNLPRIEVPFEQVNGEYLTPMPAMRQALTGAGALL--LSNPHNPMGKVFPREE 176 Query: 182 LLKLGELCLEHGVTVVSDEIHSDLMLYGHKHTPFASLSDDFADISVTCAAPSKTFNIAGL 241 LL + CLE+G ++SDEIH++L G +H P ASLS + A ++T + SK +N+AGL Sbjct: 177 LLAVANACLENGALIISDEIHAELCFDGRRHIPTASLSPEIAQRTITLMSASKAYNVAGL 236 Query: 242 QASAIIIPDRLKRAKFSASLQRNGLGGLNAFAVTAIEAAYSKGGPWLDELITYIEKNMNE 301 + +I + R +F+ + + + ++ + A AAYS+ WLD L+ Y++ N + Sbjct: 237 KTCFAVIQNAEIRERFN-NARCGMVDSVSPLGLEATRAAYSQCNDWLDALVQYLQSNRDY 295 Query: 302 AEAFLSTELPKVKMMKPDASYLIWLDFSAYGLSDAELQQRMLKKGKVILEPGTKYGPGGE 361 + T LP V M P +YL WLD SA GL D QQ L++ KV L G ++G + Sbjct: 296 LLDAVQTRLPGVVMHAPQGTYLAWLDCSALGLDDP--QQFFLEQAKVGLSAGIEFGDDSQ 353 Query: 362 GFMRLNAGCSLATLQDGLRRIKAAL 386 F+RLN GC + L++GL+R++ AL Sbjct: 354 QFVRLNFGCPRSMLEEGLQRMERAL 378 Lambda K H 0.318 0.135 0.408 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: 401 Number of extensions: 22 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: 387 Length of database: 383 Length adjustment: 30 Effective length of query: 357 Effective length of database: 353 Effective search space: 126021 Effective search space used: 126021 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: 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