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 8501086 DvMF_1822 aminotransferase class I and II (RefSeq)
Query= SwissProt::Q08432 (387 letters) >FitnessBrowser__Miya:8501086 Length = 405 Score = 318 bits (815), Expect = 2e-91 Identities = 161/397 (40%), Positives = 234/397 (58%), Gaps = 12/397 (3%) Query: 2 NFDKREERLGTQSVKWDKTGELFGVT-----DALPMWVADMDFRAPEAITEALKERLDHG 56 +FD +R T S+KWD G +F ++ +A+P+WVADMDF +P A+ +A+ + G Sbjct: 7 DFDHAPDRRNTGSLKWDDMGHMFNLSPDEAANAIPLWVADMDFPSPPAVRDAVARLAERG 66 Query: 57 IFGYTTPDQKTKDAVCGWMQNRHGWKVNPESITFSPGVVTALSMAVQAFTEPGDQVVVQP 116 +FGY ++AV W+ RHGW VNP + P VV +L ++V+ FT PGD VV+Q Sbjct: 67 VFGYPADGTACREAVSHWLAARHGWTVNPRHLLPLPTVVASLCLSVRLFTRPGDGVVIQT 126 Query: 117 PVYTPFYHMVEKNGRHILHNPLLEKDGA-----YAIDFEDLETKLSDPS--VTLFILCNP 169 P+Y PF V+ G +L NPL A + IDF+ L+T L+D + +LC+P Sbjct: 127 PIYPPFRAAVQDAGCRVLANPLTLTTDAGGNPFHEIDFDALDTALADGGRGAKVLLLCSP 186 Query: 170 HNPSGRSWSREDLLKLGELCLEHGVTVVSDEIHSDLMLYGHKHTPFASLSDDFADISVTC 229 HNP GR W+R +L ++ ELCL+HG +VSDEIH DL+L GH HT ASL+ + A+ ++T Sbjct: 187 HNPGGRVWTRAELTRVAELCLKHGTLMVSDEIHHDLLLPGHAHTVLASLAPEVAERTITA 246 Query: 230 AAPSKTFNIAGLQASAIIIPDRLKRAKFSASLQRNGLGGLNAFAVTAIEAAYSKGGPWLD 289 + +K FN+ G + ++I D R F A L G+ N F + EAA GGPWLD Sbjct: 247 VSAAKAFNVPGAGLAHVVIEDDTLRRTFRAELTGLGIRHPNMFGLATTEAACRHGGPWLD 306 Query: 290 ELITYIEKNMNEAEAFLSTELPKVKMMKPDASYLIWLDFSAYGLSDAELQQRMLKKGKVI 349 L+ YI N L+ LP V++M+P +YL W+DF GL++A+L R+ V+ Sbjct: 307 ALMAYIAGNAALVRDVLTARLPGVRVMQPQGTYLSWVDFRPLGLAEADLLHRVRFDAGVV 366 Query: 350 LEPGTKYGPGGEGFMRLNAGCSLATLQDGLRRIKAAL 386 PG+ +GP G+G++RLN GC A L+ L R+ L Sbjct: 367 PSPGSSFGPEGDGWLRLNLGCPRALLRTALERMADVL 403 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: 510 Number of extensions: 25 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: 387 Length of database: 405 Length adjustment: 31 Effective length of query: 356 Effective length of database: 374 Effective search space: 133144 Effective search space used: 133144 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