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 PfGW456L13_3090 putative aminotransferase
Query= SwissProt::Q08432 (387 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3090 Length = 384 Score = 256 bits (653), Expect = 1e-72 Identities = 144/387 (37%), Positives = 217/387 (56%), Gaps = 13/387 (3%) Query: 2 NFDKREERLGTQSVKWDKTGELFGVTDALPMWVADMDFRAPEAITEALKERLDHGIFGYT 61 +FD+ +R T S KW + D LPMWVADMDF AP I +AL++RL+H + GY+ Sbjct: 4 DFDQVFDRHNTGSTKWSRYP-----ADVLPMWVADMDFAAPPMIIQALQKRLEHPMVGYS 58 Query: 62 TPDQKTKDAVCGWMQNRHGWKVNPESITFSPGVVTALSMAVQAFTEPGDQVVVQPPVYTP 121 ++A+ + N++ W+V P+ + F PGV + +MA++A + VVVQ P Y P Sbjct: 59 VAQDDLREAIVADLWNKYAWRVEPQELIFLPGVESGFNMALKALVQAPQNVVVQVPNYPP 118 Query: 122 FYHMVEKNGRHILH-NPLLEKDGAYAIDFEDLETKLSDPSVTLFILCNPHNPSGRSWSRE 180 H G + + N + DG Y + L L L L NPHNP G+++ R Sbjct: 119 LRHAPGHWGLNKVELNFDAQADGTYTTPLDTLSQSLQGGGALL--LSNPHNPLGKAFPRT 176 Query: 181 DLLKLGELCLEHGVTVVSDEIHSDLMLYGHKHTPFASLSDDFADISVTCAAPSKTFNIAG 240 +L + ++CLEH ++SDEIH++L G +H P A+LS A ++T + SK +NIAG Sbjct: 177 ELQAIADICLEHDAWIISDEIHAELCFDGRQHIPMATLSPQVAQRTITLMSASKAYNIAG 236 Query: 241 LQASAIIIPDRLKRAKFSASLQRNGL-GGLNAFAVTAIEAAYSKGGPWLDELITYIEKNM 299 L+ S +II DR R K + + R G+ +N + A AYS+ PWL EL Y++ N Sbjct: 237 LKTSFMIIQDRHLREKVNHA--RCGMVDSVNPLGMEATRVAYSEAAPWLAELKVYLQGNR 294 Query: 300 NEAEAFLSTELPKVKMMKPDASYLIWLDFSAYGLSDAELQQRMLKKGKVILEPGTKYGPG 359 + + T LP + M P ++YL WLD +A GL D QQ L++ KV L G +G G Sbjct: 295 DYLAEAVHTRLPGITMNLPQSTYLAWLDCTALGLDDP--QQFFLEQAKVGLSAGLDFGDG 352 Query: 360 GEGFMRLNAGCSLATLQDGLRRIKAAL 386 + F+RLN GC + L++G+ R++ +L Sbjct: 353 CKQFVRLNFGCPRSLLEEGIARMERSL 379 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: 388 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: 387 Length of database: 384 Length adjustment: 30 Effective length of query: 357 Effective length of database: 354 Effective search space: 126378 Effective search space used: 126378 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