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 Pf1N1B4_4946 putative aminotransferase
Query= SwissProt::Q08432 (387 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4946 Length = 384 Score = 256 bits (655), Expect = 6e-73 Identities = 146/389 (37%), Positives = 215/389 (55%), Gaps = 17/389 (4%) Query: 2 NFDKREERLGTQSVKWDKTGELFGVTDALPMWVADMDFRAPEAITEALKERLDHGIFGYT 61 +FD+ +R GT S KW + D LPMWVADMDF AP AI +AL++RL+H + GY+ Sbjct: 4 DFDQVFDRHGTGSTKWSRYP-----ADVLPMWVADMDFAAPPAIIQALQKRLEHPMLGYS 58 Query: 62 TPDQKTKDAVCGWMQNRHGWKVNPESITFSPGVVTALSMAVQAFTEPGDQVVVQPPVYTP 121 +DA+ + +++ W+V P+ + F PG+ + +MA+ A +P VVVQ P Y P Sbjct: 59 VAKDDLRDAIVADLWSKYAWRVQPQELIFLPGIESGFNMALNALVQPQQNVVVQTPNYPP 118 Query: 122 FYHMVEKNGRHILHNPLLE----KDGAYAIDFEDLETKLSDPSVTLFILCNPHNPSGRSW 177 H G L+ L+ DG YA + L L L L NPHNP G+ + Sbjct: 119 LRH---APGHWQLNKVELDFDALADGTYATPLDALREALQGGGALL--LSNPHNPLGKVF 173 Query: 178 SREDLLKLGELCLEHGVTVVSDEIHSDLMLYGHKHTPFASLSDDFADISVTCAAPSKTFN 237 RE+L + ++CLE ++SDEIHS+L G H P ASLS A ++T + SK +N Sbjct: 174 PREELQTVADICLEQDAWIISDEIHSELCFDGRVHIPTASLSPQIAKRTITLMSASKAYN 233 Query: 238 IAGLQASAIIIPDRLKRAKFSASLQRNGLGGLNAFAVTAIEAAYSKGGPWLDELITYIEK 297 IAGL+ + +II D R + + + + + +N + A AY +GGPWL EL+ Y++ Sbjct: 234 IAGLKTAFMIIQDAALRHRVN-NARCGMVDSVNPLGLEATRVAYREGGPWLTELMAYLQS 292 Query: 298 NMNEAEAFLSTELPKVKMMKPDASYLIWLDFSAYGLSDAELQQRMLKKGKVILEPGTKYG 357 N + + T LP V M P +YL WLD +A GL + QQ L++ KV L G +G Sbjct: 293 NRDYLVEAVRTRLPGVTMNIPQGTYLAWLDCTALGLDNP--QQFFLEQAKVGLSAGLDFG 350 Query: 358 PGGEGFMRLNAGCSLATLQDGLRRIKAAL 386 F+RLN GC A L++G+ R++ +L Sbjct: 351 DHARQFVRLNFGCPRALLEEGIARMERSL 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: 423 Number of extensions: 20 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: 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