Align L-serine ammonia-lyase (EC 4.3.1.17); D-Serine ammonia-lyase (EC 4.3.1.18) (characterized)
to candidate HSERO_RS16005 HSERO_RS16005 1-aminocyclopropane-1-carboxylate deaminase
Query= BRENDA::O57809 (325 letters) >FitnessBrowser__HerbieS:HSERO_RS16005 Length = 355 Score = 165 bits (418), Expect = 1e-45 Identities = 114/327 (34%), Positives = 170/327 (51%), Gaps = 21/327 (6%) Query: 5 IFALLAKFPRVELIPWETPIQYLPNISREIGADVYIKRDDLT-GLGIGGNKIRKLEYLLG 63 + AL FPR L + +PI L +S +G +V+ KRDD++ GL GGNKIRKLE+L+ Sbjct: 1 MLALDKLFPRKTLGFFPSPIHKLERLSAMLGVEVWAKRDDVSSGLAFGGNKIRKLEWLVA 60 Query: 64 DALSKGADVVITVGAVHSNHAFVTGLAAKKLGLDAILVLRGKEELK-------GNYLLDK 116 DAL+KG D ++++G + SNH AA +G+ + V E GN LL + Sbjct: 61 DALAKGCDTLVSIGNIQSNHTRQVCAAAAAVGMKSYTVQETWLEWDDPVYDKVGNILLTR 120 Query: 117 IMGIETRVYDAKDSFELMKYAEEIAEELKREGRKPYVIPPGGAS-PIGTLGYVRAVGEIA 175 IMG + S EE++ +G KPY IP G + P+G LGY E+A Sbjct: 121 IMGGNPIMGGYGYSTTEKDTWARALEEVRAKGGKPYAIPAGASDHPLGGLGYANFADEVA 180 Query: 176 TQSE---VKFDSIVVAAGSGGTLAGLSLGLSILNEDIRPVGIAVGRFGEVMTSKLDNLIK 232 Q + V FD+IVVA +G T AG+ +G + + R +GI + + + Sbjct: 181 MQEQQLGVFFDNIVVATCTGSTQAGMVVGFAAQEKRRRVIGIDTADDEAMTRRAVTKIAN 240 Query: 233 EAAELL----GVKVEVRPE----LYDYSFGEYGKITGEVAQIIRKVGTREGIILDPVYTG 284 + +EL+ G +V VR + DYS YG + + IR E ++ DPVY G Sbjct: 241 DTSELIASKGGKRVIVRDADIEIIPDYSGPAYGLPSEQTIAAIRTAAEMEAMLTDPVYEG 300 Query: 285 KAFYGLVDLARKGEL-GEKILFIHTGG 310 K+ GL+D+A+KG G+++L+ H GG Sbjct: 301 KSIDGLIDMAKKGHFKGQRVLYAHLGG 327 Lambda K H 0.319 0.142 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: 271 Number of extensions: 19 Number of successful extensions: 6 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: 325 Length of database: 355 Length adjustment: 28 Effective length of query: 297 Effective length of database: 327 Effective search space: 97119 Effective search space used: 97119 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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