Align ornithine cyclodeaminase (EC 4.3.1.12) (characterized)
to candidate WP_048191565.1 PYRFU_RS04150 alanine dehydrogenase
Query= BRENDA::Q88H32 (350 letters) >NCBI__GCF_000223395.1:WP_048191565.1 Length = 335 Score = 137 bits (344), Expect = 5e-37 Identities = 89/263 (33%), Positives = 134/263 (50%), Gaps = 11/263 (4%) Query: 69 KYVNGHPANTARNLHTVMAFGVLADVDSGYPVLLSELTIATALRTAATSLMAAQALARPN 128 K V +P N R L TV+A L D D+G+P+ + + T+ TA RT A +AA+ +AR Sbjct: 74 KTVGVNPQNPKRGLATVIALIELVDPDTGHPLAVMDGTLITAWRTGAAGAIAAKYMARSG 133 Query: 129 ARKMALIGNGAQSEFQA-LAFHKHLGIEEIVAYDTDPLATAKLIANLKEYSGLTIRRASS 187 + M +IG G Q Q I + +D A L +++ G+ Sbjct: 134 STVMGVIGAGVQGRMQVYFTVETVRTITRVKIFDVRREAAKSLAVFVEKELGIDASIVDE 193 Query: 188 VAEAVKGVDIITTVTADKAYATIITPDMLEPGMHLNAVGGDCPGKTELHADVLRNARVFV 247 AVKGVDI+ T T A + I+ D +E G+H+NA+G D PGK EL +L+ AR+ V Sbjct: 194 PLAAVKGVDILATCT--PARSPIVRGDWIEEGLHINAIGADAPGKEELDPAILQKARIVV 251 Query: 248 EYEPQTRIEGEIQQLPADFPVV-------DLWRVLRGETEGRQSDSQVTVFDSVGFALED 300 + Q GEI +P + + +L V+ G GR D ++T+FDS G A++D Sbjct: 252 DDFVQASHSGEI-NVPLEEGYISERDIYAELGEVVAGLKPGRVDDREITIFDSTGLAIQD 310 Query: 301 YTVLRYVLQQAEKRGMGTKIDLV 323 R V + A + G+GT++ LV Sbjct: 311 VAAARVVYEAALRTGLGTRMKLV 333 Lambda K H 0.320 0.134 0.387 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: 247 Number of extensions: 15 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: 350 Length of database: 335 Length adjustment: 29 Effective length of query: 321 Effective length of database: 306 Effective search space: 98226 Effective search space used: 98226 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 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 10 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