Align ornithine decarboxylase; EC 4.1.1.17 (characterized)
to candidate WP_011383514.1 AMB_RS05600 type III PLP-dependent enzyme
Query= CharProtDB::CH_121968 (450 letters) >NCBI__GCF_000009985.1:WP_011383514.1 Length = 400 Score = 138 bits (347), Expect = 4e-37 Identities = 117/341 (34%), Positives = 156/341 (45%), Gaps = 34/341 (9%) Query: 104 AVKCNPDPEVLRLMAKLGNG-FDCASKAEIDMALSTGVDPSRIIYAQPCKTKSYLRHAAK 162 AVKCNPD VLR +A G G FD AS AE+ + + I + P K +S +R A Sbjct: 62 AVKCNPDEAVLRALAAGGIGHFDAASIAEVRLVRRLFPEAG-IHFMHPVKARSAIREAYG 120 Query: 163 V-GVKQMTFDNADELYKIKACYPEAE---LYLRILTDDSNSLCQFSMKFGASLDVARQLL 218 + GV+ D A EL KI A A L +R+ ++ S KFGAS D A +LL Sbjct: 121 LHGVRDFVLDGAGELDKIVAETEGASDLRLIVRLGLAKGDARLDLSGKFGASADDAVRLL 180 Query: 219 ELAHQLELKIVGVSFHVGSGAEDPKAFLKAVQDARLVFDQAAEIGHELHTLDVGGGFT-- 276 + VG+SFHVGS DP A+ +A+ A V AA +L LDVGGGF Sbjct: 181 RRCAAVGR--VGLSFHVGSQCCDPSAWERALAQADAVIRAAAI---QLDVLDVGGGFPVA 235 Query: 277 ------GETFEKFAAVLDSALETYFPPNIRIIAEPGRYYVGGAFTLAANIIARRGVQDPE 330 AA+ P + EPGR V G +L + ARRG Sbjct: 236 YPGMRPPPLAAFMAAIRRGVARMGLPSGCVLWCEPGRALVAGCQSLVVQVQARRGD---- 291 Query: 331 NPSKDAYMIYLNDGVYGNFSNIIFDHQHPEARILSCASEINGRPVSEDVTYSIWGPTCDG 390 M+++NDGVYG S+ R++ A G + +GPTCD Sbjct: 292 -------MLFINDGVYGTLSDAGALAWRYPCRLIKAA----GASHETLQAFGFFGPTCDS 340 Query: 391 IDVISQRSVLPGLLDVGDWLYFEEMGAYTRCSATRFNGFSD 431 +D + +LP GDW+ ++GAY C T FNGF+D Sbjct: 341 LDRMPGPFLLPADTAEGDWIEIGQLGAYGACLRTGFNGFND 381 Lambda K H 0.320 0.137 0.411 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: 426 Number of extensions: 16 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: 450 Length of database: 400 Length adjustment: 32 Effective length of query: 418 Effective length of database: 368 Effective search space: 153824 Effective search space used: 153824 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: 51 (24.3 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