Align Antizyme inhibitor 2; AzI2; Arginine decarboxylase; ADC; ARGDC; Ornithine decarboxylase-like protein; ODC-like protein; ornithine decarboxylase paralog; ODC-p (characterized)
to candidate AZOBR_RS00105 AZOBR_RS00105 ornithine decarboxylase
Query= SwissProt::Q96A70 (460 letters) >FitnessBrowser__azobra:AZOBR_RS00105 Length = 378 Score = 118 bits (296), Expect = 3e-31 Identities = 111/371 (29%), Positives = 163/371 (43%), Gaps = 27/371 (7%) Query: 35 TDEVAAFF----------VADLGAIVRKHFCFLKCLPRVRPFYAVKCNSSPGVLKVLAQL 84 TD++A FF V DL + + + LP + FYAVK N +P +L +L +L Sbjct: 2 TDKIARFFEEQRPQTPCLVVDLDVVEANYHDLEEALPDAKIFYAVKANPAPEILGLLTRL 61 Query: 85 GLGFSCANKAEMELVQHIGIPASKIICANPCKQIAQIKYAAKHGIQLLSFDNEMELAKVV 144 G F A+ E+++V G +I N K+ A I+ A + G++L +FD+E EL K+ Sbjct: 62 GSAFDTASVPEIQMVLAAGCAPERISYGNTIKKEADIRRAFELGVRLFAFDSEAELEKIA 121 Query: 145 KSHPSAKMVLCIATDDSHSLSCLSLKFGVSLKSCRHLLENAKKHHVEVVGVSFHIGSGCP 204 ++ P A++ I T + LS KFG L R LL AK +V GVSFH+GS Sbjct: 122 RAAPGARVFCRILTSGEGAEWPLSRKFGCDLAMARELLLKAKGMNVVPYGVSFHVGSQQK 181 Query: 205 DPQAYAQSIADARLVFEMGTELGHKMHVLDLGGGFPGTEGAKV-RFEEIASVINSALDLY 263 D + +I +F LG + +++LGGGFP V I +L + Sbjct: 182 DLMQWDHAIFQVAQLFRELEVLGVDLGMINLGGGFPTRYRTDVPETTAYGQAIFESLRTH 241 Query: 264 FPEGCGVDIFAELGRYYVTSAFTVAVSIIAKKEVLLDQPGREEENGSTSKTIVYHLDEGV 323 F + E GR V +A II + VL+ + ++ + K VY LD G Sbjct: 242 FGNRL-PEAIVEPGRSMVGNA-----GIIESEVVLVSR-----KSANDVKRWVY-LDIGK 289 Query: 324 YGIFNSVLFDNICPTPILQKKPSTEQPLYSSSLWGPAVDGCDCV---AEGLWLPQLHVGD 380 + + D PI E + L GP D D + AE L GD Sbjct: 290 FSGLAETM-DEAIQYPIQVMGDDGEGDSEAVVLAGPTCDSADVLYERAEYKLPMDLKAGD 348 Query: 381 WLVFDNMGAYT 391 + GAYT Sbjct: 349 RVRIHATGAYT 359 Lambda K H 0.321 0.137 0.422 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: 381 Number of extensions: 22 Number of successful extensions: 1 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: 460 Length of database: 378 Length adjustment: 31 Effective length of query: 429 Effective length of database: 347 Effective search space: 148863 Effective search space used: 148863 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 (21.9 bits) S2: 50 (23.9 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