Align ornithine decarboxylase, degradative (EC 4.1.1.17) (characterized)
to candidate AZOBR_RS27535 AZOBR_RS27535 amino acid decarboxylase
Query= ecocyc::ORNDECARBOXDEG-MONOMER (732 letters) >FitnessBrowser__azobra:AZOBR_RS27535 Length = 785 Score = 593 bits (1528), Expect = e-173 Identities = 316/698 (45%), Positives = 417/698 (59%), Gaps = 28/698 (4%) Query: 55 GYGIPVFIATENQ--ERVPAEYLPRISGVFENCESRREFYGRQLETAASHYETQLRPPFF 112 G +P+ + Q E +P + L ++ G E EF + L + Y L+ PFF Sbjct: 86 GLEMPIILLVRRQRLENIPVDVLNQVDGYVFLAEETPEFIAKNLVSRLKQYAETLKTPFF 145 Query: 113 RALVDYVNQGNSAFDCPGHQGGEFFRRHPAGNQFVEYFGEALFRADLCNADVAMGDLLIH 172 LVDY +GN + CPGH GG F+ R P G FVE+ GEA+FR D+ N+ + MGDLL+H Sbjct: 146 GELVDYAEEGNQLWTCPGHNGGIFYSRSPIGRIFVEHLGEAVFRDDIDNSVLEMGDLLVH 205 Query: 173 EGAPCIAQQHAAKVFNADKTYFVLNGTSSSNKVVLNALLTPGDLVLFDRNNHKSNHHGAL 232 EG AQ+ AAK+F A++TYFVLNGTS+SNK+VL+AL+ DLVLFDRNNHK+ HHG L Sbjct: 206 EGPALKAQKEAAKIFGAERTYFVLNGTSASNKIVLSALVAEDDLVLFDRNNHKAAHHGGL 265 Query: 233 LQAGATPVYLETARNPYGFIGGIDAHCFEESYLRELI----AEVAPQRAKEARPFRLAVI 288 G PV+LET RN YG IG ID +E +R I P K RPFR AVI Sbjct: 266 FLGGGIPVFLETDRNAYGLIGPIDHEALDEERIRAKIRGNPLVKDPDAWKRERPFRAAVI 325 Query: 289 QLGTYDGTIYNARQVVDKIGHLCDYILFDSAWVGYEQFIPMMADCSPLLLD-LNENDPGI 347 Q +YDGTIY+A ++ KIGHLCDYILFD AW G+ +F P+ + LD L++ PGI Sbjct: 326 QQCSYDGTIYSAETILAKIGHLCDYILFDEAWAGFLKFHPLFKGRFAMGLDGLHDGHPGI 385 Query: 348 LVTQSVHKQQAGFSQTSQIHKKDSHIKGQQRYVPHKRMNNAFMMHASTSPFYPLFAALNI 407 + TQS HKQ A FSQ SQIH KDSHI+GQ+R V H+R N F++HASTSPFYPLFA+L++ Sbjct: 386 IATQSTHKQLASFSQASQIHVKDSHIRGQRRRVEHRRFNETFLLHASTSPFYPLFASLDV 445 Query: 408 NAKMHEGVSGRNMWMDCVVNGINARKLILDNCQHIR-------------PFVPELV--DG 452 A+M +G SG +W D + G+ RK I + PFVP+ V DG Sbjct: 446 GAQMMKGRSGEVLWDDTIRLGVELRKKIRAIRREFEERESAPARRWFFDPFVPDRVSFDG 505 Query: 453 K--PWQSYETAQIAVDLRFFQFVPGEHWHSFEGYAENQYFVDPCKLLLTTPGIDARNGEY 510 W+ T +A D+R + F PG HWH F A DP KL L TPG D R G Y Sbjct: 506 AEIAWEEVPTDALASDVRHWVFKPGAHWHGFRHVAAGYAMTDPNKLTLLTPGFDRRTGAY 565 Query: 511 EAFGVPATILANFLRENGVVPEKCDLNSILFLLTPAEDMAKLQQLVALLVRFEKLLESDA 570 E G+PA ++A +LREN +VPEK DLNSILFLLTP + +K L++ LV F++L + +A Sbjct: 566 EEHGIPAPVVAQYLRENRIVPEKNDLNSILFLLTPGVESSKAGTLLSALVAFKRLHDDNA 625 Query: 571 PLAEVLPSIYKQHEERYAGYTLRQLCQEMHDLYARHNVKQLQKEMFRKEHFPRVSMNPQE 630 L +V+P + RYAG LR LC EMH Y +LQ+ MFR +H P + M P+E Sbjct: 626 LLEDVIPEFVARRPARYAGRRLRDLCAEMHGFYRERRTNELQRRMFRPDHLPEMVMPPRE 685 Query: 631 ANYAYLRGEVELVRLPDAEGRIAAEGALPYPPGVLCVVPGEIW---GGAVLRYFSALEEG 687 A +R +V+ + + GR+A + YPPG+ +VPGE ++ Y +EG Sbjct: 686 AVRRLVRNDVDYLPIDRIAGRVATTLFVVYPPGIATIVPGERLDERARPMIEYLQVFQEG 745 Query: 688 INLLPGFAPELQGVYIE-EHDGRKQVWCYVIKPRDAQS 724 N PGF E+QG+Y E E DG + + YV++ A + Sbjct: 746 ANRFPGFDNEIQGLYRETEPDGSVRFYTYVVREDGADA 783 Lambda K H 0.322 0.138 0.424 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: 1537 Number of extensions: 68 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: 732 Length of database: 785 Length adjustment: 40 Effective length of query: 692 Effective length of database: 745 Effective search space: 515540 Effective search space used: 515540 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: 55 (25.8 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