Align arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate AZOBR_RS27535 AZOBR_RS27535 amino acid decarboxylase
Query= BRENDA::E8X9U7 (756 letters) >FitnessBrowser__azobra:AZOBR_RS27535 Length = 785 Score = 430 bits (1106), Expect = e-124 Identities = 249/746 (33%), Positives = 400/746 (53%), Gaps = 25/746 (3%) Query: 15 DTWVGNAVERLADALSQQNVTVIKSTSFDDGYAILSANEAIDCLMFSYQMEQPDEHLSVR 74 D G V+++ + + V+++ +D + + AI C++ + + + Sbjct: 19 DELEGVRVQQIVAEVERLGFEVVRTRRVEDAELAIRTDAAIGCMIVDWGKRGLEGKPA-- 76 Query: 75 QLIGKLHERQQNVPVFLLGDREKATASLDRDLLELVDEFAWILEDTADFIAGRAVAAMTR 134 LI +R +P+ LL R++ ++ D+L VD + ++ E+T +FIA V+ + + Sbjct: 77 SLIALARKRGLEMPIILLVRRQRLE-NIPVDVLNQVDGYVFLAEETPEFIAKNLVSRLKQ 135 Query: 135 YRQQLLPPLFNALMKYSDIHEYSWAAPGHQGGVGFTKTPAGRFYHDYYGENLFRSDMGIE 194 Y + L P F L+ Y++ W PGH GG+ ++++P GR + ++ GE +FR D+ Sbjct: 136 YAETLKTPFFGELVDYAEEGNQLWTCPGHNGGIFYSRSPIGRIFVEHLGEAVFRDDIDNS 195 Query: 195 RTTLGSLLDHTGAFGESEKNAARVFGADRSWSVVVGTSGSNRTIMQACMTDNDVVVLDRN 254 +G LL H G +++K AA++FGA+R++ V+ GTS SN+ ++ A + ++D+V+ DRN Sbjct: 196 VLEMGDLLVHEGPALKAQKEAAKIFGAERTYFVLNGTSASNKIVLSALVAEDDLVLFDRN 255 Query: 255 CHKSIEQ-GLILTGAKPVYMVPSRNRYGIIGPIYPQEMQPETLQKKISASPLTKTKAGQK 313 HK+ GL L G PV++ RN YG+IGPI + + E ++ KI +PL K K Sbjct: 256 NHKAAHHGGLFLGGGIPVFLETDRNAYGLIGPIDHEALDEERIRAKIRGNPLVKDPDAWK 315 Query: 314 PS----YSVVTNCTYDGVCYNAKEAQDLLAKTSDRIHFDEAWYGYARFNPIYCDHYAMRG 369 +V+ C+YDG Y+A+ + D I FDEAW G+ +F+P++ +AM G Sbjct: 316 RERPFRAAVIQQCSYDGTIYSAETILAKIGHLCDYILFDEAWAGFLKFHPLFKGRFAM-G 374 Query: 370 EPGDHNG-PTVFATHSTHKLLNALSQASYIHVREG-----RGAVNFSRFNQAYMMHATTS 423 G H+G P + AT STHK L + SQAS IHV++ R V RFN+ +++HA+TS Sbjct: 375 LDGLHDGHPGIIATQSTHKQLASFSQASQIHVKDSHIRGQRRRVEHRRFNETFLLHASTS 434 Query: 424 PLYAICASNDVAVSMMDGNSGLSLTQEVIDEAVDFRQAMARLYKEFTDEGD-----WFFK 478 P Y + AS DV MM G SG L + I V+ R+ + + +EF + WFF Sbjct: 435 PFYPLFASLDVGAQMMKGRSGEVLWDDTIRLGVELRKKIRAIRREFEERESAPARRWFFD 494 Query: 479 PWNKDVVTDPQTGKTYDFADAPAKLLATDQNCWVMRPGETWHGFKDLPDNWSMLDPIKVS 538 P+ D V+ G + + P LA+D WV +PG WHGF+ + ++M DP K++ Sbjct: 495 PFVPDRVS--FDGAEIAWEEVPTDALASDVRHWVFKPGAHWHGFRHVAAGYAMTDPNKLT 552 Query: 539 ILAPGMG-DDGELEASGVPAALVTAWLGRHGIVPTRTTDFQIMFLFSMGVTRGKWGTLIN 597 +L PG G E G+PA +V +L + IVP + I+FL + GV K GTL++ Sbjct: 553 LLTPGFDRRTGAYEEHGIPAPVVAQYLRENRIVPEKNDLNSILFLLTPGVESSKAGTLLS 612 Query: 598 TLCSFKHHYDANTPLAQVMPELVQDYPDTYANMGIHDLGDKMFAWLRE--NNPGARLNAA 655 L +FK +D N L V+PE V P YA + DL +M + RE N R Sbjct: 613 ALVAFKRLHDDNALLEDVIPEFVARRPARYAGRRLRDLCAEMHGFYRERRTNELQRRMFR 672 Query: 656 YSTLPVAEITPRDAYNAIVNNNIEMVAIENLPGRIAANSVIPYPPGIPMLLSGENFGDEN 715 LP + PR+A +V N+++ + I+ + GR+A + YPPGI ++ GE + Sbjct: 673 PDHLPEMVMPPREAVRRLVRNDVDYLPIDRIAGRVATTLFVVYPPGIATIVPGERLDERA 732 Query: 716 SPQVGYLRSLQSWDHHFPGFEHETEG 741 P + YL+ Q + FPGF++E +G Sbjct: 733 RPMIEYLQVFQEGANRFPGFDNEIQG 758 Lambda K H 0.319 0.135 0.415 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: 1435 Number of extensions: 58 Number of successful extensions: 8 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: 756 Length of database: 785 Length adjustment: 41 Effective length of query: 715 Effective length of database: 744 Effective search space: 531960 Effective search space used: 531960 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: 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