Align arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate BWI76_RS07195 BWI76_RS07195 lysine decarboxylase CadA
Query= BRENDA::P28629 (755 letters) >FitnessBrowser__Koxy:BWI76_RS07195 Length = 715 Score = 457 bits (1175), Expect = e-132 Identities = 253/737 (34%), Positives = 397/737 (53%), Gaps = 48/737 (6%) Query: 21 VERLADALSQQNVTVIKSTSFDDGFAILSSNEAIDCLMFSYQMEHPDEHQNVRQLIGKLH 80 + L AL + + ++ DD ++ +N + ++F + + + +++ ++ Sbjct: 19 IRELHRALERLDFRIVYPNDRDDLLKLIENNARLCGVIFDWDKYNLELCEDISKM----- 73 Query: 81 ERQQNVPVFLLGDREKALAAMDRDLLELVDEFAWILEDTADFIAGRAVAAMTRYRQQLLP 140 + +P++ + L DL V F + L A+ IA + Y +LP Sbjct: 74 --NEYMPLYAFANTYSTLDVSLNDLRMQVRFFEYAL-GAAEDIANKIKQNTDEYIDTILP 130 Query: 141 PLFSALMKYSDIHEYSWAAPGHQGGVGFTKTPAGRFYHDYYGENLFRTDMGIERTSLGSL 200 PL AL KY +Y++ PGH GG F K+P G ++D++G N ++D+ I + LGSL Sbjct: 131 PLTKALFKYVREGKYTFCTPGHMGGTAFQKSPVGSIFYDFFGSNTMKSDISISVSELGSL 190 Query: 201 LDHTGAFGESEKYAARVFGADRSWSVVVGTSGSNRTIMQACMTDNDVVVVDRNCHKSIEQ 260 LDH+G E+E+Y ARVF A+RS+ V GTS +N+ + V++DRNCHKS+ Sbjct: 191 LDHSGPHKEAEEYIARVFNAERSYMVTNGTSTANKIVGMYSAPAGSTVLIDRNCHKSLTH 250 Query: 261 GLMLTGAKPVYMVPSRNRYGIIGPIYPQEMQPETLQKKISESPLTKDKAGQKPSYCVVTN 320 +M++ P+Y P+RN YGI+G I E Q T+ K++ E+P P + V+TN Sbjct: 251 LMMMSDITPIYFRPTRNAYGILGGIPQSEFQHATIAKRVKETP-----NATWPVHAVITN 305 Query: 321 CTYDGVCYNAKEAQDLLEKTSD--RLHFDEAWYGYARFNPIYADHYAMRGEPGDHNGPTV 378 TYDG+ YN D ++KT D +HFD AW Y F+PIY M G G G + Sbjct: 306 STYDGLLYNT----DYIKKTLDVKSIHFDSAWVPYTNFSPIYEGKCGMSG--GRVEGKVI 359 Query: 379 FATHSTHKLLNALSQASYIHVREGRGAINFSRFNQAYMMHATTSPLYAICASNDVAVSMM 438 + T STHKLL A SQAS IHV+ G +N FN+AYMMH TTSP Y + AS + A +MM Sbjct: 360 YETQSTHKLLAAFSQASMIHVK---GDVNEETFNEAYMMHTTTSPHYGVVASTETAAAMM 416 Query: 439 DGNSGLSLTQEVIDEAVDFRQAMARLYKEFTADGSWFFKPWNKEVVTDPQTGKTYDFADA 498 GN+G L I+ ++ FR+ + RL E +DG WFF W E + + Sbjct: 417 KGNAGKRLIDGSIERSIKFRKEIKRLKGE--SDG-WFFDVWQPEHIDGAE---------- 463 Query: 499 PTKLLTTVQDCWVMHPGESWHGFKDIPDNWSMLDPIKVSILAPGMGEDGELEETGVPAAL 558 CW + +WHGFK+I + LDPIKV++L PGM +DG +++ G+PA++ Sbjct: 464 ----------CWPLRSDSAWHGFKNIDNEHMYLDPIKVTLLTPGMKKDGTMDDFGIPASI 513 Query: 559 VTAWLGRHGIVPTRTTDFQIMFLFSMGVTRGKWGTLVNTLCSFKRHYDANTPLAQVMPEL 618 V +L HGIV +T + ++FLFS+G+ + K +L+ L FKR +D N + ++P L Sbjct: 514 VAKYLDEHGIVVEKTGPYNLLFLFSIGIDKTKALSLLRALTDFKRAFDLNLRVKNMLPSL 573 Query: 619 VEQYPDTYANMGIHDLGDTMFAWLKENNPGARLNEAYSGLPVAEVTPREAYNAIVDNNVE 678 + P+ Y NM + +L + ++ +N + A+ LP +TP A+ + E Sbjct: 574 YREDPEFYENMRVQELAQNIHKLIEHHNLPDLMFRAFEVLPTMMITPYAAFQKELHGQTE 633 Query: 679 LVSIENLPGRIAANSVIPYPPGIPMLLSGENFGDKNSPQVSYLRSLQSWDHHFPGFEHET 738 V +E + GR+ AN ++PYPPG+P+++ GE +++ P + +L+ L H+PGFE + Sbjct: 634 EVYLEEMVGRVNANMILPYPPGVPLVMPGEMITEESRPVLEFLQMLCEIGAHYPGFETDI 693 Query: 739 EGT-EIIDGIYHVMCVK 754 G DG Y V ++ Sbjct: 694 HGAYRQADGRYTVKVLR 710 Lambda K H 0.319 0.135 0.414 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: 1364 Number of extensions: 79 Number of successful extensions: 6 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: 755 Length of database: 715 Length adjustment: 40 Effective length of query: 715 Effective length of database: 675 Effective search space: 482625 Effective search space used: 482625 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 (21.7 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