Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate PP_3723 PP_3723 putative 2-ketoarginine decarboxylase AruI
Query= SwissProt::Q9HUI8 (559 letters) >FitnessBrowser__Putida:PP_3723 Length = 535 Score = 876 bits (2264), Expect = 0.0 Identities = 436/529 (82%), Positives = 466/529 (88%) Query: 29 TLTAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSGIRHVLTRHEQGAGFMADGYAR 88 TLTAGQALVRLLANYGV+TVFGIPGVHTLELYRGLPGSGIRHVLTRHEQGAGFMADGYAR Sbjct: 5 TLTAGQALVRLLANYGVETVFGIPGVHTLELYRGLPGSGIRHVLTRHEQGAGFMADGYAR 64 Query: 89 VSGKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQRA 148 VSGKPGVCFVITGPGVTNVAT IGQAYADSVP+LVISSVNH+ASLGKGWGCLHETQDQRA Sbjct: 65 VSGKPGVCFVITGPGVTNVATPIGQAYADSVPMLVISSVNHTASLGKGWGCLHETQDQRA 124 Query: 149 MTAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWSAAVAR 208 MTAPITAFSA+AL + LPELIARA+AVFDSERPRPVHIS+PLDVLAA V+ DWS V R Sbjct: 125 MTAPITAFSAVALQGDDLPELIARAWAVFDSERPRPVHISVPLDVLAASVSRDWSGEVVR 184 Query: 209 RPGRGVPCSEALRAAAERLAAARRPMLIAGGGALAAGEALAALSERLAAPLFTSVAGKGL 268 RPGRG PC E L AA +LAAA+RPM+IAGGGAL A E L LS RLAAPLFTSVAGKGL Sbjct: 185 RPGRGQPCRETLEQAALKLAAAQRPMIIAGGGALHAAEQLQQLSTRLAAPLFTSVAGKGL 244 Query: 269 LPPDAPLNAGASLCVAPGWEMIAEADLVLAVGTEMADTDFWRERLPLSGELIRVDIDPRK 328 LPPDAPLNAGASLCV PGW++I++AD+VLAVGTEMADTDFWRERLP+ GEL+RVDIDPRK Sbjct: 245 LPPDAPLNAGASLCVEPGWQLISQADVVLAVGTEMADTDFWRERLPIRGELLRVDIDPRK 304 Query: 329 FNDFYPSAVALRGDARQTLEALLVRLPQEARDSAPAAARVARLRAEIRAAHAPLQALHQA 388 FNDFYP A+AL+GDARQTL+ LL LP RD A A+A VA LR IR HAPLQA HQA Sbjct: 305 FNDFYPCAIALQGDARQTLDGLLEHLPALQRDPAQASAAVATLRQAIRNGHAPLQATHQA 364 Query: 389 ILDRIAAALPADAFVSTDMTQLAYTGNYAFASRAPRSWLHPTGYGTLGYGLPAGIGAKLG 448 ILDRIAA LP DAF+S+DMTQLAYTGNYAFASRAPRSWLHPTGYGTLGYGLPAGIG Sbjct: 365 ILDRIAAVLPDDAFISSDMTQLAYTGNYAFASRAPRSWLHPTGYGTLGYGLPAGIGGMFA 424 Query: 449 APQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWNNDALGQIRDDMLGLDIEPVGV 508 + RPGLVLVGDGGFLYTAQELATA EEL PLVVLLWNNDALGQIRDDMLGLDIEPVGV Sbjct: 425 SDHRPGLVLVGDGGFLYTAQELATAVEELHRPLVVLLWNNDALGQIRDDMLGLDIEPVGV 484 Query: 509 LPRNPDFALLGRAYGCAVRQPQDLDELERDLRAGFGQSGVTLIELRHAC 557 LPRNPDF L RA+GC V QP+DLD L+ DL +GF GVT IEL+H C Sbjct: 485 LPRNPDFIGLARAFGCTVHQPRDLDALQADLASGFATPGVTFIELKHTC 533 Lambda K H 0.321 0.136 0.412 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: 1039 Number of extensions: 34 Number of successful extensions: 2 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: 559 Length of database: 535 Length adjustment: 36 Effective length of query: 523 Effective length of database: 499 Effective search space: 260977 Effective search space used: 260977 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: 52 (24.6 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