Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate AO353_24845 AO353_24845 decarboxylase
Query= SwissProt::Q9HUI8 (559 letters) >FitnessBrowser__pseudo3_N2E3:AO353_24845 Length = 535 Score = 882 bits (2278), Expect = 0.0 Identities = 435/531 (81%), Positives = 471/531 (88%) Query: 29 TLTAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSGIRHVLTRHEQGAGFMADGYAR 88 TLT GQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSGIRHVLTRHEQGA FMADGYAR Sbjct: 5 TLTGGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSGIRHVLTRHEQGASFMADGYAR 64 Query: 89 VSGKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQRA 148 VSGKPGVCF+ITGPGVTN AT IGQAYADS+P+LVISSVNH+ASLGKGWGCLHETQDQRA Sbjct: 65 VSGKPGVCFIITGPGVTNAATGIGQAYADSIPMLVISSVNHTASLGKGWGCLHETQDQRA 124 Query: 149 MTAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWSAAVAR 208 MTAPITAFSA+ALS E LPELIARAYAVFDSERPRPVHIS+PLDVL+A V DWS V R Sbjct: 125 MTAPITAFSAVALSTEDLPELIARAYAVFDSERPRPVHISVPLDVLSAQVTRDWSHEVVR 184 Query: 209 RPGRGVPCSEALRAAAERLAAARRPMLIAGGGALAAGEALAALSERLAAPLFTSVAGKGL 268 RPGRGVP + AL A +L A+RPM+IAGGGAL A + L +LS RLA P FTSVAGKGL Sbjct: 185 RPGRGVPAATALEQAVAKLQTAKRPMIIAGGGALNAAQELQSLSTRLAVPFFTSVAGKGL 244 Query: 269 LPPDAPLNAGASLCVAPGWEMIAEADLVLAVGTEMADTDFWRERLPLSGELIRVDIDPRK 328 LPPDAPLNAG++LCV PGW++IAEAD+VLAVGTEMADTDFWRERLPL EL+RVDIDPRK Sbjct: 245 LPPDAPLNAGSTLCVEPGWQLIAEADVVLAVGTEMADTDFWRERLPLKAELLRVDIDPRK 304 Query: 329 FNDFYPSAVALRGDARQTLEALLVRLPQEARDSAPAAARVARLRAEIRAAHAPLQALHQA 388 FNDFYP AVAL GDA+QTL ALL RL RD++ A VA LR ++A H PLQ++HQA Sbjct: 305 FNDFYPCAVALHGDAQQTLAALLERLSPATRDASAPIAAVAALREAVKAGHGPLQSIHQA 364 Query: 389 ILDRIAAALPADAFVSTDMTQLAYTGNYAFASRAPRSWLHPTGYGTLGYGLPAGIGAKLG 448 IL+RIAA LP +AF+STDMTQLAYTGNYAF S APRSWLHPTGYGTLGYGLPAGIGAK G Sbjct: 365 ILERIAAELPDNAFISTDMTQLAYTGNYAFNSLAPRSWLHPTGYGTLGYGLPAGIGAKFG 424 Query: 449 APQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWNNDALGQIRDDMLGLDIEPVGV 508 APQRPGLVLVGDGGFLYTAQELATA EELDSPLVVLLWNNDALGQIRDDMLGLDIEP+GV Sbjct: 425 APQRPGLVLVGDGGFLYTAQELATAVEELDSPLVVLLWNNDALGQIRDDMLGLDIEPIGV 484 Query: 509 LPRNPDFALLGRAYGCAVRQPQDLDELERDLRAGFGQSGVTLIELRHACAR 559 LPRNPDFA LGRA+GC+V QPQ L EL+ DLR GF ++GVTLIEL+HACAR Sbjct: 485 LPRNPDFAALGRAFGCSVSQPQSLAELQTDLRHGFKRNGVTLIELKHACAR 535 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: 1032 Number of extensions: 39 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