Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate GFF3828 PGA1_262p02320 putative acetolactate synthase isozyme 1 large subunit
Query= SwissProt::Q9HUI8 (559 letters) >FitnessBrowser__Phaeo:GFF3828 Length = 551 Score = 331 bits (848), Expect = 5e-95 Identities = 216/537 (40%), Positives = 298/537 (55%), Gaps = 22/537 (4%) Query: 31 TAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSGIRHVLTRHEQGAGFMADGYARVS 90 T G+ALV LA GV VFGIPGVHT+ELYRGL S +RH+ RHEQGAGFMADGYARVS Sbjct: 10 TVGEALVEELAARGVQHVFGIPGVHTVELYRGLGRSDLRHITPRHEQGAGFMADGYARVS 69 Query: 91 GKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQRAMT 150 G+PGV FVITGPG+TN T + QA ADSVP+LV+S VN S SLG G G LHE DQ A+ Sbjct: 70 GRPGVAFVITGPGLTNTLTPMAQARADSVPMLVVSGVNESGSLGHGMGHLHELPDQHALA 129 Query: 151 APITAFSALALSPEQLPELIARAYAVFDS---ERPRPVHISIPLDVLAAPVAHDWSAAVA 207 + S +PEQL + +A+A RP P H+ IPLDV A A D + Sbjct: 130 KMVALKSEHVAAPEQLTPALDQAFAPIAGAALSRPGPTHVQIPLDV-AGSAARDGDGQES 188 Query: 208 RRPG---RGVPCSEALRAAAERLAAARRPMLIAGGGALAAGEALAALSERLAAPLFTSVA 264 G R V ++ L A +RL AA RP+++AGGGA + L L+E L AP+ +V Sbjct: 189 APTGEQDRTVSPAD-LAALMQRLTAAERPVILAGGGARFCADQLRQLAEYLGAPVVQTVN 247 Query: 265 GKGLLPPDAPLNAGASLCVAPGWEMIAEADLVLAVGTEMADTD---FWRERLPLSGELIR 321 +G++ D PL+ AS + E+I AD+VLA+GTE+ TD + +P LIR Sbjct: 248 ARGVM-FDHPLSVPASPSLGSVRELIEAADMVLALGTELGPTDYDMYATGTMPQMPGLIR 306 Query: 322 VDIDPRKFNDFYPSAVALRGDARQTLEALLVRLPQEARDSAPAAARVARLRAEIRAAHAP 381 +D+ + + + + ++GD L A L + R + +A AA Sbjct: 307 IDLCADQLAR-HRAELTVQGDVAAVLSAALAEWKPDVRSTTDWGIGLAEQTR--TAAWDE 363 Query: 382 LQALHQA---ILDRIAAALPADAFVSTDMTQLAYTGNYAFASRAPRSWLH-PTGYGTLGY 437 + ++A +L+ + AA+P A V D Q Y GN + P W + TGYG LGY Sbjct: 364 IGESYRAQVMVLNALRAAVPG-AIVVGDSAQPIYAGNLYYDHDRPGGWFNAATGYGALGY 422 Query: 438 GLPAGIGAKLGAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWNNDALGQIRDD 497 G+PA IGA + AP+ P + + GDGG ++ E+ TA +E S + ++WNN +I Sbjct: 423 GIPAAIGAAVAAPETPVICITGDGGAQFSLPEIMTAVDEALS-ITFIVWNNHGYQEIARS 481 Query: 498 MLGLDIEPVGVLPRNPDFALLGRAYGCAVRQ-PQDLDELERDLRAGFGQSGVTLIEL 553 M + + VG P PDFA R++G + R D E+ L + ++G +IE+ Sbjct: 482 MQDVGVPVVGCDPTPPDFAATARSFGISHRAVSADPQEVAVALHSAATETGPRMIEI 538 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: 866 Number of extensions: 47 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: 559 Length of database: 551 Length adjustment: 36 Effective length of query: 523 Effective length of database: 515 Effective search space: 269345 Effective search space used: 269345 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: 53 (25.0 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