Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate PfGW456L13_3207 Acetolactate synthase large subunit (EC 2.2.1.6)
Query= SwissProt::Q9HUI8 (559 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3207 Length = 535 Score = 873 bits (2256), Expect = 0.0 Identities = 433/531 (81%), Positives = 471/531 (88%) Query: 28 KTLTAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSGIRHVLTRHEQGAGFMADGYA 87 KTLT GQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSGIRHVLTRHEQGA FMADGYA Sbjct: 4 KTLTGGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSGIRHVLTRHEQGASFMADGYA 63 Query: 88 RVSGKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQR 147 RVSGKPGVCFVITGPGVTN AT IGQAYADS+P+LVISSVNHSASLGKGWG LHE QDQR Sbjct: 64 RVSGKPGVCFVITGPGVTNAATGIGQAYADSIPMLVISSVNHSASLGKGWGSLHECQDQR 123 Query: 148 AMTAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWSAAVA 207 AMTAPITAFSA+AL+ E LPELIARAYAVFDSERPRPVHIS+PLDVL+AP+A DWS V Sbjct: 124 AMTAPITAFSAVALTAEDLPELIARAYAVFDSERPRPVHISVPLDVLSAPIARDWSNEVV 183 Query: 208 RRPGRGVPCSEALRAAAERLAAARRPMLIAGGGALAAGEALAALSERLAAPLFTSVAGKG 267 RRPGRG + A+ A +L AA+RPM+IAGGGAL A L +S RLAAPLFTSVAGKG Sbjct: 184 RRPGRGPASTTAIDQAVAKLNAAKRPMIIAGGGALNATSELQEVSTRLAAPLFTSVAGKG 243 Query: 268 LLPPDAPLNAGASLCVAPGWEMIAEADLVLAVGTEMADTDFWRERLPLSGELIRVDIDPR 327 LLPPDAPLNAG+SLCV PGW +IAEAD+VLAVGTEMADTDFWRERLPL+GEL+RVDIDPR Sbjct: 244 LLPPDAPLNAGSSLCVEPGWNLIAEADVVLAVGTEMADTDFWRERLPLNGELLRVDIDPR 303 Query: 328 KFNDFYPSAVALRGDARQTLEALLVRLPQEARDSAPAAARVARLRAEIRAAHAPLQALHQ 387 KFNDFYP AVAL GDA+QTL LL RLP + R+++ A A VA LR ++A+H PLQ++HQ Sbjct: 304 KFNDFYPCAVALHGDAQQTLSGLLERLPTDVREASAAIASVAALRKAVKASHGPLQSIHQ 363 Query: 388 AILDRIAAALPADAFVSTDMTQLAYTGNYAFASRAPRSWLHPTGYGTLGYGLPAGIGAKL 447 +ILDRIAA LP +AF+STDMTQLAYTGNYAF S A RSWLHPTGYGTLGYGLPAGIGAK Sbjct: 364 SILDRIAAELPDNAFISTDMTQLAYTGNYAFDSLAIRSWLHPTGYGTLGYGLPAGIGAKF 423 Query: 448 GAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWNNDALGQIRDDMLGLDIEPVG 507 GAPQRPGLVLVGDGGFLYTAQELAT+ EELDSPLVVLLWNNDALGQIRDDMLGLDIEP+G Sbjct: 424 GAPQRPGLVLVGDGGFLYTAQELATSVEELDSPLVVLLWNNDALGQIRDDMLGLDIEPIG 483 Query: 508 VLPRNPDFALLGRAYGCAVRQPQDLDELERDLRAGFGQSGVTLIELRHACA 558 VLPRNPDFA L RA+GC V QPQ L EL+ DLR GF ++GVTLIEL+HACA Sbjct: 484 VLPRNPDFAALARAFGCTVTQPQSLAELQTDLRHGFKRNGVTLIELKHACA 534 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: 1025 Number of extensions: 37 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