Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate Ac3H11_1601 Acetolactate synthase large subunit (EC 2.2.1.6)
Query= SwissProt::Q9HUI8 (559 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1601 Length = 561 Score = 166 bits (421), Expect = 2e-45 Identities = 153/520 (29%), Positives = 232/520 (44%), Gaps = 49/520 (9%) Query: 31 TAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSGIRHVLTRHEQGAGFMADGYARVS 90 T GQ LV+ L +GV +F +PG L + L + I + R E GA MA+ +++ Sbjct: 10 TGGQILVQQLITHGVKQLFCVPGESYLAVLDALHDADIGVTVCRQEGGAAMMAEAQGKLT 69 Query: 91 GKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQRAMT 150 G+PG+CFV GPG TN + + A+ DS P+++ ++G+ + D A+ Sbjct: 70 GQPGICFVTRGPGATNASAGVHIAHQDSTPMILFVGQVARGAMGRE---AFQELDYSAVF 126 Query: 151 APITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVL--AAPVAHDWSAAVAR 208 + + P ++PELI+RA+ V S RP PV +++P D+L AA VA A+ Sbjct: 127 GTMAKWVVQIDDPARVPELISRAFHVATSGRPGPVVVALPEDMLTEAATVAD----ALPY 182 Query: 209 RPGRGVPCSEALRAAAERLAAARRPMLIAGGGALA--AGEALAALSERLAAPLFTSVAGK 266 + P + L A+RL AA+ P+ I GG + A A +E + P++ S + Sbjct: 183 QVTETHPGAAQLAELAQRLQAAKNPVAILGGSRWSEEAVREFTAFAEAWSIPVYCSFRRQ 242 Query: 267 GLLPPDAPLNAG-ASLCVAPG-WEMIAEADLVLAVG---TEMADTDFWRERLPLSGE-LI 320 L P G L V P I +DLVL VG +E+ + +P + + Sbjct: 243 MLFPATHACYGGDLGLGVNPKLLARIKASDLVLVVGGRLSEVPSQGYELFDIPTPAQSFV 302 Query: 321 RVDIDPRKFNDFYPSAVALRGDARQTLEALLVRLPQEARDSAPAAARVARLRAEIRAAHA 380 V D + Y A+ + AL R +A A +A AAHA Sbjct: 303 HVHADADELGKLYRPTQAIHATPQAFTAAL-----NAVRPTASVA-----WKAHTEAAHA 352 Query: 381 PLQALHQ-------------AILDRIAAALPADAFVSTDMTQLAYTGNYAFASRAPRSWL 427 A ++ + + LPAD A + + S L Sbjct: 353 EYLAWSDPAPIRIPGNLQMGEVMQHLKSVLPADTIFCNGAGNFATWVHRFWPFTTYASQL 412 Query: 428 HPTGYGTLGYGLPAGIGAKLGAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWN 487 PT G++GYGLPAG+G K PQR +V GDG FL QE ATA + P++V+L + Sbjct: 413 APTS-GSMGYGLPAGVGGKRLWPQREVVVFAGDGDFLMHGQEFATA-VQYGLPILVVLLD 470 Query: 488 NDALGQIRDDMLGLDIEPVGVLP----RNPDFALLGRAYG 523 N G IR + + E G + +NPDF +A+G Sbjct: 471 NAMYGTIR---MHQEREYPGRISATQLKNPDFKAYAQAFG 507 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: 738 Number of extensions: 47 Number of successful extensions: 3 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: 561 Length adjustment: 36 Effective length of query: 523 Effective length of database: 525 Effective search space: 274575 Effective search space used: 274575 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