Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate GFF4653 PS417_23810 acetolactate synthase 3 catalytic subunit
Query= SwissProt::Q9HUI8 (559 letters) >FitnessBrowser__WCS417:GFF4653 Length = 574 Score = 205 bits (521), Expect = 4e-57 Identities = 157/537 (29%), Positives = 239/537 (44%), Gaps = 29/537 (5%) Query: 30 LTAGQALVRLLANYGVDTVFGIPGVHTLELYRGL-PGSGIRHVLTRHEQGAGFMADGYAR 88 L+ G+ LVR L + GVD ++G PG L +Y L + H+L RHEQ A MADGYAR Sbjct: 4 LSGGEMLVRFLRDEGVDYIYGYPGGALLHVYDALFKEPAVTHILVRHEQAATHMADGYAR 63 Query: 89 VSGKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQRA 148 +GK GV V +GPG TN T I AY DS+P+++IS S +G ET D Sbjct: 64 ATGKAGVVLVTSGPGATNAITGIATAYMDSIPMVIISGQVPSTMVGT--DAFQET-DMIG 120 Query: 149 MTAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWSAAVAR 208 ++ PI S + P ++PE++ +A+ + S RP PV + +P D+ ++ Sbjct: 121 ISRPIVKHSFMIKHPSEIPEVMKKAFYLAQSGRPGPVVVDVPKDMTNPAEKFEYIFPKKA 180 Query: 209 RPGRGVPC----SEALRAAAERLAAARRPMLIAGGGALAAGEA--LAALSERLAAPLFTS 262 + P S +R AAE L AA+RP+L +GGG + G + L L++ L P+ + Sbjct: 181 KLRSYSPAVRGHSGQIRKAAEMLLAAKRPVLYSGGGVILGGGSAPLTELAKLLNLPVTNT 240 Query: 263 VAGKGLLPPDAPLNAGASLCVAPGWEMIA--EADLVLAVGTEMADTDF-WRERLPLSGEL 319 + G G P G +A AD++LAVG D + + ++ Sbjct: 241 LMGLGAFPGTDRQFVGMLGMHGSYTANLAMHHADVILAVGARFDDRVINGASKFCPNAKI 300 Query: 320 IRVDIDPRKFNDFYPSAVALRGDARQTLEALLVRLPQEARDSAPAAARVARLRAEIRAAH 379 I +DIDP + + V + G L ++ L P VA +I Sbjct: 301 IHIDIDPASISKTIKADVPIVGPVESVLTEMVAALKDIG--ETPNKESVASWWKQIDEWR 358 Query: 380 APLQAL-----------HQAILDRIAAALPADAFVSTDMTQLAYTGNYAFASRAPRSWLH 428 Q +++ + DAFV++D+ Q + P W++ Sbjct: 359 GDRGLFPYDKGDGSIIKPQTVIETLCEVTKGDAFVTSDVGQHQMFAAQYYKFDKPNRWIN 418 Query: 429 PTGYGTLGYGLPAGIGAKLGAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWNN 488 G GT+G+G PA +G KL P + G+G QEL+T + P+ ++ NN Sbjct: 419 SGGLGTMGFGFPAAMGVKLSFPDTDVACVTGEGSIQMNIQELSTCL-QYGLPVKIVCLNN 477 Query: 489 DALGQIR--DDMLGLDIEPVGVLPRNPDFALLGRAYGCAVRQPQDLDELERDLRAGF 543 LG +R DM + PDF L AYG + DL +L+ + F Sbjct: 478 GVLGMVRQWQDMSYNSRHSHSYMESLPDFVKLVEAYGHVGIRITDLKDLKPKMEEAF 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: 725 Number of extensions: 49 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 559 Length of database: 574 Length adjustment: 36 Effective length of query: 523 Effective length of database: 538 Effective search space: 281374 Effective search space used: 281374 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