Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate WP_057507191.1 ABB28_RS02940 acetolactate synthase large subunit
Query= SwissProt::Q9HUI8 (559 letters) >NCBI__GCF_001431535.1:WP_057507191.1 Length = 551 Score = 212 bits (540), Expect = 3e-59 Identities = 162/530 (30%), Positives = 245/530 (46%), Gaps = 23/530 (4%) Query: 36 LVRLLANYGVDTVFGIPGVHTLELYRGLPGSGIRHVLTRHEQGAGFMADGYARVSGKPGV 95 LV+ L N GVD +FG+PG L+ L S I VLTRHEQ A FMA + R++G+PGV Sbjct: 8 LVKALENEGVDRIFGVPGEENLDFLESLRNSKIELVLTRHEQAAAFMAATHGRLTGRPGV 67 Query: 96 CFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQRAMTAPITA 155 C GPG N +T A+ + P+++I+ S + + D A P+T Sbjct: 68 CLATLGPGALNFSTGAAYAHLGAWPMILITGQKAVMSAKQ---ARFQIVDIVASMKPLTK 124 Query: 156 FSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWSAAVARRPGRGVP 215 + +SP +P ++ A+ V ERP PVH+ +P D+ A D R + Sbjct: 125 MTRQIVSPASIPAMVRDAFRVAMEERPGPVHLELPEDI-AGEEVEDVPVIPIHALERPIA 183 Query: 216 CSEALRAAAERLAAARRPMLIAG--GGALAAGEALAALSERLAAPLFTSVAGKGLLPPDA 273 AL A + AA+RP+++ G G EAL+A R P F + GKG + + Sbjct: 184 APAALDRAEAAILAAKRPLVMIGAAGSRPWLTEALSAFVARTRLPFFNTQMGKGAVTGGS 243 Query: 274 PLNAGASLCVAPGW--EMIAEADLVLAVGTEMADTDFWRERLPLSGELIRVDIDPRKFND 331 L G + + E +A ADL++A+G + + + + ++I + Sbjct: 244 NLYMGTAALSEGDYVHEAVARADLIIAIGHDTIEKPPFLMKSSGGPKVIHISFQSATVEQ 303 Query: 332 FYPSAVALRGDARQTLEALLVRLPQEARDSAPAAARVARLRAEI------RAAHAPLQAL 385 Y + + GD ++EAL RL E R PA + LR +I RA Sbjct: 304 VYHPDIEVLGDIGASVEALAERL--EGR--LPADEGMTELRQKILARLNDRADEDRFPIT 359 Query: 386 HQAILDRIAAALPADAFVSTD--MTQLAYTGNYAFASRAPRSWLHPTGYGTLGYGLPAGI 443 Q I+ + A+P D V D M ++ + NY + + L T+G GLP+ + Sbjct: 360 PQRIVHDVRQAVPDDGIVCLDNGMYKIWFARNY--RTHVANTLLLDNALATMGAGLPSAM 417 Query: 444 GAKLGAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWNNDALGQIRDDMLGLDI 503 A + PQR L + GDGGF+ +QEL TA L LVV++ N+ A G IR Sbjct: 418 MAAMLYPQRRVLAVCGDGGFMMNSQELETA-VRLGLNLVVVILNDSAYGMIRWKQAVDGF 476 Query: 504 EPVGVLPRNPDFALLGRAYGCAVRQPQDLDELERDLRAGFGQSGVTLIEL 553 E G+ NPDF AYG + ++EL + A F GV ++++ Sbjct: 477 EDFGMRFGNPDFVKYAEAYGAKGSRVSAVEELVPMIEAAFAGGGVHVLDV 526 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: 664 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 24 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