Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate 1936210 b0077 acetolactate synthase III large subunit (NCBI)
Query= SwissProt::Q9HUI8 (559 letters) >FitnessBrowser__Keio:1936210 Length = 574 Score = 224 bits (570), Expect = 9e-63 Identities = 168/537 (31%), Positives = 260/537 (48%), Gaps = 27/537 (5%) Query: 30 LTAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPG-SGIRHVLTRHEQGAGFMADGYAR 88 L+ + +VR L + GV VFG PG L++Y L GI HVL RHEQ A MADG AR Sbjct: 4 LSGAEMVVRSLIDQGVKQVFGYPGGAVLDIYDALHTVGGIDHVLVRHEQAAVHMADGLAR 63 Query: 89 VSGKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQRA 148 +G+ GV V +GPG TN T I AY DS+PL+V+S ++ + G+ E D Sbjct: 64 ATGEVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVATSLI--GYDAFQEC-DMVG 120 Query: 149 MTAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVL--AAPVAHDWSAAV 206 ++ P+ S L E +P+++ +A+ + S RP PV + +P D+L A + + W +V Sbjct: 121 ISRPVVKHSFLVKQTEDIPQVLKKAFWLAASGRPGPVVVDLPKDILNPANKLPYVWPESV 180 Query: 207 ARRPGRGVPCSE--ALRAAAERLAAARRPMLIAGGGALAAG--EALAALSERLAAPLFTS 262 + R ++ A + L AA++P++ GGGA+ AG + L E L P+ S Sbjct: 181 SMRSYNPTTTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETVEALNLPVVCS 240 Query: 263 VAGKGLLPPDAPLNAGASLCVAPGWE---MIAEADLVLAVGTEMAD--TDFWRERLPLSG 317 + G G P A L + +E + AD++ AVG D T+ + P + Sbjct: 241 LMGLGAFPA-THRQALGMLGMHGTYEANMTMHNADVIFAVGVRFDDRTTNNLAKYCP-NA 298 Query: 318 ELIRVDIDPRKFNDFYPSAVALRGDARQTLEALLVRLPQEARDSAPAAAR-------VAR 370 ++ +DIDP + + + + GDARQ LE +L L QE+ R R Sbjct: 299 TVLHIDIDPTSISKTVTADIPIVGDARQVLEQMLELLSQESAHQPLDEIRDWWQQIEQWR 358 Query: 371 LRAEIRAAHAPLQALHQAILDRIAAALPADAFVSTDMTQLAYTGNYAFASRAPRSWLHPT 430 R ++ + QA+++ + DA+V++D+ Q + PR W++ Sbjct: 359 ARQCLKYDTHSEKIKPQAVIETLWRLTKGDAYVTSDVGQHQMFAALYYPFDKPRRWINSG 418 Query: 431 GYGTLGYGLPAGIGAKLGAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWNNDA 490 G GT+G+GLPA +G K+ P+ + + GDG QEL+TA + + P++V+ NN Sbjct: 419 GLGTMGFGLPAALGVKMALPEETVVCVTGDGSIQMNIQELSTAL-QYELPVLVVNLNNRY 477 Query: 491 LGQIR--DDMLGLDIEPVGVLPRNPDFALLGRAYGCAVRQPQDLDELERDLRAGFGQ 545 LG ++ DM+ + PDF L AYG Q ELE L Q Sbjct: 478 LGMVKQWQDMIYSGRHSQSYMQSLPDFVRLAEAYGHVGIQISHPHELESKLSEALEQ 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: 698 Number of extensions: 42 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: 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