Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate 6937877 Sama_2018 acetolactate synthase 3 catalytic subunit (RefSeq)
Query= SwissProt::Q9HUI8 (559 letters) >FitnessBrowser__SB2B:6937877 Length = 573 Score = 217 bits (553), Expect = 9e-61 Identities = 159/529 (30%), Positives = 255/529 (48%), Gaps = 31/529 (5%) Query: 30 LTAGQALVRLLANYGVDTVFGIPGVHTLELYRGL-PGSGIRHVLTRHEQGAGFMADGYAR 88 L+ +VR L + GV +FG PG L++Y L S I H+L RHEQ A MADGYAR Sbjct: 4 LSGASMIVRSLIDEGVKHIFGYPGGSVLDIYDALHESSNIEHILVRHEQAAVHMADGYAR 63 Query: 89 VSGKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQRA 148 +G GV V +GPG TN T I AY DSVPL+++S S+ +G + D Sbjct: 64 ATGDVGVVLVTSGPGATNAITGIATAYMDSVPLVILSGQVPSSLIGND---AFQECDMIG 120 Query: 149 MTAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVL--AAPVAHDWSAAV 206 ++ PI S L P ++PE I +A+ + + RP PV + +P D L A +++ + V Sbjct: 121 ISRPIVKHSFLVKDPTEIPETIKKAFYIAATGRPGPVVVDLPKDTLNPALKFDYEYPSEV 180 Query: 207 ARRPGRGVPCSE--ALRAAAERLAAARRPMLIAGGGAL--AAGEALAALSERLAAPLFTS 262 R +R + L A++P+L GGGA+ + + + ALSERL P+ + Sbjct: 181 KMRSYNPTVTGHKGQIRRGLQALLNAKKPVLYVGGGAIISSCDKQILALSERLNIPVVNT 240 Query: 263 VAGKGLLPPDAPLNAGASLCVAPGWE---MIAEADLVLAVGTEMAD--TDFWRERLPLSG 317 + G G P P N G L + +E + +DL+ +G D T+ ++ P + Sbjct: 241 LMGLGAFPGTHPNNIG-MLGMHGTYEANMTMHNSDLIFGIGVRFDDRTTNNVQKYCP-NA 298 Query: 318 ELIRVDIDPRKFNDFYPSAVALRGDARQTLEALL--------VRLPQEARDSAPAAARVA 369 ++ +DIDP + + + + G A + L+ +L +R + A D Sbjct: 299 TVLHIDIDPSSISKTVQAHIPIVGSADKVLDEMLSLLDGDTEMRNDEGAIDCWWNDINQW 358 Query: 370 RLRAEIRAAHAPLQALHQAILDRIAAALPADAFVSTDMTQLAYTGNYAFASRAPRSWLHP 429 R R + + Q +++ + DA+VS+D+ Q + PR W++ Sbjct: 359 RSRKCLAYETNSEKIKPQQVIETLYRLTKGDAYVSSDVGQHQMFAALYYPFDKPRRWINS 418 Query: 430 TGYGTLGYGLPAGIGAKLGAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWNND 489 G GT+G+GLPA +G K+ P + + GDG QEL+TA + D P+ ++ NN Sbjct: 419 GGLGTMGFGLPAAMGVKMAMPDETVVCVTGDGSIQMNIQELSTAL-QYDVPVKIINLNNR 477 Query: 490 ALGQIR--DDMLGLDIEPVGVLPRNPDFALLGRAY---GCAVRQPQDLD 533 LG ++ DM+ + PDFA + AY G + +P++L+ Sbjct: 478 FLGMVKQWQDMIYSGRHSHSYMDSVPDFAKIAEAYGHVGITISRPEELE 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: 682 Number of extensions: 36 Number of successful extensions: 5 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: 573 Length adjustment: 36 Effective length of query: 523 Effective length of database: 537 Effective search space: 280851 Effective search space used: 280851 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