Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate BPHYT_RS21705 BPHYT_RS21705 sulfoacetaldehyde acetyltransferase
Query= SwissProt::Q9HUI8 (559 letters) >FitnessBrowser__BFirm:BPHYT_RS21705 Length = 610 Score = 180 bits (457), Expect = 1e-49 Identities = 160/572 (27%), Positives = 254/572 (44%), Gaps = 57/572 (9%) Query: 28 KTLTAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSGIRHVLTRHEQGAGFMADGYA 87 + +T +A V LA GV +FGI G ++ +GIR + HEQGAG MADGY+ Sbjct: 21 QAMTPSEAFVETLAANGVTDMFGIMGSAFMDAMDIFAPAGIRLIPVVHEQGAGHMADGYS 80 Query: 88 RVSGKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQR 147 RVSG+ GV GPG++N TAI AY P+++++ + ++G G G E + Q Sbjct: 81 RVSGRHGVVIGQNGPGISNCVTAIAAAYWAHSPVVIVTP--EAGTMGIGLGGFQEAK-QL 137 Query: 148 AMTAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWSAAVA 207 M T + P ++ E R + +E P ++IP D V + Sbjct: 138 PMFQEFTKYQGHVTHPARMAEFTGRCFDRAMAEM-GPTQLNIPRDYFYGQVKVE--IPQP 194 Query: 208 RRPGRGVPCSEALRAAAERLAAARRPMLIAGGGALAAG--EALAALSERLAAPLFTSVAG 265 +R RG ++L AAE LA A+ P++I+GGG + A E AL+ERL AP+ S Sbjct: 195 QRLDRGAGGEQSLNEAAELLAQAKFPVIISGGGVVMADAIEECKALAERLNAPVVNSYLH 254 Query: 266 KGLLPPDAPLNAG--ASLCVAPGWEMIAEADLVLAVGTEMA--------DTDFWRERLPL 315 P + PL G ++++ AD+V+A+G+ + D+W P Sbjct: 255 NDSFPANHPLWCGPLGYQGSKAAMKLLSRADVVIALGSRLGPFGTLPQHGMDYW----PT 310 Query: 316 SGELIRVDIDPRKFNDFYPSAVALRGDARQTLEALLVRLP-QEARDSAPAAARVARLRAE 374 + ++I++D D + +V + GDA+ AL RL ++ A R A++ +E Sbjct: 311 NAKIIQIDADHKMLGLVKKISVGICGDAKAAAVALTERLAGRKLASDATREERGAQIASE 370 Query: 375 IRAAHAPLQ---------------------------ALH-QAILDRIAAALPADAFVSTD 406 A L LH + +L + A+P D VSTD Sbjct: 371 KAAWEKELDDWTHERDAYSLDMIEEQKQERTPGGGTYLHPRQVLRELEKAMPEDVMVSTD 430 Query: 407 MTQLAYTGNYAFASRAPRSWLHPTGYGTLGYGLPAGIGAKLGAPQRPGLVLVGDGGFLYT 466 + + N PRS+ +G GY P IGAK+ AP RP + GDG + + Sbjct: 431 IGNINSVANSYLRFNKPRSFFAAMSWGNCGYAFPTIIGAKVAAPHRPAVSYAGDGAWGMS 490 Query: 467 AQELATASEELDSPLVVLLWNNDALGQIRDDMLGL-DIEPVGVLPRNPDFALLGRAYGC- 524 E T + P+ ++++N G + + + + V N FA + RA G Sbjct: 491 LMETMTCVRH-NIPVTAVVFHNRQWGAEKKNQVDFYNRRFVAGELDNQSFAAIARAMGAE 549 Query: 525 --AVRQPQDL-DELERDLRAGFGQSGVTLIEL 553 V + +D+ L+R + A T+IE+ Sbjct: 550 GIVVDRLEDVGPALKRAIDAQMNHGKTTIIEI 581 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: 733 Number of extensions: 47 Number of successful extensions: 3 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: 610 Length adjustment: 36 Effective length of query: 523 Effective length of database: 574 Effective search space: 300202 Effective search space used: 300202 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