Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate RR42_RS29140 RR42_RS29140 thiamine pyrophosphate-binding protein
Query= SwissProt::Q9HUI8 (559 letters) >FitnessBrowser__Cup4G11:RR42_RS29140 Length = 558 Score = 174 bits (442), Expect = 6e-48 Identities = 171/526 (32%), Positives = 235/526 (44%), Gaps = 59/526 (11%) Query: 31 TAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGS-GIRHVLTRHEQGAGFMADGYARV 89 + G+ LV L +G +F +PG L++ L I ++ +HE A MA+ ++ Sbjct: 14 SGGRVLVDALRIHGAQRIFCVPGESFLDVLDALHDQPAIDLIVCKHEGAAANMAEADGKL 73 Query: 90 SGKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQRAM 149 +G+PG+CFV GPG T+ + + A DS P+L+ V A KG E D AM Sbjct: 74 TGRPGICFVTRGPGATHASIGVHIAAQDSTPMLLF--VGQIARGHKGREAFQEV-DYGAM 130 Query: 150 TAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWSAAVARR 209 I + P ++PEL+ARA+ S RP PV IS+P DVL D VA Sbjct: 131 FGSIAKWVVEIEDPARIPELVARAFQCATSGRPGPVVISLPEDVL------DGLCEVADT 184 Query: 210 PGRGVPCSEALRAA-----AERLAAARRPMLIAGGGALAAGEA--LAALSERLAAPLFTS 262 GR P + A RAA A LA A RP++IAGG +A A AA +R P+ + Sbjct: 185 -GRYRPVAAAPRAADADALAAALAGAERPLVIAGGANWSAQAAADFAAFVQRWNLPVACA 243 Query: 263 VAGKGLLPPDAPLNAG-ASLCVAPGW-EMIAEADLVLAVGTEMAD--TDFWR--ERLPLS 316 + + P G SL V P E + AD++LA GT + D TD + E Sbjct: 244 FRRQDVFDNRDPHYVGHLSLGVNPALAERVRTADVILAFGTRLGDIATDGYTLLEAPQPR 303 Query: 317 GELIRVDIDPRKFNDFYPSAVALRGDARQTLEALLVRLPQEARDSAPAAARVARLRAEIR 376 L + D + Y +A+ L P PAA R + R Sbjct: 304 QRLFHLHADSAELGRVYQPELAIHAGIEPGAAMLAALTP-------PAAVRWGDWTSAAR 356 Query: 377 AAH----APLQALHQAI-LDRIAAALPADAFVSTDMTQLAYTGNYA------FASRAPRS 425 AAH AP + Q +D A D + D GNY +A R PR+ Sbjct: 357 AAHGAFVAPAKPHPQLTGVDMGAVVAHLDRILPDDAVLTNGAGNYTVWLHRYYAYRQPRT 416 Query: 426 WLHPTGYGTLGYGLPAGIGAKLGAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLL 485 L PT G +GYGLPA + AKL PQR + GDG FL QELATA+ + + L+V++ Sbjct: 417 ELAPT-CGAMGYGLPAAVAAKLRDPQRTVVCFAGDGCFLMYPQELATAA-QYGANLIVVV 474 Query: 486 WNNDALGQIR--------DDMLGLDIEPVGVLPRNPDFALLGRAYG 523 NN G IR + G DI +PDF + R+ G Sbjct: 475 VNNGMYGTIRMHQEKRYPGRVSGTDIP-------SPDFVAMARSCG 513 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: 782 Number of extensions: 46 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: 558 Length adjustment: 36 Effective length of query: 523 Effective length of database: 522 Effective search space: 273006 Effective search space used: 273006 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