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_RS26245 RR42_RS26245 thiamine pyrophosphate-binding protein
Query= SwissProt::Q9HUI8 (559 letters) >FitnessBrowser__Cup4G11:RR42_RS26245 Length = 575 Score = 166 bits (421), Expect = 2e-45 Identities = 165/531 (31%), Positives = 234/531 (44%), Gaps = 77/531 (14%) Query: 33 GQALVRLLANYGVDTVFGIPGVHTLELYRGLPG--SGIRHVLTRHEQGAGFMADGYARVS 90 GQ L+ L GV VF +PG L L I+ ++ R E GAG+MA+ +++ Sbjct: 18 GQILIDQLIIQGVKRVFLVPGESYLPCIDALYDHQDKIQPIVCRQESGAGYMAEAQGKLT 77 Query: 91 GKPGVCFVITGPGVTNVATAIGQAYADSVP-LLVISSVNHSASLGKGWGCLHETQDQRAM 149 G+PG+CFV GPG TN + A+ AY DS P +L + V + + + + D R M Sbjct: 78 GEPGICFVTRGPGATNASIAVHTAYQDSTPMILFVGQVGNDFYEREAF----QEVDYRRM 133 Query: 150 TAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWSAAVAR- 208 +T + A E++PE IARA+AV S RP PV +++P D L W A Sbjct: 134 FGQMTKWVAQIDRTERIPEFIARAFAVATSGRPGPVVLALPEDTL-------WGKATVAD 186 Query: 209 ----RPGRGVPCSEALRAAAERLAAARRPMLIAGGGAL--AAGEALAALSERLAAPLFTS 262 R P +A+ + AE + A RP L+ GG AA + +ER A P+ Sbjct: 187 VPRYRRAHSAPTPDAVASLAELIEQAERPFLLLGGSGWTPAASRQMEGFAERFALPV--G 244 Query: 263 VAGKGLLPPDAPLNAGASLCVAPGWEM-------IAEADLVLAVGTEM----------AD 305 VA + L D N + GW M + E+DL++AVGT M + Sbjct: 245 VAWRRLECFD---NHHPNFAGHVGWAMPESLRKRVQESDLLIAVGTRMGEATSEGYTVVE 301 Query: 306 TDFWRERL----PLSGELIRVDIDPRKFNDFYPSAVALRGDARQTLEALLVRLPQEARDS 361 + R+RL P + EL RV F+ P A + A E R P AR++ Sbjct: 302 SPLPRQRLVHVYPDANELGRV------FHPTLPIAADVVSFAAAVAELSPSRSP-GARNA 354 Query: 362 APAAARVARLRAEIRAAHAPLQALHQAILDRIAAALPADAFVSTDMTQLAYTGNYAFASR 421 A +V E +AA L A + +P D ++ A + + + Sbjct: 355 GHDAHQVYLAEQEPKAAPGALNLNVAAC--HVRDNVPQDTCITVGAGNYALYPHAYYRFK 412 Query: 422 APRSWLHPTGYGTLGYGLPAGIGAKLGAPQRPGLVLVGDGGFLYTAQELATASEELDSPL 481 + L PT G++GYGLPA I AKL P R + GDG F QEL A + + Sbjct: 413 GVGTSLAPT-VGSMGYGLPAAIAAKLENPDRTVICYAGDGCFQMNLQELGVAM-QYRVGI 470 Query: 482 VVLLWNNDALGQIRDDM----------LGLDIEPVGVLPRNPDFALLGRAY 522 VVL++NN G IR LG D NP+F+ L RAY Sbjct: 471 VVLVFNNGIWGTIRAHQEREFPGRTVALGFD---------NPEFSELIRAY 512 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: 815 Number of extensions: 45 Number of successful extensions: 5 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: 575 Length adjustment: 36 Effective length of query: 523 Effective length of database: 539 Effective search space: 281897 Effective search space used: 281897 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