Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate SM_b20681 SM_b20681 glyoxylate carboligase
Query= SwissProt::Q9HUI8 (559 letters) >FitnessBrowser__Smeli:SM_b20681 Length = 594 Score = 173 bits (439), Expect = 1e-47 Identities = 150/501 (29%), Positives = 231/501 (46%), Gaps = 41/501 (8%) Query: 30 LTAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSG-IRHVLTRHEQGAGFMADGYAR 88 + A A V +L G+D FG+PG Y L G IRH+L RH +GA MA+GY R Sbjct: 4 MRAVDAAVYVLEKEGIDCAFGVPGAAINPFYSALRARGSIRHILARHVEGASHMAEGYTR 63 Query: 89 VS-GKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQR 147 G GVC +GP T++ T + A ADS+P+L I+ A L K + D Sbjct: 64 ARHGNIGVCIGTSGPAGTDMITGLYSASADSIPILCITGQAPRARLDKED---FQAVDIA 120 Query: 148 AMTAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHD---WSA 204 + AP+T ++ + P +P + +A+ + S RP PV I +P+DV A + D + Sbjct: 121 KIAAPVTKWAVTVMEPALVPFVFQKAFHLMRSGRPGPVLIDLPVDVQLAEIEFDPETYEP 180 Query: 205 AVARRPGRGVPCSEALRAAAERLAA----ARRPMLIAGGGALAA--GEALAALSERLAAP 258 A +P A RA AE+ A A RP+++AGGG + A + L +E P Sbjct: 181 LSAYKPA-------ATRAQAEKALAMLNEAERPLIVAGGGIINADASDLLTEFAEITGVP 233 Query: 259 LFTSVAGKGLLPPDAPLNAGASLCVAP-----GWEMIAEADLVLAVGTEMADTDFWRERL 313 + ++ G G++P D PL AG +C G + +D V +G A+ Sbjct: 234 VVPTLMGWGVIPDDHPLMAG--MCGLQTSHRYGNATLLASDFVFGIGNRWANRHTGNIPT 291 Query: 314 PLSG-ELIRVDIDPRKFNDFYPSAVALRGDARQTLEALLV-----RLPQEARD-SAPAAA 366 G + I VDI+P + + + DA L+ L + + RD SA A Sbjct: 292 YTEGRKFIHVDIEPTQIGRVFAPDFGIVSDAGAALKLFLDVATEWKTAGKLRDWSAWAEE 351 Query: 367 RVARLRAEIRAAHAPLQALH-QAILDRIAAALPADA-FVST-DMTQLAYTGNYAFASRAP 423 R R+ +R H L Q + + + D +VST ++Q+A G P Sbjct: 352 CRERKRSMLRKTHFDQTPLKPQRVYEEMNKTFGRDTCYVSTIGLSQIA--GAQFLHVYKP 409 Query: 424 RSWLHPTGYGTLGYGLPAGIGAKLGAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVV 483 R+W++ G LG+ LPA +G + P R + L GD F + +ELA ++ P + Sbjct: 410 RNWINCGQAGPLGWTLPAALGVRAADPNRQIVALSGDYDFQFLIEELAVGAQH-KLPYLH 468 Query: 484 LLWNNDALGQIRDDMLGLDIE 504 ++ NN LG IR G +++ Sbjct: 469 VVVNNSYLGLIRQAQRGFNMD 489 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: 726 Number of extensions: 49 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: 594 Length adjustment: 36 Effective length of query: 523 Effective length of database: 558 Effective search space: 291834 Effective search space used: 291834 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