Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate GFF1148 Psest_1181 glyoxylate carboligase
Query= SwissProt::Q9HUI8 (559 letters) >FitnessBrowser__psRCH2:GFF1148 Length = 593 Score = 184 bits (467), Expect = 8e-51 Identities = 152/497 (30%), Positives = 231/497 (46%), Gaps = 33/497 (6%) Query: 30 LTAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSG-IRHVLTRHEQGAGFMADGYAR 88 + A A V +L G+DT FGIPG LY L G IRH+L RH +GA MA+GY R Sbjct: 4 MRAIDAAVAVLRKEGIDTAFGIPGAAINPLYSALRADGSIRHILARHVEGASHMAEGYTR 63 Query: 89 V-SGKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQR 147 +G GVC +GP T++ T + A+ADS+P+L I+ A L K + D Sbjct: 64 TKAGNIGVCIGTSGPAGTDMITGLYSAWADSIPILCITGQAPRARLYKED---FQAVDIE 120 Query: 148 AMTAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWSAAVA 207 ++ P+T ++ P +P + +A+ V S RP PV I +P DV A + D Sbjct: 121 SIAKPVTKWAVTVREPALVPRVFQQAFHVMRSGRPGPVLIDLPFDVQMAEIEFDIETYEP 180 Query: 208 RRPGRGVPCSEALRAAAERLAAARRPMLIAGGGALAAGEA--LAALSERLAAPLFTSVAG 265 + + + A + L AA RP+++AGGG AG L +E + P+ ++ G Sbjct: 181 LAVYKPAATRKQIEKAIDMLCAAERPLIVAGGGIYNAGAEALLVEFAETVGVPVIPTLMG 240 Query: 266 KGLLPPDAPLNAGASLCVAP-----GWEMIAEADLVLAVGTEMADTDFWR-ERLPLSGEL 319 G +P D PL AG +C G + +D VL +G A+ E Sbjct: 241 WGSIPDDHPLMAG--MCGLQTSHRYGNANMLASDFVLGIGNRWANRHTGSVEVYTKDRTF 298 Query: 320 IRVDIDPRKFNDFYPSAVALRGDARQTLEALLVRLPQEAR------DSAPAAARVA-RLR 372 + VDI+P + + + DA L AL V + +E + D P AA R R Sbjct: 299 VHVDIEPTQIGRVFSPDFGITSDAGAAL-ALFVEVAKERKAAGQLPDRTPWAADCQERKR 357 Query: 373 AEIRAAH---APLQALHQAILDRIAAALPADA-FVST-DMTQLAYTGNYAFASRAPRSWL 427 +R H P++ Q + + A DA +VST ++Q+A + + PR W+ Sbjct: 358 TMLRKTHFDSVPMKP--QRVYQCMNNAFGKDACYVSTIGLSQIA-AAQFLHVYK-PRHWI 413 Query: 428 HPTGYGTLGYGLPAGIGAKLGAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWN 487 + G LG+ +PA +G P R + L GD F + +ELA + + P + +L N Sbjct: 414 NCGQAGPLGWTIPAALGVVAADPTRKVVALSGDYDFQFMIEELAVGA-QFKLPYIHILVN 472 Query: 488 NDALGQIRDDMLGLDIE 504 N LG IR G +++ Sbjct: 473 NAYLGLIRQSQRGFEMD 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: 735 Number of extensions: 47 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: 593 Length adjustment: 36 Effective length of query: 523 Effective length of database: 557 Effective search space: 291311 Effective search space used: 291311 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