Align Carbon-nitrogen hydrolase family protein; EC 3.5.-.- (characterized, see rationale)
to candidate 350403 BT0875 beta-ureidopropionase (NCBI ptt file)
Query= uniprot:Q5NHL7_FRATT (286 letters) >FitnessBrowser__Btheta:350403 Length = 294 Score = 206 bits (525), Expect = 4e-58 Identities = 118/294 (40%), Positives = 166/294 (56%), Gaps = 10/294 (3%) Query: 1 MANIKVAVVQLSFNDNEAENLAKLESKIIQAAKNGAKIILTPELPSYLYFCKKQNSKYFD 60 M IKV ++Q S + NL L I A +GA++I+ EL + LYFC+ +N+ FD Sbjct: 1 MKKIKVGLIQQSNTADIRVNLMNLAKSIEACAAHGAQLIVLQELHNSLYFCQTENTNLFD 60 Query: 61 LAKTIDESPIVKLYKLLAHKYNIVLPASFFERDGNACYNSIAMI-DADGSIMGVYRKAHI 119 LA+ I P Y LA +VL AS FE+ Y++ A++ D DGSI G YRK HI Sbjct: 61 LAEPIP-GPSTGFYSELAAANKVVLVASLFEKRAPGLYHNTAVVFDRDGSIAGKYRKMHI 119 Query: 120 PDGIGYQEKYYFSPGSAGFKVWDTKYAKVGVGICWDQWFPEAARVMALKGAEILLYPTAI 179 PD Y EK+YF+PG GF+ T K+GV +CWDQW+PEAAR+MALKGAE+L+YPTAI Sbjct: 120 PDDPAYYEKFYFTPGDIGFEPIQTSLGKLGVLVCWDQWYPEAARLMALKGAELLIYPTAI 179 Query: 180 GSEPHLPDYDSK----DHWQRVMQGHAAANMLPVLASNRYATEANDDITAT---YYGSSF 232 G E D D K + W + HA AN LPV++ NR E + ++G+SF Sbjct: 180 GWESSDTD-DEKARQLNAWIISQRAHAVANGLPVISVNRVGHEPDPSGQTNGIQFWGNSF 238 Query: 233 ITDHTGDKIAEADRSGDDILYATFDFAELQQQRFYWGLFRDRRPELYDEIVRKY 286 + G+ +A+A + + D + R +W RDRR + YD + +++ Sbjct: 239 VAGPQGEFLAQASNDHPENMVVEIDMERSENVRRWWPFLRDRRIDEYDGLTKRF 292 Lambda K H 0.320 0.136 0.413 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: 253 Number of extensions: 15 Number of successful extensions: 4 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: 286 Length of database: 294 Length adjustment: 26 Effective length of query: 260 Effective length of database: 268 Effective search space: 69680 Effective search space used: 69680 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: 48 (23.1 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