Align Carbon-nitrogen hydrolase family protein; EC 3.5.-.- (characterized, see rationale)
to candidate Pf1N1B4_4326 N-carbamoylputrescine amidase (3.5.1.53)
Query= uniprot:Q5NHL7_FRATT (286 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4326 Length = 302 Score = 298 bits (763), Expect = 1e-85 Identities = 139/286 (48%), Positives = 197/286 (68%), Gaps = 3/286 (1%) Query: 1 MANIKVAVVQLSFNDNEAENLAKLESKIIQAAKNGAKIILTPELPSYLYFCKKQNSKYFD 60 M + +A Q+ + NL + E + +AA GA++IL EL + YFC +Q+ K+ Sbjct: 1 MTLLTIATTQMPCTWDLQHNLDQAERLVREAAAKGAQVILLQELFATPYFCIEQSHKHLA 60 Query: 61 LAKTIDESPIVKLYKLLAHKYNIVLPASFFERDGNACYNSIAMIDADGSIMGVYRKAHIP 120 LA+ +SP++K + LA + +VLP S+FE+ GNA +NS+++ DADG ++GVYRK HIP Sbjct: 61 LAEEYRDSPVLKRFAALAKELGVVLPLSWFEKAGNAYFNSLSVADADGRLLGVYRKTHIP 120 Query: 121 DGIGYQEKYYFSPGSAGFKVWDTKYAKVGVGICWDQWFPEAARVMALKGAEILLYPTAIG 180 + IGYQEK YFSPG GF+VWDT + ++GVGICWDQWFPE AR +AL GAE+LL+PTAIG Sbjct: 121 NAIGYQEKEYFSPGDTGFRVWDTAFGRIGVGICWDQWFPETARCLALMGAEVLLFPTAIG 180 Query: 181 SEPHLPDYDSKDHWQRVMQGHAAANMLPVLASNRYATE---ANDDITATYYGSSFITDHT 237 SEP DS+DHWQ M+GHAAAN+LPV+A+NR E + + +YGSSFI +H Sbjct: 181 SEPGCAALDSRDHWQMTMRGHAAANILPVVAANRVGPEVATTDPTLQMNFYGSSFICNHK 240 Query: 238 GDKIAEADRSGDDILYATFDFAELQQQRFYWGLFRDRRPELYDEIV 283 G +AEADR +L + D ++++R WG++RDRRP++Y ++ Sbjct: 241 GKLLAEADRDSTGVLVHSLDLTAMREERLSWGIYRDRRPDMYGALL 286 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: 272 Number of extensions: 5 Number of successful extensions: 2 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: 302 Length adjustment: 26 Effective length of query: 260 Effective length of database: 276 Effective search space: 71760 Effective search space used: 71760 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