Align Carbon-nitrogen hydrolase family protein; EC 3.5.-.- (characterized, see rationale)
to candidate WP_086509072.1 BZY95_RS05890 nitrilase-related carbon-nitrogen hydrolase
Query= uniprot:Q5NHL7_FRATT (286 letters) >NCBI__GCF_002151265.1:WP_086509072.1 Length = 288 Score = 169 bits (428), Expect = 7e-47 Identities = 95/258 (36%), Positives = 144/258 (55%), Gaps = 12/258 (4%) Query: 28 IIQAAKNGAKIILTPELPSYLYFCKKQNSKYFDLAKTIDESPIVKLYKLLAHKYNIVLPA 87 I QAA+ G +++ E+ + YFC Q+ K++ A+ + + P ++ + LA ++ +V+ Sbjct: 36 IQQAAQAGVQVLCFQEVFNQPYFCPSQDPKWYAAAERVPDGPTCRMMQKLAAEHRMVMIV 95 Query: 88 SFFERDGNACY-NSIAMIDADGSIMGVYRKAHIPDGIGYQEKYYFSPGSAGFKVWDTKYA 146 +E Y NS A+ DADGS +G Y K HIP G+ EK++F PG +G+ V+DT Y Sbjct: 96 PIYEETVTGVYYNSAAVFDADGSYLGKYHKTHIPQVAGFWEKFFFKPGRSGWPVFDTAYG 155 Query: 147 KVGVGICWDQWFPEAARVMALKGAEILLYP--TAIGSEPHLPDYDSKDHWQRVMQGHAAA 204 K+GV IC+D+ FPE R +AL GAE++ P T G +L W+ AAA Sbjct: 156 KIGVYICYDRHFPEGWRALALNGAEVIFNPSATVAGLSQYL--------WELEQPASAAA 207 Query: 205 NMLPVLASNRYATEANDDITATYYGSSFITDHTGDKIAEADRSGDDILYATFDFAELQQQ 264 N + A NR +EA +I +YGSS+I + G A+A D++L D A +++ Sbjct: 208 NGCFIAAINRVGSEAPWNI-GEFYGSSYIVNPRGQIEAQASDRADELLVHEIDLAMVREI 266 Query: 265 RFYWGLFRDRRPELYDEI 282 R W FRDRRPE Y + Sbjct: 267 RNNWQFFRDRRPEAYGRL 284 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: 256 Number of extensions: 9 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: 288 Length adjustment: 26 Effective length of query: 260 Effective length of database: 262 Effective search space: 68120 Effective search space used: 68120 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: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. 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