Align Carbon-nitrogen hydrolase family protein; EC 3.5.-.- (characterized, see rationale)
to candidate PP_0382 PP_0382 5-aminopentanamidase
Query= uniprot:Q5NHL7_FRATT (286 letters) >FitnessBrowser__Putida:PP_0382 Length = 264 Score = 90.5 bits (223), Expect = 4e-23 Identities = 83/261 (31%), Positives = 126/261 (48%), Gaps = 19/261 (7%) Query: 20 NLAKLESKIIQAAKNGAKIILTPELPSYLYFCKKQNSKYFDLAKTIDESPIVKLYKLLAH 79 NL +L + AA GA++++ PE+ +L ++ LA+ D P +A Sbjct: 18 NLQRLRHQAQLAADRGAQLLVCPEM--FLSGYNIGLAQVERLAEAAD-GPAAMTVVEIAQ 74 Query: 80 KYNIVLPASFFER-DGNACYNSIAMIDADGSIMGVYRKAHIPDGIGYQEKYYFSPGSAGF 138 + I + + ER D A YNS+ +IDA G + YRK H+ G ++ FSPG+ F Sbjct: 75 AHRIAIVYGYPERGDDGAIYNSVQLIDAHGRSLSNYRKTHL---FGELDRSMFSPGADHF 131 Query: 139 KVWDTKYAKVGVGICWDQWFPEAARVMALKGAEILLYPTAIGSEPHLPDYDSKDHWQRVM 198 V + + KVG+ IC+D FPE AR +AL GAE++L PTA ++ YD Q + Sbjct: 132 PVVELEGWKVGLLICYDIEFPENARRLALDGAELILVPTA-----NMTPYDFT--CQVTV 184 Query: 199 QGHAAANMLPVLASNRYATEANDDITATYYGSSFITDHTGDKIAEADRSGDDILYATFDF 258 + A N ++ +N E D+I Y G S I G +A A R +L A + Sbjct: 185 RARAQENQCYLVYANYCGAE--DEI--EYCGQSSIIGPDGSLLAMAGRDECQLL-AELEH 239 Query: 259 AELQQQRFYWGLFRDRRPELY 279 + Q R + D R EL+ Sbjct: 240 ERVVQGRRAFPYLTDLRQELH 260 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: 184 Number of extensions: 13 Number of successful extensions: 3 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: 264 Length adjustment: 25 Effective length of query: 261 Effective length of database: 239 Effective search space: 62379 Effective search space used: 62379 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 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