Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate BWI76_RS07990 BWI76_RS07990 carbon-nitrogen hydrolase
Query= BRENDA::B3IVI7 (264 letters) >FitnessBrowser__Koxy:BWI76_RS07990 Length = 262 Score = 107 bits (268), Expect = 2e-28 Identities = 83/261 (31%), Positives = 125/261 (47%), Gaps = 11/261 (4%) Query: 1 MRIALYQGAPKPLDVPGNLQRLRHQAQLAAERGAQLLVCPEMFLTGYNIGLAQVERLAEA 60 M +A Q A P D GN Q + AAERGA LLV PE L + + A+ Sbjct: 1 MFVAAGQFAVMP-DWTGNAQTCVSMMRQAAERGASLLVLPEALLARDDNDADLSVKSAQQ 59 Query: 61 ADGPAAMTVVEIAQAHRIAIVYGYPERGDDGAIYNSVQLIDAHGRSLSNYRKTHLFGEL- 119 DG ++ ++ + V +G N++ + G+ ++ Y+K HL+ Sbjct: 60 LDGGFLQLLLAESENSALTTVLTLHIPSGEGRATNTLVAL-RQGKIVAQYQKLHLYDAFN 118 Query: 120 --DRSMFSPGADHFPVVELEGWKVGLLICYDIEFPENARRLALDGAELILVPTANMTP-- 175 + + G P++E++G +VGL+ CYD+ FPE A LAL GA+LI++P A + Sbjct: 119 IQESRLVDAGRQIPPLIEVDGMRVGLMTCYDLRFPELALSLALSGAQLIVLPAAWVKGPL 178 Query: 176 YDFTCQVTVRARAQENQCYLVYANYCGAEDEIEYCGQSSIIGPDGSLLAMAGRDECQLLA 235 + + ARA + CY+V A CG + GQS II P G+ LA AG + A Sbjct: 179 KEHHWATLLAARALDTTCYIVAAGECGTRN----IGQSRIIDPLGTTLAGAGERPQLIFA 234 Query: 236 ELEHERVVQGRTAFPYLTDLR 256 EL + + Q R P L + R Sbjct: 235 ELSADYIQQVRERLPVLRNRR 255 Lambda K H 0.322 0.139 0.416 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: 185 Number of extensions: 11 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: 264 Length of database: 262 Length adjustment: 25 Effective length of query: 239 Effective length of database: 237 Effective search space: 56643 Effective search space used: 56643 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 (21.9 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