Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate 350332 BT0804 putative carbon-nitrogen hydrolase (NCBI ptt file)
Query= reanno::pseudo5_N2C3_1:AO356_14225 (264 letters) >FitnessBrowser__Btheta:350332 Length = 512 Score = 85.5 bits (210), Expect = 2e-21 Identities = 77/251 (30%), Positives = 121/251 (48%), Gaps = 27/251 (10%) Query: 32 ADVLVLPEMF----MTGYNIGVD--AVNVLAEVYNGEWAQQIGRIAKAANLAIVYG-YPE 84 +D ++ PE F M+ +N + A+ LA+ Y E + +A + N+ I+ G P Sbjct: 261 SDFVLFPEYFNAPLMSKFNDKGESQAIRGLAK-YTDEIRDRFINLAISYNINIITGSMPY 319 Query: 85 RGEDGQIYNAVQLIDAQGERLANYRKSHLFGDLDHAMFSAGDSALPIVELNGWKLGLLIC 144 EDG +YN L G Y K H+ D + +G L + + K+G+LIC Sbjct: 320 VKEDGLLYNVGFLCRRDGT-YEMYEKMHVTPDEIKSWGLSGGKLLQTFDTDCAKVGVLIC 378 Query: 145 YDLEFPENARRLALAGAELILVP--TANMQPYEFIADVTVRARAIENQCFVAYANYCG-- 200 YD+EFPE +R +A G +++ VP T Y + V +ARAIEN+CFV A G Sbjct: 379 YDVEFPELSRLMADQGMQILFVPFLTDTQNAYSRVR-VCAQARAIENECFVVIAGCVGNL 437 Query: 201 ---HEAELQYCGQSSIAAP-------NGSRPALAGLDEALIVGELDRQLLD--DSRAAYN 248 H ++QY QS + P +G R E ++V ++D LL+ + + Sbjct: 438 PRVHNMDIQY-AQSGVFTPCDFAFPTDGKRAEATPNTEMILVSDVDLDLLNALHTYGSVR 496 Query: 249 YLHDRRPELYD 259 L DRR ++Y+ Sbjct: 497 NLKDRRNDVYE 507 Lambda K H 0.321 0.139 0.419 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: 315 Number of extensions: 12 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: 264 Length of database: 512 Length adjustment: 30 Effective length of query: 234 Effective length of database: 482 Effective search space: 112788 Effective search space used: 112788 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: 49 (23.5 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