Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate Pf1N1B4_4326 N-carbamoylputrescine amidase (3.5.1.53)
Query= reanno::pseudo3_N2E3:AO353_07425 (264 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4326 Length = 302 Score = 104 bits (260), Expect = 2e-27 Identities = 86/275 (31%), Positives = 136/275 (49%), Gaps = 24/275 (8%) Query: 10 PLPLDVAGNLQRLQKLATEA--KGADLLVFPEMFLTGYNIGAEAVGALA---EAQDGTCA 64 P D+ NL + ++L EA KGA +++ E+F T Y ++ LA E +D Sbjct: 12 PCTWDLQHNLDQAERLVREAAAKGAQVILLQELFATPYFCIEQSHKHLALAEEYRDSPVL 71 Query: 65 QYIASIAKASGIAIVYGYPERAEDGQIYNAVQLIDSRGQRLANYRKTHL---FGELDHSM 121 + A++AK G+ + + E+A + +N++ + D+ G+ L YRKTH+ G + Sbjct: 72 KRFAALAKELGVVLPLSWFEKAGNAY-FNSLSVADADGRLLGVYRKTHIPNAIGYQEKEY 130 Query: 122 FSVGPDEFPLVELNGWKLGFLICYDLEFPENARRLALAGAELILVPTANMIPYDFIA--- 178 FS G F + + ++G IC+D FPE AR LAL GAE++L PTA A Sbjct: 131 FSPGDTGFRVWDTAFGRIGVGICWDQWFPETARCLALMGAEVLLFPTAIGSEPGCAALDS 190 Query: 179 ----DVTVRSRAFENQCYVAYANYCGHEG-------EIHYCGQSSIAAPDGSRIAQAGLD 227 +T+R A N V AN G E ++++ G S I G +A+A D Sbjct: 191 RDHWQMTMRGHAAANILPVVAANRVGPEVATTDPTLQMNFYGSSFICNHKGKLLAEADRD 250 Query: 228 E-ALIVGTLDRQLMVDSRAANRYFLDRRPELYGEL 261 ++V +LD M + R + + DRRP++YG L Sbjct: 251 STGVLVHSLDLTAMREERLSWGIYRDRRPDMYGAL 285 Lambda K H 0.322 0.139 0.414 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: 14 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: 302 Length adjustment: 26 Effective length of query: 238 Effective length of database: 276 Effective search space: 65688 Effective search space used: 65688 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