Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate SMc02442 SMc02442 hydrolase
Query= reanno::pseudo6_N2E2:Pf6N2E2_4777 (264 letters) >FitnessBrowser__Smeli:SMc02442 Length = 285 Score = 103 bits (256), Expect = 5e-27 Identities = 90/263 (34%), Positives = 131/263 (49%), Gaps = 15/263 (5%) Query: 13 LDPAGNLHRLHQVALEA--RGADVLVLPEMFMTGYNIGVDAVNVLAEVYNGEWAQQIARI 70 +DPAGN + ++ EA RGA + PEM +VL + N ++ +R+ Sbjct: 14 VDPAGNAETMAKLVREAASRGATYVQTPEMTGAVQRDRTGLRSVLKDGENDVVVREASRL 73 Query: 71 AKAAGLAIVYGY-PERGEDGQIYNAVQLIDAQGERLANYRKSHLFG-DLDH-------AM 121 A+ G+ + G P DG+I N L G ++ +Y K H+F DL++ A Sbjct: 74 ARELGIYLHVGSTPIARADGKIANRGFLFGPDGAKICDYDKIHMFDVDLENGESWRESAA 133 Query: 122 FSAGDAALPIVELNGWKLGLLICYDLEFPENARRLALAGAELILVPTA-NMQPYEFIADV 180 + G+ A +L KLG ICYD+ FPE R+ A+AGAE++ VP A Q E ++ Sbjct: 134 YHPGNTART-ADLPFGKLGFSICYDVRFPELFRQQAVAGAEIMSVPAAFTRQTGEAHWEI 192 Query: 181 TVRARAIENQCFVAYANYCG-HEGELQYCGQSSIAAPNGSRPALAG-LDEALIVAELDRQ 238 +RARAIEN FV A G HE + G S I P G A AG E +IVAE+D Sbjct: 193 LLRARAIENGLFVIAAAQAGTHEDGRETFGHSMIVDPWGRVLAEAGATGEEIIVAEIDVA 252 Query: 239 LMDDSRAAYNYLHDRRPELYDDL 261 + +RA L + R + D++ Sbjct: 253 AVHAARAKIPNLRNARSFVLDEV 275 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: 197 Number of extensions: 9 Number of successful extensions: 5 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: 285 Length adjustment: 25 Effective length of query: 239 Effective length of database: 260 Effective search space: 62140 Effective search space used: 62140 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