Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate SMc01962 SMc01962 hypothetical protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_2504 (264 letters) >FitnessBrowser__Smeli:SMc01962 Length = 259 Score = 198 bits (504), Expect = 8e-56 Identities = 114/257 (44%), Positives = 159/257 (61%), Gaps = 8/257 (3%) Query: 1 MRVALYQCPPLPLDVAGNLQRLHQLALEA--KGADLLVLPEMFLTGYNIGIDAVSVLAEV 58 M+ A Q + DVA NL R+ + A+ A +GA LLV PE+ +TGY G +A+ LAE Sbjct: 2 MKFAALQMKSIGGDVAANLARIERAAIGASGEGASLLVAPELAITGYGAG-EAIRRLAEP 60 Query: 59 HNGESAQQIARIAKTTGIAILYGYPERTEDGQIYNAVQLIDANGERLCNYRKTHLFGDLD 118 +G +++ RI+ TGIAI+ G+ E+ D +YN+ +D + + YRK+HL+GD + Sbjct: 61 ADGRIVRELGRISLKTGIAIVAGFAEQGADA-VYNSAVHVDGDAVPVV-YRKSHLYGDYE 118 Query: 119 HSMFSPGPDEFPLVELNGWKLGFLICYDLEFPENARRLALAGAELILVPTANMIPYD--F 176 S+F+P L + G G LICYD+EFPEN RRLALAGA+ +LVPTA + F Sbjct: 119 RSLFTPAEPSTRLFKHRGVTCGMLICYDVEFPENVRRLALAGADAVLVPTALPAGWSGTF 178 Query: 177 IADVTVRARAFENQCYVAYANYCGHEGEIQYCGQSSIAAPDGSRIAQAG-LDEALIVGEL 235 I D ++ RAFENQ +VAY N+CG + + G S IA+PDG +A+AG DE LI+ E+ Sbjct: 179 ITDHMIQTRAFENQVFVAYVNHCGSDDMFSFAGLSLIASPDGQALAKAGSSDETLIIAEI 238 Query: 236 DRQLMIDSRAANRYFLD 252 D Q SRA N Y +D Sbjct: 239 DPQAFAISRAENTYLMD 255 Lambda K H 0.322 0.140 0.420 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: 207 Number of extensions: 12 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: 259 Length adjustment: 25 Effective length of query: 239 Effective length of database: 234 Effective search space: 55926 Effective search space used: 55926 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