Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate 5207893 Shew_0409 Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase (RefSeq)
Query= reanno::pseudo1_N1B4:Pf1N1B4_2504 (264 letters) >FitnessBrowser__PV4:5207893 Length = 276 Score = 80.1 bits (196), Expect = 5e-20 Identities = 72/238 (30%), Positives = 115/238 (48%), Gaps = 26/238 (10%) Query: 1 MRVALYQCPPLPLDVAGNLQRLHQLALEAKGAD---LLVLPEMFLTGYNIGIDAVSVLAE 57 M+V+L QC DV NL + + G + L+VLPE L ++ + Sbjct: 1 MQVSLLQCQS-GRDVEENLSFIREQLDALAGGERPHLVVLPECCLLFGGHERQQLAYAGD 59 Query: 58 VHNGESAQQIARIAKTTGIAILYG-YPERTEDGQIYNAVQLIDANGERLCNYRKTHLFG- 115 E Q +A +AK GI ++ G P ++G++++ L D +GE L +Y K HLF Sbjct: 60 DAGSELKQTLAALAKQYGIYLVAGTIPILADEGRVFSRSYLFDDSGETLGHYDKLHLFDV 119 Query: 116 DLDHSM--------FSPGPDEFPLVELNGWKLGFLICYDLEFPENARRLALAGAELILVP 167 D+D F PG + +V+ K+G ICYDL F + R + L GAE+I++P Sbjct: 120 DVDDGTKSYRESDTFCPG-EGVTVVDTPFGKVGMAICYDLRFADLFRAMRLQGAEIIVLP 178 Query: 168 TANMIPYDFIADVT-----VRARAFENQCYVAYANYCG--HEGEIQYCGQSSIAAPDG 218 A + + T ++ARA E QC++ A G ++G+ + G S + +P G Sbjct: 179 AA----FTRVTGRTHWLPLLQARAIETQCFLLAAAQWGEHNQGKRETWGHSCVISPWG 232 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: 186 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: 276 Length adjustment: 25 Effective length of query: 239 Effective length of database: 251 Effective search space: 59989 Effective search space used: 59989 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