Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate 3610125 Dshi_3506 Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase (RefSeq)
Query= reanno::pseudo1_N1B4:Pf1N1B4_2504 (264 letters) >FitnessBrowser__Dino:3610125 Length = 277 Score = 61.6 bits (148), Expect = 2e-14 Identities = 77/257 (29%), Positives = 106/257 (41%), Gaps = 23/257 (8%) Query: 1 MRVALYQCPPLPLDVAGNLQRLHQLALEA--KGADLLVLPEMFLTGYNIGIDAVSVLAEV 58 MR AL Q D NL +L LA +A +GA ++ PE+ +VL Sbjct: 1 MRAALVQMTSGD-DPEANLAQLQGLAAQAVAEGAGFVLSPEVSNCLSTSRTRQRAVLRRE 59 Query: 59 HNGESAQQIARIAKTTGIAILYG-YPERTED--GQIYNAVQLIDANGERLCNYRKTHLFG 115 + + A G+ +L G TED G+ N LIDA G Y K H+F Sbjct: 60 ADDPMLAAMREFAARRGVWVLLGSLAVTTEDAEGRFANRSILIDAGGGIAARYDKIHMFD 119 Query: 116 DL--------DHSMFSPGPDEFPLVELNGWKLGFLICYDLEFPENARRLALAGAELILVP 167 + + PG D L + K+G +CYDL FP R LA AGAE++ VP Sbjct: 120 VAVSEAETYRESDGYRPG-DRAVLADTPFGKIGMTVCYDLRFPHLFRDLARAGAEILTVP 178 Query: 168 TANMIPYDFIA--DVTVRARAFENQCYVAYANYCG----HEGEIQYC-GQSSIAAPDGSR 220 +A P A + +RARA E +V G G+ + G S P G Sbjct: 179 SA-FSPVTGAAHWEPLLRARAIECGAWVLAPAQTGTHPATRGKARSTHGHSLAVDPWGRV 237 Query: 221 IAQAGLDEALIVGELDR 237 +A G + +LDR Sbjct: 238 LADGGTAPGVCFVDLDR 254 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: 151 Number of extensions: 4 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: 277 Length adjustment: 25 Effective length of query: 239 Effective length of database: 252 Effective search space: 60228 Effective search space used: 60228 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