Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate 14358 b0219 predicted C-N hydrolase family amidase, NAD(P)-binding (NCBI)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1170 (264 letters) >FitnessBrowser__Keio:14358 Length = 256 Score = 90.9 bits (224), Expect = 2e-23 Identities = 75/226 (33%), Positives = 106/226 (46%), Gaps = 11/226 (4%) Query: 1 MRVALYQCPPLPLDVAGNLQRLQQLALEAKGADLLVLPEMFLTGYNIGVDAVSVLAE-VY 59 +++ L Q P + +D NL+ + G D++VLPEMF +G+ + A S+ + V Sbjct: 4 LKITLLQQPLVWMDGPANLRHFDRQLEGITGRDVIVLPEMFTSGFAMEAAASSLAQDDVV 63 Query: 60 NGESAQQVARIAKAAGIAILYGYPERTEDGQIYNAVQLIDSDGERVCNYRKTHLFGDLDH 119 N +A+ A AG L +TE G + N L++ G V Y K HLF D Sbjct: 64 NWMTAKAQQCNALIAGSVAL-----QTESGSV-NRFLLVEPGGT-VHFYDKRHLFRMADE 116 Query: 120 SMFSAGSDEFPIVELNGWKLGFLICYDLEFPENARRLALAGAELILVPTANMIPFDFVAD 179 + + IVE GW++ L+CYDL FP +R L +L L P Sbjct: 117 HLHYKAGNARVIVEWRGWRILPLVCYDLRFPVWSRN--LNDYDLALYVANWPAPRSLHWQ 174 Query: 180 VTVRARAFENQCYVAYANYCGHEGD-IHYCGQSSIAAPDGSRIAQA 224 + ARA ENQ YVA N G +G+ HY G S + P G IA A Sbjct: 175 ALLTARAIENQAYVAGCNRVGSDGNGCHYRGDSRVINPQGEIIATA 220 Lambda K H 0.321 0.139 0.411 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: 177 Number of extensions: 12 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: 256 Length adjustment: 24 Effective length of query: 240 Effective length of database: 232 Effective search space: 55680 Effective search space used: 55680 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 (21.8 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