Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate AZOBR_RS30770 AZOBR_RS30770 carbon-nitrogen hydrolase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1170 (264 letters) >lcl|FitnessBrowser__azobra:AZOBR_RS30770 AZOBR_RS30770 carbon-nitrogen hydrolase Length = 268 Score = 265 bits (678), Expect = 6e-76 Identities = 140/266 (52%), Positives = 179/266 (67%), Gaps = 6/266 (2%) Query: 1 MRVALYQCPPLPLDVAGNLQRLQQLALEA--KGADLLVLPEMFLTGYNIGVDAVSVLAEV 58 MR+ L+Q P NL RL++ A EA +G LLV PEM LT Y+IG + V LAE Sbjct: 1 MRLTLFQTDAEPGAPHRNLDRLERAAAEAAERGPALLVGPEMGLTSYDIGAETVRALAEP 60 Query: 59 YNGESAQQVARIAKAAGIAILYGYPERTEDGQIYNAVQLIDSDGERVCNYRKTHLFGDLD 118 +G A +VA IA+ GIAILYGYPER DG +YNA QLI SDG+ + N RKTHL+GDLD Sbjct: 61 VDGPMAARVAEIARRHGIAILYGYPERGADGAVYNAAQLIGSDGQSLLNQRKTHLYGDLD 120 Query: 119 HSMFSAGSDEFPIVELNGWKLGFLICYDLEFPENARRLALAGAELILVPTANMIPFDFVA 178 F+ G D FP E++G ++G ICYD+EFPE RR ALAG +++LVPTA M P++ VA Sbjct: 121 RGSFAPGGDAFPTAEVDGMRVGVAICYDVEFPELVRRHALAGVDVLLVPTALMTPYEIVA 180 Query: 179 DVTVRARAFENQCYVAYANYCGHEGDIHYCGQSSIAAPDGSRIAQAGLDESLIVGELDRQ 238 + ARAFEN +VAYAN CG EG + YCG SS+AAPDGS +A+AG E+L+ +LD Sbjct: 181 TTVIPARAFENGIFVAYANRCGREGTLRYCGLSSVAAPDGSVLARAGDGEALLTVDLDAA 240 Query: 239 LMVDSRAANRYLLDRRPELYGELNKS 264 L R +L DRRP+LYG ++ + Sbjct: 241 L----RRVGTHLADRRPDLYGAVSST 262 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: 251 Number of extensions: 13 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: 268 Length adjustment: 25 Effective length of query: 239 Effective length of database: 243 Effective search space: 58077 Effective search space used: 58077 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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