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) >FitnessBrowser__azobra:AZOBR_RS30770 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:
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