Align N-carbamoylputrescine amidase; EC 3.5.1.53 (characterized)
to candidate AO353_15200 AO353_15200 hydratase
Query= SwissProt::Q9XGI9 (300 letters) >FitnessBrowser__pseudo3_N2E3:AO353_15200 Length = 295 Score = 110 bits (275), Expect = 4e-29 Identities = 94/304 (30%), Positives = 147/304 (48%), Gaps = 32/304 (10%) Query: 1 MAEKNRLVTVAALQF---ACTDDVSTNVATAERLVRAAHQKGANIILIQELFE-GYYFCQ 56 M+E V VA +QF ++ N+ + L A GAN+I++ EL GY+F Sbjct: 1 MSESTSPVRVAVVQFDPQVGIENREGNLHHSLELALQAVNGGANLIVMPELTNTGYFF-- 58 Query: 57 AQKEEFFHRAKPYPGHPTIVRMQNLAKELGVVIPVSFFEEANNAHYNSVAIIDADGTDLG 116 + +++ F ++ PG P+ + A + V + E +N+ ++ DG +G Sbjct: 59 SNRQDAFDHSEAVPGGPSTQSWVDFACKHKVYLVAGLTERDGMRLFNTGILVGPDGF-IG 117 Query: 117 LYRKSHIPDGPGYQEKYYFNPGDTGFKVFQTKYAKIGVAICWDQWFPEAARAMALQGAEV 176 YRK+H+ + EK +F PGD GF VF T +IG+ ICWD WFPE R ++ QGA++ Sbjct: 118 KYRKAHLWN----LEKLWFTPGDLGFPVFDTPIGRIGLLICWDIWFPEVPRILSQQGADI 173 Query: 177 L-FYPTAIGSEPQ--DDGLDSRDHWRRVMQGHAGANVVPLVASNRIGKEIIETEHGNSEI 233 + + + P DD + + H N V + A++RIG+E Sbjct: 174 ICSLNNWVWTPPPLFDDAGKCMASYLTMTAAH--VNNVFIAAASRIGEE--------RGA 223 Query: 234 TFYGYSFIAGPTGELV--AAAGDKEEAVLVAQFDLDKIKSKRHGWG----VYRDRRPDLY 287 + G S IAG G + A+ DK+E +L A DL +S W ++RDRR DLY Sbjct: 224 RYLGCSLIAGTNGWPIGAVASADKQE-ILFADIDLTSSRSAPI-WNNLNDLHRDRRADLY 281 Query: 288 KVLL 291 +L Sbjct: 282 DQML 285 Lambda K H 0.319 0.137 0.414 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: 258 Number of extensions: 20 Number of successful extensions: 3 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: 300 Length of database: 295 Length adjustment: 26 Effective length of query: 274 Effective length of database: 269 Effective search space: 73706 Effective search space used: 73706 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: 48 (23.1 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