Align electron transfer component of the anthranilate 1,2-dioxygenase system (EC 1.14.12.1) (characterized)
to candidate PP_3163 PP_3163 benzoate 1,2-dioxygenase electron transfer component
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2738 (343 letters) >FitnessBrowser__Putida:PP_3163 Length = 336 Score = 274 bits (700), Expect = 3e-78 Identities = 148/337 (43%), Positives = 203/337 (60%), Gaps = 6/337 (1%) Query: 1 MNHKVAFSFADGKTSFFEVKPNELLLDAALRNGVNIPLDCREGVCGTCQGRCESGRYTQ- 59 M++++A +F DG T F E E + DAA R G+NIPLDCR+G CGTC+ + ESGRY Sbjct: 1 MSYQIALNFEDGVTRFIEATGQETVADAAYRQGMNIPLDCRDGACGTCKCKAESGRYDLG 60 Query: 60 DYVDDEALSEQDLAQRKMLSCQTRVQSDASFYFDFDSSLCNAGATQLLQAVITGVEQVSA 119 D ++ALSE ++A+ +L+CQ R +SD S LC +A I+ V Q+S Sbjct: 61 DNFIEDALSEDEIAEGYVLTCQMRAESDCVIRIPASSQLCKTEQATF-EAAISDVRQLSV 119 Query: 120 TTAILHLDACSHPRQLDFLPGQYARLHVPGTDEWRSYSFANRPNPDNQLQFLIRLLPDGV 179 +T L + + R L FLPGQY L VPG+++ R+YSF++ D ++ FLIR +P G+ Sbjct: 120 STIALSIKGEALSR-LAFLPGQYVNLKVPGSEQSRAYSFSSLQK-DGEVSFLIRNVPGGL 177 Query: 180 MSNFIREHCRPGEVLEFEAPLGSFYLRQVSKPLVLVAGGTGLSAFLGMLDTIAEQGGCGH 239 MS+F+ + G+ L PLGSFYLR + +PL+L+AGGTGL+ F ML+ IAEQG H Sbjct: 178 MSSFLTNLAKAGDSLSLAGPLGSFYLRPIQRPLLLLAGGTGLAPFTAMLEKIAEQGS-EH 236 Query: 240 PIQLFYGVTQDNDLCETQRLADYRDKIANFDYHLVVSKPSEHWKGKTGWIPDHFDRQSFE 299 P+ L YGVT D DL E RL +I NF Y V+ P + K G++ H + + Sbjct: 237 PLHLIYGVTNDFDLVELDRLQALAARIPNFTYSACVANPDSQYPQK-GYVTQHIEPRHLN 295 Query: 300 ANPFDIYLCGPPPMVEAVKTWFSDQKIERFQMYYEKF 336 D+YLCGPPPMVEAV + +Q I YYEKF Sbjct: 296 DGDVDVYLCGPPPMVEAVSQYVREQGITPANFYYEKF 332 Lambda K H 0.322 0.138 0.431 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: 354 Number of extensions: 17 Number of successful extensions: 6 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: 343 Length of database: 336 Length adjustment: 28 Effective length of query: 315 Effective length of database: 308 Effective search space: 97020 Effective search space used: 97020 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: 49 (23.5 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