Align neutral invertase (InvA; sll0626) (EC 3.2.1.26) (characterized)
to candidate Synpcc7942_0397 Synpcc7942_0397 putative neutral invertase
Query= CAZy::CAD33848.1 (489 letters) >FitnessBrowser__SynE:Synpcc7942_0397 Length = 463 Score = 402 bits (1034), Expect = e-116 Identities = 201/458 (43%), Positives = 284/458 (62%), Gaps = 25/458 (5%) Query: 7 QQILDQARRLLYEKAMVKINGQYVGTVAAIPQSDH-HDLNYTEVFIRDNVPVMIFLLLQN 65 Q L A +LL+++A+V+ + Q+ G +AA+P+ NY E+FIRDNVPVM++LLLQ Sbjct: 12 QTALQTAEQLLWDRALVRYHDQWAGAIAALPEDQELAAANYREIFIRDNVPVMLYLLLQG 71 Query: 66 ETEIVQNFLEICLTLQSKGFPTYGIFPTSFVETENHELKADYGQRAIGRVCSVDASLWWP 125 +T++V++FL++ L+LQS+ TYGI PTSFV E H + ADYGQRAIGRV S D SLWWP Sbjct: 72 KTDVVRDFLQLSLSLQSQALQTYGILPTSFVCEETHCV-ADYGQRAIGRVVSADPSLWWP 130 Query: 126 ILAYYYVQRTGNEAWARQTHVQLGLQKFLNLILHPVFRDAPTLFVPDGAFMIDRPMDVWG 185 +L Y + + ++A+ VQ GLQ+ L +L PVF P L VPDGAFM+DRP+DV G Sbjct: 131 VLLQAYRRASHDDAFVHSPTVQQGLQRLLAFLLRPVFNQNPLLEVPDGAFMVDRPLDVAG 190 Query: 186 APLEIQTLLYGALKSAAGLLLIDLKAKGYCSNKDHPFDSFTMEQSHQFNLSVDWLKKLRT 245 APLEIQ LLYGAL++ LL + + N + ++LR Sbjct: 191 APLEIQVLLYGALRACGQLL----------------------QYTEAANAAHVQARRLRQ 228 Query: 246 YLLKHYWINCNIVQALRRRPTEQYGEEASNEHNVHTETIPNWLQDWLGDRGGYLIGNIRT 305 YL HYW+ + ++ ++ PTE++G+ + N +N+ IP+W++ WLG+ GGY +GNIR Sbjct: 229 YLCWHYWVTPDRLRRWQQWPTEEFGDRSHNPYNIQPIAIPDWVEPWLGESGGYFLGNIRA 288 Query: 306 GRPDFRFFSLGNCLGAIFDVTSLAQQRSFFRLVLNNQRELCAQMPLRICHPPLKDDDWRS 365 GRPDFRFFSLGN L +FDV L QQ + RL+L N+ ++ Q+PLR+C+P L W+ Sbjct: 289 GRPDFRFFSLGNLLAIVFDVLPLNQQGAILRLILQNEAQILGQVPLRLCYPALTGSAWKI 348 Query: 366 KTGFDRKNLPWCYHNAGHWPCLFWFLVVAVLRHSCHSNYGTVEYAEMGNLIRNNYEVLLR 425 TG D KN PW YHN G WP L W+L AVL + + + N +++ + Sbjct: 349 LTGCDPKNQPWSYHNGGSWPSLLWYLSAAVLHYQQRGGDRNLCQVWL-NKLQHYHTQQCE 407 Query: 426 RLPKHKWAEYFDGPTGFWVGQQSRSYQTWTIVGLLLVH 463 +LP +W EY++G + ++ YQTWT GLLL H Sbjct: 408 QLPGDEWPEYYEGQDSVQIATRACRYQTWTFTGLLLNH 445 Lambda K H 0.324 0.139 0.455 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: 736 Number of extensions: 37 Number of successful extensions: 5 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: 489 Length of database: 463 Length adjustment: 33 Effective length of query: 456 Effective length of database: 430 Effective search space: 196080 Effective search space used: 196080 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 51 (24.3 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