Align phosphate acetyltransferase (EC 2.3.1.8) (characterized)
to candidate 351497 BT1969 NADP-dependent malate dehydrogenase (NCBI ptt file)
Query= BRENDA::O52593 (332 letters) >FitnessBrowser__Btheta:351497 Length = 763 Score = 163 bits (413), Expect = 1e-44 Identities = 110/333 (33%), Positives = 178/333 (53%), Gaps = 14/333 (4%) Query: 6 QIIERAKSDVKTIVLPESTDLRVIKAASMIMKKGIAKVVLIGNEKEIKSLAGDIDL--EG 63 Q+ + A+ + + +V E ++KAA +GI +L+GN++ I LA ++DL EG Sbjct: 432 QLYDTARRNPQRVVFAEGIHPNMLKAAVEAKAEGICHPILLGNDEAIGKLAEELDLSLEG 491 Query: 64 VMIEDSLN---SEKLEDYANTLYELRKSKGMTIEAARETIKDPLYYGVMMVKKGEADGMV 120 + I + + SE+ E Y+ L E R +G T E A + + + Y+G+MMV+ G+AD + Sbjct: 492 IEIVNLRHPDESERRERYSRILAEKRAREGFTYEEANDKMFERNYFGMMMVETGDADAFI 551 Query: 121 AGAVNSTANTLRPALQILKTAPGTKLVSSFFVMVVPNCEYGHNGTFVYADCGLVENPDAD 180 G +NT++ A +++ PG + F M + N + GT+ AD + +PD + Sbjct: 552 TGLYTRYSNTIKVAKEVIGIQPG---FNHFGTMHILNSK---KGTYFLADTLINRHPDTE 605 Query: 181 QLSEIAISASKSFEMLVGAKPQVAMLSYSSYGSAKSELTEKVIKATQLAKEKAPHLAIDG 240 L +IA A K+ P ++MLSYS++G+ S KV A +++ P LAIDG Sbjct: 606 TLIDIAKLADKTVRFF-NHTPVISMLSYSNFGADTSGSPVKVHGAVNYMQKEYPELAIDG 664 Query: 241 ELQVDAAIVPEVAKSKAKGSSVAGK-ANVLIFPDLDAGNIAYKLTQRL-AKAEAYGPITQ 298 E+QV+ A+ E+ +K + + GK N LIFP+L + N YKL Q + E GPI Sbjct: 665 EMQVNFAMNRELRDAKYPFTRLKGKDVNTLIFPNLSSANAGYKLLQAMDPDTEFIGPIQM 724 Query: 299 GLARPVNDLSRGCSAEDIVGVAAITAVQAQYVK 331 GL +P++ S DIV + A+ + A VK Sbjct: 725 GLNKPIHFTDFESSVRDIVNITAVAVIDAIVVK 757 Lambda K H 0.313 0.129 0.346 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: 485 Number of extensions: 21 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: 332 Length of database: 763 Length adjustment: 34 Effective length of query: 298 Effective length of database: 729 Effective search space: 217242 Effective search space used: 217242 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 52 (24.6 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