Align phosphate acetyltransferase (EC 2.3.1.8) (characterized)
to candidate HSERO_RS05745 HSERO_RS05745 NADP-dependent malic enzyme oxidoreductase
Query= BRENDA::P41790 (338 letters) >FitnessBrowser__HerbieS:HSERO_RS05745 Length = 758 Score = 142 bits (358), Expect = 3e-38 Identities = 112/336 (33%), Positives = 175/336 (52%), Gaps = 20/336 (5%) Query: 1 MIIERARELAVRAPARVVFPDALDERVLKAAHYLQQYGLARPVLVASPFA----LRQFAL 56 M ++ A AP RVV+ D DERVL+A ++ GLA P+LV +P A +++ L Sbjct: 435 MFMQPVFNTAKVAPQRVVYADGQDERVLRAVQFVADEGLAAPILVGAPAAIEAGIKKAGL 494 Query: 57 SHRMAMDGIQVIDPHSNLSMRQRFAQRWLARAGEKTPPDAVEKLSDPLMFAAAMVSAGEA 116 ++ + +QVIDP ++ + Q AQ K +A + S L+ AA MV AG+A Sbjct: 495 RIKIGQN-VQVIDPATDARVAQYAAQ-------YKDGGEADVRASGSLL-AALMVKAGDA 545 Query: 117 DVCIAGNLSSTANVLRAGLRVIGLQPGCKTLSSI-FLMLPQYAGPALGFADCSVVPQPTA 175 D + G + L +VIGL+ G + +++ ++LP L D V P A Sbjct: 546 DAMLCGLDGNYDGHLAHVEKVIGLKQGAQEFAALNAVLLPD---QTLFITDTYVNDTPDA 602 Query: 176 AQLADIALASADTWRAITGEEPRVAMLSFSSNGSARHPNVANVQQATELVRERAPQLLVD 235 QLA IA A+A+ A G P+VA LS S+ GS+ P+ + A E ++ AP++ Sbjct: 603 EQLARIAQAAAEE-VARFGVPPKVAFLSHSNRGSSSRPSARKMAAAHEAFKKLAPEVESA 661 Query: 236 GELQFDAAFVPEVAAQKA-PDSPLQGRANVMIFPSLEAGNIGYKITQRLGGY-RAVGPLI 293 GEL DAA ++ DS L G ANV++ P+L+A NI + + + G +GP++ Sbjct: 662 GELHGDAALSEKIRNNAGLADSGLTGAANVLVCPNLDAANILFNVLKTSSGQGTTIGPIL 721 Query: 294 QGLAAPLHDLSRGCSVQEIIELALVAAVPRQADVSR 329 G AAP+H L+ +V+ +I + +AA Q S+ Sbjct: 722 LGAAAPVHVLTPSSTVRRVINMTALAAAKAQDGKSK 757 Lambda K H 0.321 0.134 0.384 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: 525 Number of extensions: 30 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: 338 Length of database: 758 Length adjustment: 34 Effective length of query: 304 Effective length of database: 724 Effective search space: 220096 Effective search space used: 220096 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: 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