Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate BPHYT_RS34305 BPHYT_RS34305 succinate-semialdehyde dehydrogenase
Query= BRENDA::Q5P171 (474 letters) >FitnessBrowser__BFirm:BPHYT_RS34305 Length = 479 Score = 319 bits (818), Expect = 1e-91 Identities = 192/465 (41%), Positives = 256/465 (55%), Gaps = 10/465 (2%) Query: 8 INGKPVRAGSTFDVVNPATGEVFARVQAGDASHVDQAVAAARAAFPGWSRTPDAERKRLM 67 I G+ T+ V+NPATGEV A V G A+ QA+AAA AFP W ER + Sbjct: 11 IGGEWYEGADTYAVLNPATGEVVAHVAKGGAAETAQAIAAAERAFPAWRALTAKERSARV 70 Query: 68 HALGAALEAHMPELMELVTKEAGKPLGGLNGVGSGMEVGGAIA---WTHVTADLELPVEV 124 G + + L EL+T E GKPL G EVG A + W A + Sbjct: 71 KRWGELMLENRDALAELLTLEQGKPLAEARG-----EVGYAASFFEWFAEEAKRAYGDVI 125 Query: 125 IQDNDDARIEVHRKPLGVVGSITPWNWPLMIAIWHVIPALRAGNTVVIKPSGMTPTATIR 184 N +A+I V R+P+GVV +ITPWN+PL + PAL AG T+V+KPS TP + Sbjct: 126 PSPNPNAKIIVTREPVGVVAAITPWNFPLAMITRKAGPALAAGCTMVLKPSEETPLSAFA 185 Query: 185 FVELA-NAILPPGVLNIVTGES-GVGSAIAKHPDINKIVFTGSTPTGKNIMQNAAGNLKR 242 LA A +PPGV NIV+G++ +G A+ + + K+ FTGST GK + + +A LK+ Sbjct: 186 LAVLAAKAGIPPGVFNIVSGDAVAIGGALTESDVVRKLSFTGSTRVGKLLAKQSADTLKK 245 Query: 243 LTLELGGNDAGIVLPDVDPKAIAPKLFGVGFHNNGQTCACLKRLYVHDSIYEKVCAELAR 302 L+LELGGN IV D D A F N GQTC C+ R YV D IY+ + L + Sbjct: 246 LSLELGGNAPFIVFDDADLDAAVQGAMASKFRNTGQTCVCVNRFYVQDGIYDAFTSALTQ 305 Query: 303 IAKETVVGDGLVEGTELGPVQNKAQLDFVQELVEDARAHGARILSGGKARSGGGFFFEPT 362 ++ VG+ L E GP+ N+A L V+ V DA GA+IL+GGK + GG F+EPT Sbjct: 306 AVRKMRVGNALQGEVEQGPLINQAALKKVETHVADALQKGAKILTGGKPHTLGGTFYEPT 365 Query: 363 VIADAKDGMRVVDEEQFGPVLPVIRYSDIEEVIARANNNENGLGGSIWSKDHAKAAELAL 422 V+ADA + M + EE FGPV R+ E I AN+ GL +++D A+A + Sbjct: 366 VLADADNSMLIAGEETFGPVAACFRFKTEAEAIEAANDTPFGLSAYFYTRDLARAWRVGE 425 Query: 423 RLECGTAWVNEHGAVQPDAPFGGVKQSGLGVEFGRYGLEEYTSIQ 467 LE G +NE APFGGVKQSGLG E +YGL+EYT ++ Sbjct: 426 ALESGMVGINEGIVSTEVAPFGGVKQSGLGREGSKYGLDEYTELK 470 Lambda K H 0.317 0.136 0.405 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: 593 Number of extensions: 25 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: 474 Length of database: 479 Length adjustment: 33 Effective length of query: 441 Effective length of database: 446 Effective search space: 196686 Effective search space used: 196686 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (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