Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate WP_090274723.1 BLU11_RS14925 NADP-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::Q5P171 (474 letters) >NCBI__GCF_900105005.1:WP_090274723.1 Length = 486 Score = 286 bits (732), Expect = 1e-81 Identities = 170/462 (36%), Positives = 249/462 (53%), Gaps = 13/462 (2%) Query: 16 GSTFDVVNPATGEVFARVQAGDASHVDQAVAAARAAFPGWSRTPDAERKRLMHALGAALE 75 G ++VNPA+GE V A +A+AAA+AA P W R ER ++ + Sbjct: 25 GQRVEIVNPASGERLGSVPDMGADETRRAIAAAQAAQPVWRRRTAKERAGVLRRWYELIL 84 Query: 76 AHMPELMELVTKEAGKPLGGLNGVGSGMEVGGAIAWTHVTADLELPV--EVIQDND-DAR 132 H +L ++T E GKPL G E+ A ++ A+ V +VI + D R Sbjct: 85 QHQEDLARIMTAEQGKPLTEARG-----EIAYAASFIEWFAEEAKRVYGDVIPGHQTDKR 139 Query: 133 IEVHRKPLGVVGSITPWNWPLMIAIWHVIPALRAGNTVVIKPSGMTPTATIRFVELAN-A 191 + V ++P+GV +ITPWN+P + PAL AG +V+KP+ TP + + V LA A Sbjct: 140 LIVQKEPVGVTAAITPWNFPSAMITRKAGPALAAGCAMVLKPAPQTPFSALALVALAEQA 199 Query: 192 ILPPGVLNIVTG----ESGVGSAIAKHPDINKIVFTGSTPTGKNIMQNAAGNLKRLTLEL 247 LP G+L++VT VG + +P + K+ FTGST G +MQ A +LK+L+LEL Sbjct: 200 GLPAGLLSVVTAGVDNARAVGGELCANPVVRKLSFTGSTAVGIQLMQQCAPSLKKLSLEL 259 Query: 248 GGNDAGIVLPDVDPKAIAPKLFGVGFHNNGQTCACLKRLYVHDSIYEKVCAELARIAKET 307 GGN IV D D + + N GQTC C R+YV D++Y+ +LA + Sbjct: 260 GGNAPFIVFEDADLDEAVEGVMISKYRNAGQTCVCANRIYVQDAVYDAFAEKLAAAVRRL 319 Query: 308 VVGDGLVEGTELGPVQNKAQLDFVQELVEDARAHGARILSGGKARSGGGFFFEPTVIADA 367 VGDG+ EG GP+ N + +Q ++DA GA +L+GGK + GG FFEPT++ Sbjct: 320 EVGDGMREGVTTGPLINAEAVSKIQRHLQDALDGGATLLAGGKPHALGGLFFEPTILTGV 379 Query: 368 KDGMRVVDEEQFGPVLPVIRYSDIEEVIARANNNENGLGGSIWSKDHAKAAELALRLECG 427 M + EE FGPV P+ R+ D +V+ +AN+ E GL +++D ++ +A LE G Sbjct: 380 DSSMLIAREETFGPVAPLFRFDDEADVVRQANDTEFGLAAYFYARDLSRVFRVAEALEYG 439 Query: 428 TAWVNEHGAVQPDAPFGGVKQSGLGVEFGRYGLEEYTSIQTL 469 +N APFGG+K SGLG E +YG++EY I+ L Sbjct: 440 MVGINTGLISTEVAPFGGMKASGLGREGSKYGMDEYLEIKYL 481 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: 597 Number of extensions: 31 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: 474 Length of database: 486 Length adjustment: 34 Effective length of query: 440 Effective length of database: 452 Effective search space: 198880 Effective search space used: 198880 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 24 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