Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate WP_057507768.1 ABB28_RS05980 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::Q5P171 (474 letters) >NCBI__GCF_001431535.1:WP_057507768.1 Length = 454 Score = 236 bits (603), Expect = 9e-67 Identities = 150/458 (32%), Positives = 226/458 (49%), Gaps = 10/458 (2%) Query: 18 TFDVVNPATGEVFARVQAGDASHVDQAVAAARAAFPGWSRTPDAERKRLMHALGAALEAH 77 T ++VNP TG V R + D + ++Q + AA AFP WS T ER ++ A+GA L Sbjct: 2 TVEIVNPTTGRVDYRHELLDKAGIEQRLQAAAGAFPAWSATSLQERAAVLRAIGAQLRER 61 Query: 78 MPELMELVTKEAGKPLGGLNGVGSGMEVGGAIAWTHVTADLE---LPVEVIQDNDDARIE 134 ++ +T+E GK V + EV A AD L ++I D + R Sbjct: 62 KDDIQGAMTREMGKLK-----VEALAEVEKCAAACEYYADHAADYLKPQLI-DTEAQRSY 115 Query: 135 VHRKPLGVVGSITPWNWPLMIAIWHVIPALRAGNTVVIKPSGMTPTATIRFVELANAI-L 193 V +P+G V ++ PWN+P+ + PA AGN ++K + P E+ A L Sbjct: 116 VRYEPIGCVFAVMPWNFPIWQVFRFLAPAFMAGNVALLKHASNVPQCADLINEVVRAGGL 175 Query: 194 PPGVLNIVTGESGVGSAIAKHPDINKIVFTGSTPTGKNIMQNAAGNLKRLTLELGGNDAG 253 P GV +++ ++ + + + + + TGS G++I NA LK+ +ELGG+DA Sbjct: 176 PDGVFDVLHIDNDQAADVLRDRRVKAVTLTGSERAGRSIAANAGDQLKKCVMELGGSDAF 235 Query: 254 IVLPDVDPKAIAPKLFGVGFHNNGQTCACLKRLYVHDSIYEKVCAELARIAKETVVGDGL 313 +VL D D F N+GQTC KR V +++ + A E GD Sbjct: 236 VVLDDADLDKAIDAAVKSRFDNSGQTCIAAKRFIVVEAVADAFTERFVAAAGERRYGDPA 295 Query: 314 VEGTELGPVQNKAQLDFVQELVEDARAHGARILSGGKARSGGGFFFEPTVIADAKDGMRV 373 T L P+ D + + V+ + A GAR+L+GG+ G + TV+ GM Sbjct: 296 DARTTLAPMARADLRDELHKQVQASVAKGARVLAGGEPVDGSHAGYPATVLDQVGPGMPA 355 Query: 374 VDEEQFGPVLPVIRYSDIEEVIARANNNENGLGGSIWSKDHAKAAELALRLECGTAWVNE 433 DEE FGPV VIR D E + AN+ GLGGS+W+ D A+ A ++ECG A+VN Sbjct: 356 YDEELFGPVAAVIRVKDEAEALKVANDTRFGLGGSVWTTDAARGEAFAQQMECGAAFVNS 415 Query: 434 HGAVQPDAPFGGVKQSGLGVEFGRYGLEEYTSIQTLKI 471 PFGG K+SG G E +G+ E+ +I+T+ + Sbjct: 416 IVKSDVRLPFGGSKESGFGRELAEHGIHEFMNIKTIYV 453 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: 519 Number of extensions: 25 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: 454 Length adjustment: 33 Effective length of query: 441 Effective length of database: 421 Effective search space: 185661 Effective search space used: 185661 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 Apr 09 2024. 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