Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate Pf6N2E2_3131 4-aminobutyraldehyde dehydrogenase (EC 1.2.1.19)
Query= BRENDA::Q88RC0 (480 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3131 Length = 474 Score = 321 bits (822), Expect = 4e-92 Identities = 178/466 (38%), Positives = 269/466 (57%), Gaps = 6/466 (1%) Query: 15 INGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTAKERSA 74 ING ++ + G V NP+ G V+ + + A+ A+ +AD A AW + K+RS Sbjct: 7 INGHLVNGE-GPGQAVFNPSLGRVLVEINEASEAQVDAAVRSADAAFEAWSQVPPKDRSL 65 Query: 75 KLRRWFELMIENQDDLARLMTTEQGKPLAEA-KGEIAYAASFIEWFAEEAKRIYGDTIPG 133 L + + + + ++LA+L + GKPL+ A EI A +FA ++ + G Sbjct: 66 LLLKLADAIEAHGEELAKLESDNCGKPLSAALNDEIPAIADVFRFFAGASRCMSGSAGGE 125 Query: 134 HQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPYSALALV 193 + P ++ + P+GV A+I PWN+P M+ K PALAAG T+VLKP+ QTP +AL L Sbjct: 126 YLPGHTSMIRRDPVGVIASIAPWNYPLMMVAWKIAPALAAGNTVVLKPSEQTPLTALRLA 185 Query: 194 ELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQLMEECAKDIKKVS 253 ELA PAGVL+V+ G VG L + VR +S TGS G ++ + +K++ Sbjct: 186 ELASEI-FPAGVLNVIFGRGQTVGNPLVTHPKVRMVSLTGSIATGSNIISSTSDSVKRMH 244 Query: 254 LELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYDAFAEKLAAAV 313 +ELGG AP I+FDDAD+D AVEG + N GQ C A RIY Q G+Y+ F EKL AAV Sbjct: 245 MELGGKAPVIIFDDADIDAAVEGIRTFGFYNAGQDCTAACRIYAQQGIYEQFVEKLGAAV 304 Query: 314 AKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSK-GAKVLSGGKLIEGN--FFEPTI 370 +K G T GPLI + +V +E A+++ ++++GGK ++GN FFEPT+ Sbjct: 305 GSIKYGLQTAPDTEMGPLITAQHRDRVAAFVERAIAQPHIRLITGGKAVDGNGFFFEPTV 364 Query: 371 LVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDMSRVFRVAEA 430 L D + + + E FGP+ + F DEA+V+A +ND+++GLAS + D+ R R++ Sbjct: 365 LADAQQDDEIVRREVFGPVVSVTSFLDEAQVLAWANDSDYGLASSVWTADIGRAHRLSAR 424 Query: 431 LEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYL 476 L+YG +NT + P GG K SG G++ S YG+EDY ++++ Sbjct: 425 LQYGCTWVNTHFMLVSEMPHGGQKRSGYGKDMSMYGLEDYTVVRHV 470 Lambda K H 0.317 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: 553 Number of extensions: 18 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: 480 Length of database: 474 Length adjustment: 33 Effective length of query: 447 Effective length of database: 441 Effective search space: 197127 Effective search space used: 197127 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