Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate GFF1165 PS417_05920 gamma-aminobutyraldehyde dehydrogenase
Query= BRENDA::Q88RC0 (480 letters) >FitnessBrowser__WCS417:GFF1165 Length = 474 Score = 323 bits (828), Expect = 8e-93 Identities = 181/466 (38%), Positives = 270/466 (57%), Gaps = 6/466 (1%) Query: 15 INGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTAKERSA 74 ING+ ++ + G V NPA G V+ + + A+ A+ AAD A +W K+RS Sbjct: 7 INGQLVEGE-GPAQAVFNPALGRVLVEINEASEAQVDAAVRAADAAFESWSQTAPKDRSL 65 Query: 75 KLRRWFELMIENQDDLARLMTTEQGKPLAEA-KGEIAYAASFIEWFAEEAKRIYGDTIPG 133 L + +++ + ++LA+L + GKP + A EI A +FA ++ + G Sbjct: 66 LLLKLADVIEAHGEELAQLESDNCGKPYSAALNDEIPAIADVFRFFAGASRCMSGSAGGE 125 Query: 134 HQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPYSALALV 193 + P ++ + P+GV A+I PWN+P M+ K PALAAG T+VLKP+ QTP +AL +V Sbjct: 126 YLPGHTSMIRRDPVGVIASIAPWNYPLMMVAWKIAPALAAGNTVVLKPSEQTPLTALRMV 185 Query: 194 ELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQLMEECAKDIKKVS 253 ELA PAGVL++V G VG L + VR +S TGS G ++ A +K++ Sbjct: 186 ELAADL-FPAGVLNLVFGRGPTVGSPLVNHPKVRMVSLTGSIATGANIISSTADSVKRMH 244 Query: 254 LELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYDAFAEKLAAAV 313 +ELGG AP I+F DAD+D AVEG + N GQ C A RIY Q +Y+ F EKL AAV Sbjct: 245 MELGGKAPVIIFSDADIDAAVEGIRTFGFYNAGQDCTAACRIYAQAEIYEQFVEKLGAAV 304 Query: 314 AKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKG-AKVLSGGKLIEGN--FFEPTI 370 A +K G + T GPLI + +V +E AV++ ++++GGK +EGN FFEPT+ Sbjct: 305 ASIKYGLQDDPATELGPLITAQHRDRVAGFVERAVAQSHIRLVTGGKAVEGNGFFFEPTV 364 Query: 371 LVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDMSRVFRVAEA 430 L D + + + E FGP+ + RF DEA+V+ +ND+++GLAS + D+ R R+A Sbjct: 365 LADAQQDDEIVRREVFGPVVSVTRFTDEAQVLGWANDSDYGLASSVWTADVGRAHRLAAR 424 Query: 431 LEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYL 476 L+YG +NT + P GG K SG G++ S YG+EDY ++++ Sbjct: 425 LQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSMYGLEDYTSVRHV 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: 554 Number of extensions: 20 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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