Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate Pf1N1B4_3024 4-aminobutyraldehyde dehydrogenase (EC 1.2.1.19)
Query= BRENDA::Q83XU8 (485 letters) >lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3024 4-aminobutyraldehyde dehydrogenase (EC 1.2.1.19) Length = 474 Score = 303 bits (775), Expect = 1e-86 Identities = 170/463 (36%), Positives = 263/463 (56%), Gaps = 14/463 (3%) Query: 24 SPLNNAVIAKVHEAGRAEVDAAVAAAQAALKGAWGRMSLAQRVEVLYAVADGINRRFDDF 83 +P V+ +++EA A+VDAAV AA A + AW + + +R +L +AD I ++ Sbjct: 23 NPALGRVLVEINEASEAQVDAAVRAADNAFQ-AWSQTTPKERSLLLLKLADIIEAHGEEL 81 Query: 84 LAAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTPDGVGAINYAVRRP 143 E ++ GKP S A + +IP A F+ FA + + P I R P Sbjct: 82 AKLESDNCGKPYSAALNDEIPAIADVFRFFAGANRCMSGALGGEYLPGHTSMIR---RDP 138 Query: 144 VGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPPGVY 203 VGV+ I PWN PL+++ WK+ PALA GNTVV+KPSE+TP TA L E+ + P GV Sbjct: 139 VGVIASIAPWNYPLMMVAWKIAPALAAGNTVVLKPSEQTPLTALRLAELASDI-FPAGVL 197 Query: 204 NVVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADGARPVSLELGGKNAAIVF 263 N+V+G G ++ G L +HP V ++ TG TG I+ + A + + +ELGGK I+F Sbjct: 198 NLVYGRG-SAVGTALVNHPKVRMVSLTGSIATGSNIISSTAGNVKRLHMELGGKAPVIIF 256 Query: 264 ADCDLDKAIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLKKGAEGMQLGRPEDLA 323 D D+D A+EG F N GQ C R+Y + I+D+FV +L ++ G +D + Sbjct: 257 DDADIDAAVEGIRTFGFYNAGQDCTAACRIYAQAGIYDQFVEKLGAAVSSIKYGLQDDPS 316 Query: 324 TGMGPLISQEHREKVLSYYKKAV-EAGATVVTGGGVPEMPEALKG-GAWVQPTIWTGLGD 381 T +GPLIS +HR++V + ++A+ + ++TGG +A++G G + +PT+ + Sbjct: 317 TELGPLISAQHRDRVTALVERAMAQPHIRLITGG------KAVEGNGFFFEPTVLADVQQ 370 Query: 382 DSVVAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVAGAIEVGIA 441 D + R E+FGP V F E + + AND+DYGLA +WTT++ RAHR++ ++ G Sbjct: 371 DDEIVRREVFGPVVSVTRFTDEAQALAWANDSDYGLASSVWTTDVGRAHRLSARLQYGCT 430 Query: 442 WVNSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNVCIK 484 WVN+ F+ GG K SG G++ ++ LE YT +++V K Sbjct: 431 WVNTHFMLVSEMPHGGQKLSGYGKDMSMYGLEDYTVVRHVMFK 473 Lambda K H 0.318 0.135 0.406 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: 496 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: 485 Length of database: 474 Length adjustment: 34 Effective length of query: 451 Effective length of database: 440 Effective search space: 198440 Effective search space used: 198440 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 (21.7 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