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) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3024 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:
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