Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate GFF1133 HP15_1111 betaine aldehyde dehydrogenase
Query= BRENDA::Q83XU8 (485 letters) >FitnessBrowser__Marino:GFF1133 Length = 493 Score = 728 bits (1879), Expect = 0.0 Identities = 347/462 (75%), Positives = 389/462 (84%) Query: 24 SPLNNAVIAKVHEAGRAEVDAAVAAAQAALKGAWGRMSLAQRVEVLYAVADGINRRFDDF 83 +P N +I+KVHEAGR EVDAAV AA+AAL+G WG+M+L +R +L+ VADGIN RFD+F Sbjct: 32 NPANGKIISKVHEAGREEVDAAVKAARAALRGPWGKMTLDERTSILHKVADGINARFDEF 91 Query: 84 LAAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTPDGVGAINYAVRRP 143 L E DTGKP S+A H+DIPRGAANFK+FAD++KNVPTE FEMPTPDG GA+NYAVRRP Sbjct: 92 LEGECLDTGKPKSMASHIDIPRGAANFKVFADMIKNVPTESFEMPTPDGTGALNYAVRRP 151 Query: 144 VGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPPGVY 203 GV+GVI PWNLPLLLMTWKVGPALACGNTVVVKPSEETP T LLGEVM AGVP GV+ Sbjct: 152 KGVIGVISPWNLPLLLMTWKVGPALACGNTVVVKPSEETPTTTTLLGEVMKEAGVPDGVF 211 Query: 204 NVVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADGARPVSLELGGKNAAIVF 263 NVVHGFG +S G FLT HP V+ ITFTGE GTGE IMKAAA G R +SLELGGKNA +VF Sbjct: 212 NVVHGFGGDSAGAFLTEHPQVDGITFTGEIGTGEVIMKAAAKGIRDISLELGGKNAGVVF 271 Query: 264 ADCDLDKAIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLKKGAEGMQLGRPEDLA 323 ADCD+DKAIEGT+RS FANCGQVCLGTERVYVER IFD FV RLK+ AEGM++G P+D Sbjct: 272 ADCDIDKAIEGTMRSAFANCGQVCLGTERVYVERSIFDEFVGRLKEAAEGMKIGPPDDAE 331 Query: 324 TGMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKGGAWVQPTIWTGLGDDS 383 MGPL+S HREKVLSYY+KAV+ GATVVTGGGVPEMPEAL GGAWVQPTIWTGL +DS Sbjct: 332 ADMGPLVSLNHREKVLSYYQKAVDDGATVVTGGGVPEMPEALAGGAWVQPTIWTGLPEDS 391 Query: 384 VVAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVAGAIEVGIAWV 443 V +EIFGPC + PFD+EEE I AN YGLA IW+ N++RAHRVAG IE GI WV Sbjct: 392 AVITDEIFGPCCHIRPFDTEEEAIELANSLPYGLASAIWSENITRAHRVAGQIEAGIIWV 451 Query: 444 NSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNVCIKL 485 NSWFLRDLRT FGGSKQSGIGREGGVHSLEFYTE+KN+C+KL Sbjct: 452 NSWFLRDLRTPFGGSKQSGIGREGGVHSLEFYTEMKNICVKL 493 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: 753 Number of extensions: 16 Number of successful extensions: 1 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: 493 Length adjustment: 34 Effective length of query: 451 Effective length of database: 459 Effective search space: 207009 Effective search space used: 207009 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: 52 (24.6 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