Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate GFF2918 PGA1_c29650 succinate-semialdehyde dehdyrogenase GabD
Query= BRENDA::Q83XU8 (485 letters) >FitnessBrowser__Phaeo:GFF2918 Length = 491 Score = 295 bits (754), Expect = 3e-84 Identities = 171/462 (37%), Positives = 254/462 (54%), Gaps = 10/462 (2%) Query: 24 SPLNNAVIAKVHEAGRAEVDAAVAAAQAALKGAWGRMSLAQRVEVLYAVADGINRRFDDF 83 +P VIA V + R++V A+A A+ A K W + + +R VL D + +D Sbjct: 40 NPARGDVIANVADVSRSQVAGAIAQAEVAQKD-WAKWTGKERANVLRKWFDLMMENQEDL 98 Query: 84 LAAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTPDGVGAINYAVRRP 143 + GKP++ +R +I GA+ + FA+ K + E D + +++P Sbjct: 99 AVILTAEMGKPLAESRG-EIGYGASFIEFFAEEAKRIYGETIPGHQRDKRITV---LKQP 154 Query: 144 VGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPPGVY 203 +GV I PWN P ++T K GPALA G V +P+E TP +A L + + AG+P GV+ Sbjct: 155 IGVAASITPWNFPNAMITRKAGPALAAGCAFVARPAELTPLSATALAVLADRAGIPAGVF 214 Query: 204 NVVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADGARPVSLELGGKNAAIVF 263 NVV + TG+ + V +TFTG T G +M+ AAD S+ELGG IVF Sbjct: 215 NVVTSSNASETGKEFCENNAVRKLTFTGSTEVGRILMRQAADTVMKCSMELGGNAPFIVF 274 Query: 264 ADCDLDKAIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLKKGAEGMQLGRPEDLA 323 D DLD A+EG + F N GQ C+ R+YV+ ++D F ++LK+ M +G Sbjct: 275 DDADLDAAVEGAIMCKFRNNGQTCVCANRIYVQAGVYDAFAAKLKEAVAKMTVGDGLAEG 334 Query: 324 TGMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKGGAWVQPTIWTGLGDDS 383 T GPLI+++ EKV ++ A E GA V+ GG E+ GG + +PTI TG D Sbjct: 335 TQFGPLINEKAVEKVQAHIADAKEKGAEVILGGNPSEL-----GGTFFEPTIITGATQDM 389 Query: 384 VVAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVAGAIEVGIAWV 443 V +++E FGP A + F++E++VI AND +GLA + +LSR ++VA A+E GI V Sbjct: 390 VFSQDETFGPMAPLFKFETEDDVIEMANDTIFGLASYFYAKDLSRVYKVAEALEYGIVGV 449 Query: 444 NSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNVCIKL 485 N+ + FGG KQSG+GREG H +E Y E+K +C+ + Sbjct: 450 NTGIISTELAPFGGVKQSGLGREGSHHGIEDYLEMKYICMSV 491 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: 534 Number of extensions: 31 Number of successful extensions: 2 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: 491 Length adjustment: 34 Effective length of query: 451 Effective length of database: 457 Effective search space: 206107 Effective search space used: 206107 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