Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate WP_012757758.1 RLEG_RS11275 aldehyde dehydrogenase family protein
Query= BRENDA::Q83XU8 (485 letters) >NCBI__GCF_000023185.1:WP_012757758.1 Length = 795 Score = 310 bits (795), Expect = 9e-89 Identities = 180/444 (40%), Positives = 247/444 (55%), Gaps = 22/444 (4%) Query: 25 PLNNAVIAKVHEAGRAEVDAAVAAAQAALKGAWGRMSLAQRVEVLYAVADGINRRFDDFL 84 P V+AK+ G A+VD AVAAA+ A + +W R+ R LYA+A I R Sbjct: 55 PATGKVLAKLANGGAADVDNAVAAARKA-QASWARLPGHARARHLYALARMIQRHARLIA 113 Query: 85 AAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTPDGVGAINYAVRRPV 144 E D GKP+ R +D+P A +F A + TEF A PV Sbjct: 114 VVEAIDNGKPIRETRDLDVPLAARHFYHHAGWAQIQDTEF--------------ADHVPV 159 Query: 145 GVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPPGVYN 204 GVVG I PWN P L++ WKV PALA GNTV++KP+E T TA L E+ + AG+PPGV N Sbjct: 160 GVVGQIIPWNFPFLMLAWKVAPALALGNTVILKPAEFTSLTALLFAELASAAGLPPGVLN 219 Query: 205 VVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADGARPVSLELGGKNAAIVFA 264 +V G G TG L H D++ I FTG T G I + A + ++LELGGK+ +VF Sbjct: 220 IVTGEG--ETGALLVGHADIDKIAFTGSTEVGRVIRERTAGSGKSLTLELGGKSPFVVFD 277 Query: 265 DCDLDKAIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLKKGAEGMQLGRPEDLAT 324 D D+D A+EG + + + N GQVC R+ V+ I D F RLK+ E +++G+P D Sbjct: 278 DADIDGAVEGVVDAIWFNQGQVCCAGSRLLVQEGIADLFHERLKRRMETLRVGQPLDKCI 337 Query: 325 GMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKGGAWVQPTIWTGLGDDSV 384 MG +I+ ++ + KK V GAT+ ++P KGG++ PT+ +G+ S+ Sbjct: 338 DMGAIIAPVQLTRIEALVKKGVSEGATL--HQAKIDLP---KGGSFYPPTLLSGVQPTSI 392 Query: 385 VAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVAGAIEVGIAWVN 444 VA EEIFGP A+ M F + EE I+ AN YGLA +W+ + A VA + G+ WVN Sbjct: 393 VATEEIFGPVAVSMTFRTPEEAIQLANHTRYGLAASVWSETIGLALNVAAKLAAGVVWVN 452 Query: 445 SWFLRDLRTAFGGSKQSGIGREGG 468 + L D FGG ++SG GREGG Sbjct: 453 ATNLFDAAVGFGGKRESGFGREGG 476 Score = 92.8 bits (229), Expect = 4e-23 Identities = 68/233 (29%), Positives = 109/233 (46%), Gaps = 9/233 (3%) Query: 23 SSPLNNAVIAKVHEAGRAEVDAAVAAAQAALKGAWGRMSLAQRVEVLYAVADGINRRFDD 82 +SP A I +V E+ R ++ AV AAQAA AW + R ++LY +A+ ++ R D+ Sbjct: 540 ASPKGKA-IGEVGESNRKDIRNAVVAAQAA--SAWSNATTHNRAQILYYIAENLSGRADE 596 Query: 83 FLAAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTPDGVGAINYAVRR 142 F + TG + A + ++ + +A + P + + A+ Sbjct: 597 FASRITAMTGASAANA-NAEVDAAISRLFTYAAWADKYEGGIHQPP----LRGVALAMPE 651 Query: 143 PVGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPPGV 202 +GVVGVICP PLL + P +A GN VV PSE P +A V+ T+ VP GV Sbjct: 652 AIGVVGVICPPEAPLLGFISLIAPLIATGNRVVAVPSEAFPLSATDFYSVLETSDVPAGV 711 Query: 203 YNVVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADGARPVSLELG 255 N+V G + L +H DV+A+ G + K ++ + ++ G Sbjct: 712 VNIVTG-SAIELAKILAAHNDVDALWAFGSAELSTTVEKLSSGNLKRTFVDNG 763 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: 918 Number of extensions: 38 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 485 Length of database: 795 Length adjustment: 37 Effective length of query: 448 Effective length of database: 758 Effective search space: 339584 Effective search space used: 339584 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: 53 (25.0 bits)
This GapMind analysis is from Apr 09 2024. 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