Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate GFF4232 Psest_4305 NAD-dependent aldehyde dehydrogenases
Query= BRENDA::Q83XU8 (485 letters) >FitnessBrowser__psRCH2:GFF4232 Length = 497 Score = 317 bits (812), Expect = 6e-91 Identities = 185/465 (39%), Positives = 268/465 (57%), Gaps = 11/465 (2%) Query: 24 SPLNNAVIAKVHEAGRAEVDAAVAAAQAALK-GAWGRMSLAQRVEVLYAVADGINRRFDD 82 SP++ V+A+V +A+ + AVA+A+AA G+W R++ A+R VL AD + ++ Sbjct: 41 SPVDGRVLAQVASCEQADAERAVASARAAFDAGSWSRLAPAKRKAVLIRFADLLEANREE 100 Query: 83 FLAAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTPDGVGAINYAVRR 142 E D GKP+ + VDIP A + + + + E P D +G + R Sbjct: 101 LALLETLDMGKPIGDSLAVDIPGAARALRWSGEAIDKIYDEVAATPH-DQLGLVT---RE 156 Query: 143 PVGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPPGV 202 PVGVV I PWN PL++ WK+GPALA GN+VV+KPSE++P TA + ++ AG+P GV Sbjct: 157 PVGVVAAIVPWNFPLMMACWKLGPALATGNSVVLKPSEKSPLTAIRIAQLAIDAGIPAGV 216 Query: 203 YNVVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADG-ARPVSLELGGKNAAI 261 NV+ G+G ++ G+ L H DV+ + FTG T + +M A + + V LE GGK+ I Sbjct: 217 LNVLPGYG-HTVGKALALHMDVDTLVFTGSTRVAKQLMIYAGESNMKRVWLEAGGKSPNI 275 Query: 262 VFADC-DLDKAIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLKKGAEGMQLGRPE 320 VFAD DL A + + N G+VC R+ VER I +RF+ + + +G + G P Sbjct: 276 VFADAPDLQAAAQAAAGAIAFNQGEVCTAGSRLLVERSIRERFLPMVVEALKGWKPGNPL 335 Query: 321 DLATGMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKGGAWVQPTIWTGLG 380 D AT +G L+ + VL Y +AGA V+ GG + GG +V+PTI+ G+ Sbjct: 336 DPATNVGALVDTQQLNTVLGYIDAGRQAGAQVLIGG---QRTLEETGGLYVEPTIFDGVD 392 Query: 381 DDSVVAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVAGAIEVGI 440 + +A+EEIFGP V+ FDS EE + AND YGLA +WT +LS+AHR A A+ G Sbjct: 393 NAMRIAQEEIFGPVLSVITFDSAEEAVAIANDTPYGLAAAVWTADLSKAHRTARALRAGS 452 Query: 441 AWVNSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNVCIKL 485 WVN + D+ FGG KQSG GR+ +H+ + YTELK I+L Sbjct: 453 VWVNQYDGGDMTAPFGGFKQSGNGRDKSLHAFDKYTELKATWIQL 497 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: 550 Number of extensions: 29 Number of successful extensions: 6 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: 497 Length adjustment: 34 Effective length of query: 451 Effective length of database: 463 Effective search space: 208813 Effective search space used: 208813 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