Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate CCNA_03243 CCNA_03243 NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase
Query= BRENDA::Q83XU8 (485 letters) >FitnessBrowser__Caulo:CCNA_03243 Length = 499 Score = 330 bits (845), Expect = 9e-95 Identities = 192/465 (41%), Positives = 267/465 (57%), Gaps = 11/465 (2%) Query: 24 SPLNNAVIAKVHEAGRAEVDAAVAAAQAALK-GAWGRMSLAQRVEVLYAVADGINRRFDD 82 SP + V+ V +V+ AVA A+AA + G W Q+ VL+ +A+ + R D+ Sbjct: 42 SPRDGQVLNLVTACQADDVERAVAGARAAFEDGRWRDQGPRQKKAVLFRLAELMERDADE 101 Query: 83 FLAAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTPDGVGAINYAVRR 142 E D GKP+S AR+VDIP + +A+ + V E P ++YAV Sbjct: 102 LALLESLDVGKPISDARNVDIPLAINTCRWYAEALDKVYGEVGTSPAD----RLSYAVHE 157 Query: 143 PVGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPPGV 202 P+GV+G I PWN PL + WKV PALA GN+VV+KP+E++P TA LG + AG+PPGV Sbjct: 158 PLGVIGAIVPWNFPLHMAMWKVAPALAMGNSVVLKPAEQSPLTALKLGALALEAGLPPGV 217 Query: 203 YNVVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMK-AAADGARPVSLELGGKNAAI 261 NV+ G G GE L DV+ I FTG G +M+ +A + VSLELGGK+ I Sbjct: 218 LNVIPGLG-GVAGEALALSMDVDMIAFTGSGPVGRRLMEYSARSNLKRVSLELGGKSPQI 276 Query: 262 VFADC-DLDKAIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLKKGAEGMQLGRPE 320 VFADC DL+ A + F N G+VC R+ VE PI D F++R+ + A+GM++G P Sbjct: 277 VFADCPDLEAAAQAAAWGVFYNQGEVCTAASRLLVEAPIKDAFLARVIEVAKGMKVGDPL 336 Query: 321 DLATGMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKGGAWVQPTIWTGLG 380 D +T G ++S+ L Y A GA V GG + GG +V+PTI+ + Sbjct: 337 DPSTQFGAMVSERQMNTALDYIATADSQGARRVLGG---QRVRQEAGGFYVEPTIFDQVR 393 Query: 381 DDSVVAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVAGAIEVGI 440 D +AREE+FGP VM F SE+E +R AND YGLA +WT ++S+A R A ++ G+ Sbjct: 394 PDQTLAREEVFGPVLGVMTFSSEDEAMRLANDTVYGLAAGLWTADVSKALRGARRLKAGL 453 Query: 441 AWVNSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNVCIKL 485 WVN W D+ FGG KQSG GR+ +H+L Y +LK+V + L Sbjct: 454 VWVNGWDACDITMPFGGFKQSGFGRDRSLHALHKYADLKSVSVTL 498 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: 555 Number of extensions: 32 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: 499 Length adjustment: 34 Effective length of query: 451 Effective length of database: 465 Effective search space: 209715 Effective search space used: 209715 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