Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate CCNA_03243 CCNA_03243 NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__Caulo:CCNA_03243 Length = 499 Score = 357 bits (915), Expect = e-103 Identities = 190/475 (40%), Positives = 284/475 (59%), Gaps = 4/475 (0%) Query: 15 IDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKAL-NGPWKKMTANER 73 IDG V + G TF N++P + L V A +++ AV A+ A +G W+ ++ Sbjct: 25 IDGDLVEAASGATFHNVSPRDGQVLNLVTACQADDVERAVAGARAAFEDGRWRDQGPRQK 84 Query: 74 IAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEAT 133 AVL ++ +L+ +EL++LESLD GKP + ++DIP A ++++ + + E Sbjct: 85 KAVLFRLAELMERDADELALLESLDVGKPISDARNVDIPLAINTCRWYAEALDKVYGEVG 144 Query: 134 QMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATVL 193 L+YA+ P+GVIG I PWN PL + WK+APALA GN+VV+KPAE +P+TA L Sbjct: 145 TSPADRLSYAVHEPLGVIGAIVPWNFPLHMAMWKVAPALAMGNSVVLKPAEQSPLTALKL 204 Query: 194 AEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMA-SAAKTLK 252 + +AG+P GV+N++ G G AG AL DV+ I+FTG G+ +M SA LK Sbjct: 205 GALALEAGLPPGVLNVIPGLG-GVAGEALALSMDVDMIAFTGSGPVGRRLMEYSARSNLK 263 Query: 253 RLSYELGGKNPNVIFADS-NLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKF 311 R+S ELGGK+P ++FAD +L+ + F NQGEVC SR+ VE P +AFL + Sbjct: 264 RVSLELGGKSPQIVFADCPDLEAAAQAAAWGVFYNQGEVCTAASRLLVEAPIKDAFLARV 323 Query: 312 VAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEGLEKGYF 371 + K + VGDP D T+ GA++S+ YI A +G + GG+R G++ Sbjct: 324 IEVAKGMKVGDPLDPSTQFGAMVSERQMNTALDYIATADSQGARRVLGGQRVRQEAGGFY 383 Query: 372 LEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRRAH 431 +EPTI + D + +EE+FGPV+ V+ F +E+E + NDT YGL+A +WT D+ +A Sbjct: 384 VEPTIFDQVRPDQTLAREEVFGPVLGVMTFSSEDEAMRLANDTVYGLAAGLWTADVSKAL 443 Query: 432 RVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICIKL 486 R A +++AG+VWVN W D+ PFGG KQSG GR+ LH+ Y++L ++ + L Sbjct: 444 RGARRLKAGLVWVNGWDACDITMPFGGFKQSGFGRDRSLHALHKYADLKSVSVTL 498 Lambda K H 0.318 0.136 0.404 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: 564 Number of extensions: 21 Number of successful extensions: 5 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: 486 Length of database: 499 Length adjustment: 34 Effective length of query: 452 Effective length of database: 465 Effective search space: 210180 Effective search space used: 210180 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