Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate 6938545 Sama_2648 aldehyde dehydrogenase (RefSeq)
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__SB2B:6938545 Length = 498 Score = 341 bits (874), Expect = 4e-98 Identities = 182/476 (38%), Positives = 281/476 (59%), Gaps = 4/476 (0%) Query: 14 FIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKAL-NGPWKKMTANE 72 FI+G + ++ +TFD I+P L VA A+ D+AV A+ +G W + + Sbjct: 24 FINGHYCDAVGKETFDCISPVDGRLLTQVASCQQADADIAVANARAVFESGVWSLQSPVK 83 Query: 73 RIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEA 132 R V+ + +L+ +EL++LE+LD GKP S ++D+ AA + + I I +E Sbjct: 84 RKKVMIRFAELLEAHADELALLETLDMGKPIAHSKAVDVAGAARAIRWSGEAIDKIYDEL 143 Query: 133 TQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATV 192 + R PVGV+ I PWN P+L+ WKL PALA GN+VV+KP+E +P+TA Sbjct: 144 APTPHNEIGMITREPVGVVAAIVPWNFPMLMACWKLGPALATGNSVVLKPSEKSPLTAIR 203 Query: 193 LAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKT-L 251 +A++ ++AG+PDGV+N++ GFG ++ G AL H DV+ + FTG T K +M A ++ + Sbjct: 204 MAQLAKEAGLPDGVLNVLPGFG-HTVGQALALHMDVDTLVFTGSTKIAKQLMVYAGQSNM 262 Query: 252 KRLSYELGGKNPNVIFADS-NLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEK 310 KR+ E GGK+PN++F D+ +L E + NQGEVC GSR+ VE + ++ Sbjct: 263 KRVWLEAGGKSPNIVFNDAPDLKAAAEAAASAIAFNQGEVCTAGSRLLVESGVKDELIKL 322 Query: 311 FVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEGLEKGY 370 V + + G P D T GA++ + + V GYIK +EG ++ GG + G Sbjct: 323 IVKEMEAWQPGHPLDPATTCGAVVDKQQLDTVLGYIKAGHDEGAKLMCGGSQVLAETGGV 382 Query: 371 FLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRRA 430 ++ PT+ G+T ++ +EEIFGPV++VI FD +E + NDT YGL+A VWT+D+ +A Sbjct: 383 YVAPTVFDGVTNQMKIAREEIFGPVMSVITFDGMDEAVAIANDTIYGLAAGVWTSDISKA 442 Query: 431 HRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICIKL 486 H+ A + +G+VW+N + D+ PFGG KQSG GR+ LH+FE Y+E+ I L Sbjct: 443 HKTAKALRSGMVWINHYDGGDMTAPFGGYKQSGNGRDKSLHAFEKYTEVKATWIAL 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: 619 Number of extensions: 24 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: 498 Length adjustment: 34 Effective length of query: 452 Effective length of database: 464 Effective search space: 209728 Effective search space used: 209728 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 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