Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_045582953.1 AL072_RS17755 aldehyde dehydrogenase
Query= metacyc::MONOMER-15108 (486 letters) >NCBI__GCF_001305595.1:WP_045582953.1 Length = 503 Score = 346 bits (888), Expect = e-100 Identities = 185/475 (38%), Positives = 279/475 (58%), Gaps = 8/475 (1%) Query: 15 IDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGP-WKKMTANER 73 I G+FV G+ + +P T E +A+ G ++D AV AA+ A P W++MT ++R Sbjct: 17 IGGRFVEPKSGRYIPSYDPTTAEPWYELADAGPEDVDDAVAAARAAFVDPAWRRMTQSDR 76 Query: 74 IAVLRKVGDLILERKEELSVLESLDTGK--PTWLSGSIDIPRAAYNFHFFSDYIRTITNE 131 ++R++ +LIL EEL+++E+ D GK + +P + F +D ++ T Sbjct: 77 GKLVRRLAELILVNAEELALMETRDNGKLIKEMRAQMRAMPDSYTYFAGMADKLQGDTIP 136 Query: 132 ATQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTAT 191 ++D LN+ +R P+GV+G+I PWN PL+L+T LAP LA GNTVV+KP+E + Sbjct: 137 VNKLD--MLNFNLREPLGVVGMITPWNSPLMLLTGTLAPCLAIGNTVVIKPSEHATASTL 194 Query: 192 VLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTL 251 LAE+ +AG P GVVN+V G G +AG ALT HP + I FTG T TG I A+AA L Sbjct: 195 ALAELVAEAGFPAGVVNVVSGAGA-TAGEALTRHPGIAKIVFTGSTQTGSRIAANAAGNL 253 Query: 252 KRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKF 311 ELGGK+P+V+F D +++ + + F G+ C+ GSR +VE Y+ F+E Sbjct: 254 VPCQMELGGKSPHVVFGDVDIERAVNGVVAGVFAAAGQTCVAGSRCFVEASIYDRFVEAL 313 Query: 312 VAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPE--GLEKG 369 VA+T + VG P + T +G L +V Y+ +G + GG+RP+ GL++G Sbjct: 314 VARTGRIAVGHPMEEGTDIGPLALSPQLAKVEEYVASGQRDGARLAAGGRRPQAAGLDRG 373 Query: 370 YFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRR 429 ++ EPT++ D +++EIFGPVV V+PF +E+E++ NDT YGL++ +WT D+ R Sbjct: 374 WYFEPTVLADARNDMGFMRDEIFGPVVGVVPFASEDEMIAMANDTRYGLASGIWTGDIDR 433 Query: 430 AHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICI 484 A R A +I+AG VW+NT+ + GG KQSG GR GG +S N+ I Sbjct: 434 AMRFATRIDAGTVWINTYRAAAYMSSNGGFKQSGYGRRGGFDVMREFSRSKNVVI 488 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: 622 Number of extensions: 32 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: 503 Length adjustment: 34 Effective length of query: 452 Effective length of database: 469 Effective search space: 211988 Effective search space used: 211988 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 24 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