Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate AZOBR_RS22315 AZOBR_RS22315 aldehyde dehydrogenase
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__azobra:AZOBR_RS22315 Length = 497 Score = 321 bits (822), Expect = 4e-92 Identities = 181/478 (37%), Positives = 265/478 (55%), Gaps = 7/478 (1%) Query: 13 HFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANE 72 HF G+F P+ GK F +NPAT E + A G AA++D AV AA A W K E Sbjct: 22 HFFGGEFRPASSGKGFPVVNPATGETVAEAAFGEAADVDAAVAAAVAAQK-EWAKRPVRE 80 Query: 73 RIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEA 132 R ++ + G ++ KEE++ L +L+TGK ++ + F FF + E Sbjct: 81 RGKLVAECGRVLDAHKEEIAKLIALETGKALRTESRVEAGVLSDAFVFFGGLAPELKGET 140 Query: 133 TQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATV 192 + L +R PVGV+G I PWN+PLLLM K+APA+ AGN VV+K AE P+ Sbjct: 141 IPFNPSMLTMTVREPVGVVGAIIPWNVPLLLMALKIAPAMVAGNAVVVKSAEEAPLAVLR 200 Query: 193 LAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLK 252 + ++ +P GVVN++ G+GP GA L H DV ++FTG TGKI+ +AA+ L Sbjct: 201 VVQLINTV-IPAGVVNILSGYGPE-CGAPLVAHKDVKKVTFTGSVETGKIVYKTAAEKLI 258 Query: 253 RLSYELGGKNPNVIFADSNLDEVIETTMKSS-FINQGEVCLCGSRIYVERPAYEAFLEKF 311 ++ ELGGK+P ++ D++LD+ I + F QG+ C SRI+V ++AF+EK Sbjct: 259 PVTLELGGKSPMIVCGDADLDQAIAGAIAGMRFTRQGQSCTASSRIFVHDSIHDAFVEKL 318 Query: 312 VAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEG--LEKG 369 K + +GDP D T +G ++S + +RV YI + E G T P L KG Sbjct: 319 KEKVNAMKMGDPLDESTDIGTIVSPQQLDRVQSYIAIGKEGGATPHVCSAMPSDPKLTKG 378 Query: 370 YFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRR 429 +++P I TG+ R+ +EEIFGPV VI + EEV+ Q NDT YGL+A++WT DL+ Sbjct: 379 LYVQPHIFTGVKNSDRIAQEEIFGPVCCVIRWTDYEEVIAQANDTEYGLAATIWTRDLKV 438 Query: 430 AHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHS-FEFYSELTNICIKL 486 A ++EAG V VN + +GG+K SG+G+E L + E ++ I I + Sbjct: 439 AMDAVHRLEAGFVQVNQNLVVQPNLSYGGVKSSGLGKEASLEAMLEHFTHKKTIIINM 496 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: 583 Number of extensions: 25 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: 486 Length of database: 497 Length adjustment: 34 Effective length of query: 452 Effective length of database: 463 Effective search space: 209276 Effective search space used: 209276 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