Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate AO353_29295 AO353_29295 aldehyde dehydrogenase
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__pseudo3_N2E3:AO353_29295 Length = 496 Score = 358 bits (920), Expect = e-103 Identities = 197/476 (41%), Positives = 282/476 (59%), Gaps = 4/476 (0%) Query: 14 FIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALN-GPWKKMTANE 72 FIDG + +L TF+ ++P L VA A+ + AVQ A++A + G W K+ E Sbjct: 22 FIDGHYCSALSRDTFECVSPVDGRFLANVASTDEADANAAVQVARRAFDSGVWAKLAPAE 81 Query: 73 RIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEA 132 R +L + DLIL +EEL++LE+LD GKP S +IDIP A + ++ I I +E Sbjct: 82 RKRILIRFADLILANQEELALLETLDMGKPISDSMAIDIPATANAIRWSAEAIDKIYDEV 141 Query: 133 TQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATV 192 L R P GV+ I PWN PL++ +WK APALAAGN+ ++KP+E +P+TA Sbjct: 142 AATPHDQLGLVTREPSGVVAAIVPWNFPLIMASWKFAPALAAGNSFILKPSEKSPLTAIR 201 Query: 193 LAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKT-L 251 +A++ DAG+P GV N++ GFG ++ G AL H DV+ ++FTG T K ++ A ++ + Sbjct: 202 IAQLALDAGIPKGVFNVLPGFG-HTVGKALALHMDVDVLAFTGSTAIAKQLLIYAGQSNM 260 Query: 252 KRLSYELGGKNPNVIFADSNLDEVIETTMKSSF-INQGEVCLCGSRIYVERPAYEAFLEK 310 KR+ E GGK+PNV+FAD+ T S+ NQGEVC GSR+ VER E F+ Sbjct: 261 KRVWLEAGGKSPNVVFADAPDLRAAATAAASAIAFNQGEVCTAGSRLLVERSIREQFIPL 320 Query: 311 FVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEGLEKGY 370 V + G D +T VGA++ + V YI + E+G ++ GG R G Sbjct: 321 LVEALQAWKPGHALDPETTVGAVVDQRQLDNVLRYISIGKEQGAQLIAGGNRALEDTGGL 380 Query: 371 FLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRRA 430 ++EP I G+T + +EEIFGPV+++I FDT EE L ND+ +GL+A VWT++L +A Sbjct: 381 YVEPAIFDGVTNAMTIAREEIFGPVLSLITFDTAEEALAIANDSIFGLAAGVWTSNLSKA 440 Query: 431 HRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICIKL 486 H A + AG VWVN + D+ PFGG KQSG GR+ LH+F+ Y+EL IKL Sbjct: 441 HTFARGLRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHAFDKYTELKATWIKL 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: 587 Number of extensions: 25 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: 496 Length adjustment: 34 Effective length of query: 452 Effective length of database: 462 Effective search space: 208824 Effective search space used: 208824 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