Align acetaldehyde dehydrogenase (EC 1.2.1.3) (characterized)
to candidate HSERO_RS05115 HSERO_RS05115 aldehyde dehydrogenase
Query= reanno::Burk376:H281DRAFT_01117 (795 letters) >FitnessBrowser__HerbieS:HSERO_RS05115 Length = 793 Score = 1072 bits (2772), Expect = 0.0 Identities = 538/797 (67%), Positives = 621/797 (77%), Gaps = 6/797 (0%) Query: 1 MSVAEYFSSMDYGPAPEDDQPARQWLAQHEARFGHFIGGAWHAPASGAQFVSHAPASGER 60 MSV+ YF +MDYGPAPE D+ AR WLA HEA FGHFI G + P + + PASG+ Sbjct: 1 MSVSTYFDTMDYGPAPESDKDARAWLASHEASFGHFIAGRFTQPKADLDDID--PASGKL 58 Query: 61 LADIAQGDAADIDAALAAARAAQPGWLALGGKGRARHLYALARMVQRHSRLFAVLEALDN 120 LA ++QG AAD+DAA+ AA+AA PGW ALGG GRARHLYALAR VQRH+RL AVLE LDN Sbjct: 59 LAHLSQGSAADVDAAVQAAQAALPGWQALGGHGRARHLYALARTVQRHARLLAVLETLDN 118 Query: 121 GKPIRETRDLDVPLVARHFLHHAGWAQLQDSEFADHAPLGVIGQIVPWNFPLLMLAWKIA 180 GKP+RE+RD+DVPLVARHF H+AGWAQLQ+SEF DH P+GV+GQIVPWNFPLLMLAWKIA Sbjct: 119 GKPLRESRDVDVPLVARHFYHYAGWAQLQESEFPDHVPVGVVGQIVPWNFPLLMLAWKIA 178 Query: 181 PAIATGNCVVLKPAEYTPLTALLFAELAHQAGLPAGVLNVVTGDGSTGAALVEHPQVDKI 240 PA+A GN VVLKPAE T LTALLFAELA QAGLPAGVLN+VTGDG+TGAA+V HP + KI Sbjct: 179 PALALGNTVVLKPAENTSLTALLFAELAQQAGLPAGVLNIVTGDGATGAAVVAHPGIQKI 238 Query: 241 AFTGSTEVGKLIRSVTAGSGKSLTLELGGKSPFIVFDDADLDGAVEGVVDAIWFNQGQVC 300 AFTGSTEVG+LIR TAGSGKSLTLELGGKSPFIVF+DAD+D A+EGVVDAIWFNQGQVC Sbjct: 239 AFTGSTEVGRLIREQTAGSGKSLTLELGGKSPFIVFEDADIDAAIEGVVDAIWFNQGQVC 298 Query: 301 CAGSRLLVQEGIEARFIAKLKRRMETLRVGPSLDKSIDMGAIVDPVQLERIHSLVETGRR 360 CAGSRLLVQEGI FIA+LK RM+ L+VG LDK DMGA++ PVQLER+ SLVE G R Sbjct: 299 CAGSRLLVQEGIHDLFIARLKTRMQKLKVGAPLDKCSDMGALISPVQLERVRSLVEQGVR 358 Query: 361 EGCAIWQAA-DTPLPANGCFYPPTLVTNVAPASTLAQEEIFGPVLVTMSFRTPDEAIALA 419 EG Q DTP GCFYPPTL+T V PA+T+A EEIFGPVLV MSFRTPDEA+ LA Sbjct: 359 EGAQCHQVVLDTP--PGGCFYPPTLLTGVHPAATVASEEIFGPVLVAMSFRTPDEAVQLA 416 Query: 420 NNSRYGLAASVWSETIGRALDVAPRLAAGVVWVNATNLFDAAVGFGGYRESGYGREGGRE 479 NNSRYGLAAS+WSETIG AL VAP+L AGVVW+N+TN FDAAVGFGG RESGYGREGGRE Sbjct: 417 NNSRYGLAASIWSETIGLALGVAPQLKAGVVWINSTNQFDAAVGFGGVRESGYGREGGRE 476 Query: 480 GIHEYLKPRAWLNLPKRQPVSAATNASDDRQVSNLALVDRTAKLFIGGKQVRPDSGYSLP 539 G +EYLKPR RQP + +D +DRTAKL+IGGKQVRPD S+ Sbjct: 477 GCYEYLKPRRQQAGSLRQPSARRAIRADADSPLQGGAIDRTAKLYIGGKQVRPDGEVSMA 536 Query: 540 VHAPDGTRVGEVGEGNRKDIRNAVQAARAAQKWSQASTHNRAQVLFYLAENLAVRADEFA 599 H+ G R+ +VG GNRKDIRNAV AA A W+ AS H RAQ L+Y+AENL+ R +EFA Sbjct: 537 CHSTQGERLEDVGLGNRKDIRNAVAAAVKAGGWTSASPHRRAQGLYYIAENLSARTEEFA 596 Query: 600 HQLTVRNGATDAAAHAEVEASVTRLFTYAAWADKFDGAVHTPPLRGVALAMHEPLGVIGI 659 ++ G T A AEV+AS+ RLFTY AWADKF+GAVH PP+RGVALAM E +GV+G+ Sbjct: 597 RRIASTTGVTADEARAEVDASIKRLFTYGAWADKFEGAVHQPPMRGVALAMPEAIGVVGV 656 Query: 660 ACPDEAPLLAFVSLAAPALAMGNRVVVLPGEACPLAVTDFYQVVETSDVPGGVVNIVTGK 719 CP+E PLLA +SL AP +AMGNRVVV+P E PL TD YQV++TSD+P GV+NIVTGK Sbjct: 657 VCPEEKPLLALISLVAPLIAMGNRVVVVPSEQAPLVATDLYQVLDTSDLPAGVINIVTGK 716 Query: 720 REALLPALARHDDVDAVWCFGSAADATLIERESVGNLKRTFTDYGRQFDWFDRA-SEGLP 778 LLP LA HD+V+A+W G A + ER S GNLKR F D+G DW D A EG Sbjct: 717 SAELLPVLAEHDEVEALWVRGPAEFSATAERLSTGNLKRCFVDHGYVTDWHDAAQGEGAQ 776 Query: 779 FLRQAVQVKNIWIPYGD 795 +LRQA +KN+WIPYG+ Sbjct: 777 YLRQATHIKNVWIPYGE 793 Lambda K H 0.320 0.135 0.411 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: 1850 Number of extensions: 65 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: 795 Length of database: 793 Length adjustment: 41 Effective length of query: 754 Effective length of database: 752 Effective search space: 567008 Effective search space used: 567008 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 55 (25.8 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