Align acetaldehyde dehydrogenase (EC 1.2.1.3) (characterized)
to candidate GFF3227 PGA1_c32800 aldehyde dehydrogenase
Query= reanno::BFirm:BPHYT_RS25810 (796 letters) >FitnessBrowser__Phaeo:GFF3227 Length = 802 Score = 943 bits (2437), Expect = 0.0 Identities = 484/799 (60%), Positives = 582/799 (72%), Gaps = 24/799 (3%) Query: 1 MSVAEYFSSMEYGPAPEDDQPARAWLAQHEDGFGHFIGGAWHAPAAGERFASNAPATGEQ 60 ++V E F +M+YGPAPE A AWL FGHFI G + AP G+ F S PATGE Sbjct: 25 LTVKEIFETMDYGPAPESAADALAWLVDQGARFGHFINGEFTAP--GDGFDSKNPATGEV 82 Query: 61 LAQVAQGDAADIDAAVAAARAAQPGWLALGGAGRARHLYALARMVQRHSRLFAVLEALDN 120 LA ++Q +D+D+AV AAR AQ W A GGA RAR+LYA+AR++Q+H+RLFAVLE LDN Sbjct: 83 LATLSQATQSDVDSAVDAARKAQTKWSAAGGAARARYLYAIARLMQKHARLFAVLETLDN 142 Query: 121 GKPIRETRDIDVPLVARHFLHHAGWAQLQESEFADYAPLGVVGQIVPWNFPLLMLAWKIA 180 GKPIRE+RDIDVPL RHF +HAG AQL ESE D LGV GQI+PWNFPLLMLAWK+A Sbjct: 143 GKPIRESRDIDVPLAQRHFYYHAGMAQLMESELPDREALGVCGQIIPWNFPLLMLAWKVA 202 Query: 181 PAIATGNCVVLKPAEYTPLTALLFAELAHRAGLPAGVLNVVTGDGRTGAALVEHPQVDKI 240 PAIA GN VVLKPAEYT LTALLFA++ +AGLP GV+N+VTGDG G +V VDKI Sbjct: 203 PAIAMGNTVVLKPAEYTSLTALLFADICRQAGLPKGVVNIVTGDGAVGEMIV-GADVDKI 261 Query: 241 AFTGSTEVGRLIRSATAGSGKSLTLELGGKSPFIVFDDADLDGAVEGVVDAIWFNQGQVC 300 AFTGST VGR IR ATAGSGK+LTLELGGKSP+IVFDDAD+D A+EG+VDAIWFNQGQVC Sbjct: 262 AFTGSTAVGRRIREATAGSGKALTLELGGKSPYIVFDDADIDSAIEGLVDAIWFNQGQVC 321 Query: 301 CAGSRLLVQEGIEARFIAKLKRRMETLRVGTSLDKSIDLGAIVDPVQLERIQSLV---ET 357 CAGSRLLVQEGI RF KL+ RM+ LR+G LDKSID+GAIVDPVQL I +V Sbjct: 322 CAGSRLLVQEGIAERFHTKLRVRMDKLRIGNPLDKSIDVGAIVDPVQLTTISEMVAANTA 381 Query: 358 GRREGCSVWQSPDTTIPSGGCFFPPTLVTGVAPASTLAQEEIFGPVLVTMSFRTPDEAIA 417 GR V +P GCF+PPTL+ G+AP+ L QEEIFGPVLV+ +FRTP EA+ Sbjct: 382 GRMHQAQV------AVPERGCFYPPTLIEGLAPSDALMQEEIFGPVLVSTTFRTPSEAVE 435 Query: 418 LANNSRYGLAASVWSETIGRALDVAPRLASGVVWINATNLFDAAVGFGGYRESGYGREGG 477 LANN+RYGLAA++W+E + ALD+AP+L +GVVW+NATNLFDAA GFGG RESG+GREGG Sbjct: 436 LANNTRYGLAATLWTENVNLALDIAPKLVAGVVWVNATNLFDAAAGFGGTRESGFGREGG 495 Query: 478 REGIYEYLKPRAWLKLAERRAAQDVVRDAAALDPLSNVTSIDRTAKLFIGGKQARPDSGY 537 EG+ Y KP+ K E+ D A +D ++DRTAK ++GGKQ RPD GY Sbjct: 496 WEGLSAYTKPKGKTKALEK--VTGFSGDGAPVD------AVDRTAKFYVGGKQTRPDGGY 547 Query: 538 SLPVLAPDGTPVGEVAAGNRKDIRNAVEAARAAQKWSQASTHNRAQVLFYLAENLAVRAD 597 S + + G +G V GNRKD+RNAVEAA A WS+ + H RAQ+L+Y+ ENL+ R Sbjct: 548 SKAIHSKSGGLLGHVGLGNRKDVRNAVEAAAGANAWSKTTGHLRAQILYYIGENLSARVG 607 Query: 598 EFVRQLVVRNGATEAAARAEVDASVQRLFTYAAWADKFDGAVHTPPLRGVALAMHEPLGV 657 EF ++ G ++ A EV+AS+QRLFT AAWADK+DG H P+RGVALAM EP+GV Sbjct: 608 EFADRIDRMTGKSQGA--QEVEASIQRLFTAAAWADKYDGQAHGVPIRGVALAMKEPVGV 665 Query: 658 IGIACPDEAPLLGFVSLAAPALAMGNRVVVLPSEASPLTVTDFYQVAETSDVPGGVLNIV 717 IG C DEAPLLG VS+ APA+AMGNRVV+ SEA PL+ TDFYQV ETSD+PGGV+NI+ Sbjct: 666 IGALCADEAPLLGLVSVMAPAIAMGNRVVLAASEAYPLSATDFYQVLETSDLPGGVVNIL 725 Query: 718 TGERGALLPALVKHDDVDAVWCFGSAADSTLVERESVGNLKRTFVDYGRQFDWFDRASEG 777 TG + L H +VDAVW F S+ S ++E S GNLKRT+V+ G DW A Sbjct: 726 TGRHAEMASPLASHLNVDAVWSFSSSDLSAMIEEASAGNLKRTWVNNGLAMDW--SADHS 783 Query: 778 RPFLRQAVQVKNIWIPYGD 796 R FL A +VKNIWIPYG+ Sbjct: 784 RRFLEAATEVKNIWIPYGE 802 Lambda K H 0.319 0.135 0.408 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: 1702 Number of extensions: 67 Number of successful extensions: 9 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: 796 Length of database: 802 Length adjustment: 41 Effective length of query: 755 Effective length of database: 761 Effective search space: 574555 Effective search space used: 574555 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