Align aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized)
to candidate 5209439 Shew_1910 bifunctional acetaldehyde-CoA/alcohol dehydrogenase (RefSeq)
Query= CharProtDB::CH_018413 (862 letters) >FitnessBrowser__PV4:5209439 Length = 872 Score = 1016 bits (2627), Expect = 0.0 Identities = 503/865 (58%), Positives = 653/865 (75%), Gaps = 9/865 (1%) Query: 1 MKVTTVKELDEKLKVIKEAQKKFSCYSQEMVDEIFRNAAMAAIDARIELAKAAVLETGMG 60 M V+ +ELD+ ++ + +AQ +F+ +SQE VD+IFR AA+AA DARI LAK A ETGMG Sbjct: 1 MTVSNQQELDQLVERVAKAQAQFANFSQEQVDKIFRAAALAAADARISLAKMAANETGMG 60 Query: 61 LVEDKVIKNHFAGEYIYNKYKDEKTCGIIERNEPYGITKIAEPIGVVAAIIPVTNPTSTT 120 ++EDKVIKNHFA EYIYNKYKD+KTCGI+E + +G IAEP+G++ I+P TNPTST Sbjct: 61 VLEDKVIKNHFASEYIYNKYKDDKTCGILEEDPTFGTITIAEPVGLICGIVPTTNPTSTA 120 Query: 121 IFKSLISLKTRNGIFFSPHPRAKKSTILAAKTILDAAVKSGAPENIIGWIDEPSIELTQY 180 IFK+LISLKTRNGI FSPHPRAK ST AA+ +L+AAV++GAP++IIGWIDEPS+ L+ Sbjct: 121 IFKALISLKTRNGIIFSPHPRAKVSTTTAARLVLEAAVEAGAPKDIIGWIDEPSVALSNQ 180 Query: 181 LM--QKADITLATGGPSLVKSAYSSGKPAIGVGPGNTPVIIDESAHIKMAVSSIILSKTY 238 LM K ++ LATGGP +VK+AYSSGKPAIGVG GNTP++IDE+A IK AVSSI++SKT+ Sbjct: 181 LMTHDKINLILATGGPGMVKAAYSSGKPAIGVGAGNTPIVIDETADIKRAVSSILMSKTF 240 Query: 239 DNGVICASEQSVIVLKSIYNKVKDEFQERGAYIIKKNELDKVREVIFKDGSVNPKIVGQS 298 DNGV+CASEQ+V+V+ ++Y+ VK+ F G Y++ E +++VI K+G++N IVGQS Sbjct: 241 DNGVVCASEQAVVVVDAVYDAVKERFASHGGYMLSSKEAKAMQKVILKNGALNADIVGQS 300 Query: 299 AYTIAAMAGIKVPKTTRILIGEVTSLGEEEPFAHEKLSPVLAMYEADNFDDALKKAVTLI 358 A TIAAMA IKVP +T++LIG+ T + E E FAHEKLSP+LAMY A +FDDAL KA L+ Sbjct: 301 AATIAAMANIKVPASTKVLIGQATEISESEAFAHEKLSPLLAMYRASDFDDALNKAEALV 360 Query: 359 NLGGLGHTSGIYADEIKARDKIDRFSSAMKTVRTFVNIPTSQGASGDLYNFRIPPSFTLG 418 LGG+GHTSG+Y D+ +++ F MKT R +N P SQG GDLYNF++ PS TLG Sbjct: 361 TLGGIGHTSGLYTDQDTQTERVRTFGFRMKTARILINTPASQGGIGDLYNFKLAPSLTLG 420 Query: 419 CGFWGGNSVSENVGPKHLLNIKTVAERRENMLWFRVPHKVYFKFGCLQFALKDLKDLKKK 478 CG WGGNS+SENVGP HL+N KTVA+R ENMLW ++P +YF+ G L AL++L D KK Sbjct: 421 CGSWGGNSISENVGPSHLINKKTVAKRAENMLWHKLPSSIYFRRGSLPIALEELSD--KK 478 Query: 479 RAFIVTDSDPYNLNYVDSIIKILEHLDIDFKVFNKVGREADLKTIKKATEEMSSFMPDTI 538 RA IVTD +N Y D IKIL+ ++ +VF +V + L + + SF PD I Sbjct: 479 RALIVTDKYLFNNGYCDETIKILKSQGLETEVFYEVEADPTLAIVNQGASVAKSFQPDVI 538 Query: 539 IALGGTPEMSSAKLMWVLYEHPEVKFEDLAIKFMDIRKRIYTFPKLGKKAMLVAITTSAG 598 IALGG M +AK++WV+YEHPEV F DLA++FMDIRKRIY FPKLGKKA +VAI T++G Sbjct: 539 IALGGGSPMDAAKIIWVMYEHPEVDFADLALRFMDIRKRIYKFPKLGKKAKMVAIPTTSG 598 Query: 599 SGSEVTPFALVTDNNTGNKYMLADYEMTPNMAIVDAELMMKMPKGLTAYSGIDALVNSIE 658 +GSEVTPFA+VTD TG KY +ADYE+TPNMAIVD L+M MPK LTA+ GIDA+ +++E Sbjct: 599 TGSEVTPFAVVTDEQTGMKYPIADYELTPNMAIVDPNLVMDMPKSLTAFGGIDAITHALE 658 Query: 659 AYTSVYASEYTNGLALEAIRLIFKYLPEAYKNGRTNEKAREKMAHASTMAGMASANAFLG 718 AY SV A+EY++G AL+A+ L+ KYLP++Y G AREK+ + +T+AG+A ANAFLG Sbjct: 659 AYVSVMANEYSDGQALQALDLLVKYLPDSYALGAQAPVAREKVHNGATIAGIAFANAFLG 718 Query: 719 LCHSMAIKLSSEHNIPSGIANALLIEEVIKFNAVDNPVKQAPCPQYKYPNTIFRYARIAD 778 +CHSMA KL +E ++ G+ANALLI VI+FNA D P KQA QY P + RYA+IA+ Sbjct: 719 ICHSMAHKLGAEFHLAHGLANALLISNVIRFNATDLPTKQAAFSQYDRPKALCRYAKIAE 778 Query: 779 YIKLGGNT-----DEEKVDLLINKIHELKKALNIPTSIKDAGVLEENFYSSLDRISELAL 833 ++KL G T DEEKV+ L+ KI ELKK + IP SI++AGV E +F++ LD ++E A Sbjct: 779 HLKLKGATGEGISDEEKVEALLEKIDELKKTIGIPASIQEAGVNEADFFAKLDELAEDAF 838 Query: 834 DDQCTGANPRFPLTSEIKEMYINCF 858 DDQCTGANPR+PL +E+K + F Sbjct: 839 DDQCTGANPRYPLIAELKAILTASF 863 Lambda K H 0.317 0.134 0.378 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: 1761 Number of extensions: 82 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: 862 Length of database: 872 Length adjustment: 42 Effective length of query: 820 Effective length of database: 830 Effective search space: 680600 Effective search space used: 680600 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 (21.6 bits) S2: 56 (26.2 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