Align aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized)
to candidate AZOBR_RS32240 AZOBR_RS32240 acetaldehyde dehydrogenase
Query= CharProtDB::CH_018413 (862 letters) >FitnessBrowser__azobra:AZOBR_RS32240 Length = 886 Score = 1009 bits (2610), Expect = 0.0 Identities = 495/860 (57%), Positives = 654/860 (76%), Gaps = 4/860 (0%) Query: 1 MKVTTVKELDEKLKVIKEAQKKFSCYSQEMVDEIFRNAAMAAIDARIELAKAAVLETGMG 60 M VTT+ +L++ + ++EAQK ++ + QE VD IFR+AA+AA +ARI LAK AV ET MG Sbjct: 1 MPVTTLADLNDLVLRVREAQKVYAGFPQETVDRIFRSAALAAANARIPLAKLAVAETRMG 60 Query: 61 LVEDKVIKNHFAGEYIYNKYKDEKTCGIIERNEPYGITKIAEPIGVVAAIIPVTNPTSTT 120 ++EDKV+KNHFA EYIYNKYKDEKTCGI+E + YGI IAEP+G++ AI+P TNPTST Sbjct: 61 VMEDKVVKNHFASEYIYNKYKDEKTCGILEEDPEYGIMTIAEPVGLICAIVPTTNPTSTA 120 Query: 121 IFKSLISLKTRNGIFFSPHPRAKKSTILAAKTILDAAVKSGAPENIIGWIDEPSIELTQY 180 IFK+LISLKTRNGI FSPHPRA+K+T AA+ +L AAV++GAP +IIGWIDEPS++L+ Sbjct: 121 IFKALISLKTRNGIVFSPHPRARKATCEAARIVLQAAVEAGAPADIIGWIDEPSVDLSNA 180 Query: 181 LMQKADITL--ATGGPSLVKSAYSSGKPAIGVGPGNTPVIIDESAHIKMAVSSIILSKTY 238 +M DI L ATGGP +VK+AYSSGKPAIGVG GNTP +IDE A IK AV+SI++SKT+ Sbjct: 181 VMHHPDINLILATGGPGMVKAAYSSGKPAIGVGAGNTPAVIDEFADIKRAVASILMSKTF 240 Query: 239 DNGVICASEQSVIVLKSIYNKVKDEFQERGAYIIKKNELDKVREVIFKDGSVNPKIVGQS 298 DNGV+CASEQS IV+ ++Y+ V+D F G +I+ + D VR+V+ K+G++N IVGQS Sbjct: 241 DNGVVCASEQSAIVVDAVYDAVRDRFAHHGGHILSGTDADAVRKVLLKNGALNADIVGQS 300 Query: 299 AYTIAAMAGIKVPKTTRILIGEVTSLGEEEPFAHEKLSPVLAMYEADNFDDALKKAVTLI 358 A IAAMAG+ VP T++LI EV ++ E+EPFAHEKLSP LA+Y A +F DA KA L+ Sbjct: 301 AGAIAAMAGVSVPANTKVLIAEVEAVTEDEPFAHEKLSPTLALYRARDFMDACDKAAALV 360 Query: 359 NLGGLGHTSGIYADEIKARDKIDRFSSAMKTVRTFVNIPTSQGASGDLYNFRIPPSFTLG 418 LGG+GHTS +Y D+ + ++I F AMKT R +N P+SQG GDLYNFR+ PS TLG Sbjct: 361 ALGGIGHTSALYTDQDQQPERIRHFGQAMKTARILINTPSSQGGIGDLYNFRLAPSLTLG 420 Query: 419 CGFWGGNSVSENVGPKHLLNIKTVAERRENMLWFRVPHKVYFKFGCLQFALKDLKDLKKK 478 CG WGGNS+SENVGP+HL+N KTVA+R ENMLW ++P +YF+ GCL FAL++L+ KK Sbjct: 421 CGSWGGNSISENVGPQHLINRKTVAKRAENMLWHKLPKSIYFRRGCLPFALEELRG--KK 478 Query: 479 RAFIVTDSDPYNLNYVDSIIKILEHLDIDFKVFNKVGREADLKTIKKATEEMSSFMPDTI 538 R IVTD + +VD ++IL+ L + + F +V + L +++ ++F PD I Sbjct: 479 RCLIVTDRFLFENGHVDETVRILKGLGLAVETFFEVAADPTLAVVRRGLALANAFQPDVI 538 Query: 539 IALGGTPEMSSAKLMWVLYEHPEVKFEDLAIKFMDIRKRIYTFPKLGKKAMLVAITTSAG 598 +ALGG M +AK+MWV+YE P+V FEDLA++FMDIRKRIYTFPKLG KA VA+ T++G Sbjct: 539 LALGGGSPMDAAKIMWVMYEAPDVAFEDLALRFMDIRKRIYTFPKLGVKAQFVAVPTTSG 598 Query: 599 SGSEVTPFALVTDNNTGNKYMLADYEMTPNMAIVDAELMMKMPKGLTAYSGIDALVNSIE 658 +GSEVTPFA+VTD TG KY +ADYE+TPNMAI+DA L+M MPKGLTA GIDA+ +++E Sbjct: 599 TGSEVTPFAVVTDERTGIKYPIADYELTPNMAIIDANLVMDMPKGLTAAGGIDAVTHALE 658 Query: 659 AYTSVYASEYTNGLALEAIRLIFKYLPEAYKNGRTNEKAREKMAHASTMAGMASANAFLG 718 AY SV A+EYT+G AL+A++L+ ++LP AY NG + KARE++ A+T+AG+A ANAFLG Sbjct: 659 AYVSVLANEYTDGQALQALKLLKEHLPSAYANGGKDPKAREQVHSAATLAGIAFANAFLG 718 Query: 719 LCHSMAIKLSSEHNIPSGIANALLIEEVIKFNAVDNPVKQAPCPQYKYPNTIFRYARIAD 778 +CHSMA KL +E ++P G+ANALLI VI++NA D P KQ QY P + RYA IA Sbjct: 719 VCHSMAHKLGAEFHLPHGVANALLIANVIRYNAADIPTKQTAFSQYDRPKGVARYAEIAR 778 Query: 779 YIKLGGNTDEEKVDLLINKIHELKKALNIPTSIKDAGVLEENFYSSLDRISELALDDQCT 838 ++ LGG+ D E+V+ L+ + ELK+ L+IP SI+ AGV E F + LD I+E A DDQCT Sbjct: 779 HLGLGGSRDHERVETLVAWVEELKRTLDIPASIQAAGVPEAEFLARLDAIAEAAFDDQCT 838 Query: 839 GANPRFPLTSEIKEMYINCF 858 GANPRFPL +EI+++ ++ + Sbjct: 839 GANPRFPLVAEIRQLLLDSY 858 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: 1771 Number of extensions: 79 Number of successful extensions: 3 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: 886 Length adjustment: 42 Effective length of query: 820 Effective length of database: 844 Effective search space: 692080 Effective search space used: 692080 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