Align aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized)
to candidate WP_089136810.1 CES79_RS07645 bifunctional acetaldehyde-CoA/alcohol dehydrogenase
Query= CharProtDB::CH_018413 (862 letters) >NCBI__GCF_002217945.1:WP_089136810.1 Length = 873 Score = 705 bits (1819), Expect = 0.0 Identities = 387/860 (45%), Positives = 567/860 (65%), Gaps = 19/860 (2%) Query: 3 VTTVKELDEKLKVIKEAQKKFSCYSQEMVDEIFRNAAMAAIDARIELAKAAVLETGMGLV 62 V+ + +D + +A ++QE VD I A+A +D + LAK AV ETG G+ Sbjct: 18 VSVNEHIDALVNKAHDALCGMDDFTQEKVDHIVHQMAIAGLDQHMRLAKLAVDETGRGVW 77 Query: 63 EDKVIKNHFAGEYIYNKYKDEKTCGIIERNEPYGITKIAEPIGVVAAIIPVTNPTSTTIF 122 EDK IKN FA E I++ K++KT GIIE ++ + K+AEP+G++A + PVTNPTSTT+F Sbjct: 78 EDKAIKNMFATEEIWHSIKNDKTVGIIEDDKERQLIKVAEPLGILAGVTPVTNPTSTTMF 137 Query: 123 KSLISLKTRNGIFFSPHPRAKKSTILAAKTILDAAVKSGAPENIIGWIDEPSIELTQYLM 182 KSLI++KTRN I F HP+A+KS++ AAK + DAA+ +GAPE +I WI+EPS+E T LM Sbjct: 138 KSLIAVKTRNPIIFGFHPQAQKSSVAAAKVMRDAAIAAGAPEGVIQWIEEPSLEATTALM 197 Query: 183 Q--KADITLATGGPSLVKSAYSSGKPAIGVGPGNTPVIIDESAHIKMAVSSIILSKTYDN 240 K LATGGP +VK+AYS+GKPA+GVGPGN P I+++A+IK AV+ I+LSKT+DN Sbjct: 198 NHPKVASVLATGGPGMVKAAYSTGKPALGVGPGNGPAYIEKTANIKRAVNDIVLSKTFDN 257 Query: 241 GVICASEQSVIVLKSIYNKVKDEFQERGAYIIKKNELDKVREVIF--KDGSVNPKIVGQS 298 G+ICA+E SVI+ IYN VK E + R + IKK + + + ++ K GSV I G + Sbjct: 258 GMICATENSVIIDADIYNDVKQEMKARKVFFIKKADQKALADAMYDPKRGSVKGPIAGMA 317 Query: 299 AYTIAAMAGIKVPKTTRILIGEVTSLGEEEPFAHEKLSPVLAMYEADNFDDALKKAVTLI 358 A IA +AGI VP+ T++L E+T++G + + EKL PV+++Y++ + + K A L+ Sbjct: 318 AVKIAKLAGIDVPEDTKVLAAELTTVGPDNMLSAEKLCPVISVYKSADHKEGFKIANDLL 377 Query: 359 NLGGLGHTSGIYADEIKARDKIDRFSSAMKTVRTFVNIPTSQGASGDLYNFRIPPSFTLG 418 + GGLGHT+ I+ ++ D + MK R VN P++ G G+LYN I PS TLG Sbjct: 378 HFGGLGHTAAIHTED---EDLATEYGIKMKASRVLVNTPSALGGIGNLYNEMI-PSLTLG 433 Query: 419 CGFWGGNSVSENVGPKHLLNIKTVAERRENMLWFRVPHKVYFKFGCLQFALKDLKDLKKK 478 G WG NSVS NV LLNIKT+A+RR NM W ++P +VYF+ +++ L + +KK Sbjct: 434 TGSWGKNSVSHNVSSFDLLNIKTIAKRRNNMQWIKLP-RVYFEKTSVRY-LGSMPGVKK- 490 Query: 479 RAFIVTDSDPYNLNYVDSIIKILEHL--DIDFKVFNKVGREADLKTIKKATEEMSSFMPD 536 AFIV D +L YVD ++ L+ I++++F+ + + T++K +M +F PD Sbjct: 491 -AFIVADPAMISLGYVDKVLGELKRRPDGIEYQLFSVMESDPTTDTVEKGYAQMKAFKPD 549 Query: 537 TIIALGGTPEMSSAKLMWVLYEHPEVKFEDLAIKFMDIRKRIYTFPKLGKKAMLVAITTS 596 TIIALGG M +AK MW+ YEHP+ F KF+DIRKR Y F K KKA VAI T+ Sbjct: 550 TIIALGGGSPMDAAKCMWLFYEHPDASFFGAKQKFLDIRKRTYQFEK-AKKAQFVAIPTT 608 Query: 597 AGSGSEVTPFALVTDNNTGNKYMLADYEMTPNMAIVDAELMMKMPKGLTAYSGIDALVNS 656 +G+GSEVTPFA++TD+ T KY LADY +TP++AIVD++ + +PK +++G+D L + Sbjct: 609 SGTGSEVTPFAVITDSKTHVKYPLADYALTPDVAIVDSQFIESLPKKTISWAGLDVLTHG 668 Query: 657 IEAYTSVYASEYTNGLALEAIRLIFKYLPEAYKNGRTNEKAREKMAHASTMAGMASANAF 716 IE++ S AS+YT +L+AI+L+F L +Y NG ++ ARE+M +A+T+AGMA ANAF Sbjct: 669 IESFVSNMASDYTRPWSLQAIKLVFDNLTASY-NG--DQHAREEMHNAATIAGMAFANAF 725 Query: 717 LGLCHSMAIKLSSEHNIPSGIANALLIEEVIKFNAVDNPVKQAPCPQYKYPNTIFRYARI 776 LG+ HS+A KL E +P G+A A+ + VI++N P K P+Y+Y YA I Sbjct: 726 LGVNHSIAHKLGGEFGLPHGLAIAITLPHVIRYN-FKEPRKLTTWPKYEYFRADEDYAEI 784 Query: 777 ADYIKLGGNTDEEKVDLLINKIHELKKALNIPTSIKDAGVLEENFYSSLDRISELALDDQ 836 A Y+ L G +EE + L++KI +L ++++ S+K GV +++F +D ++ELA +DQ Sbjct: 785 ARYVGLTGKNNEELKEALVHKIIDLAHSVDVTLSLKANGVDKKHFDEKVDDLAELAYEDQ 844 Query: 837 CTGANPRFPLTSEIKEMYIN 856 CT ANP+ PL E++++ I+ Sbjct: 845 CTTANPKEPLIGELRQIMID 864 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: 1773 Number of extensions: 84 Number of successful extensions: 11 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: 873 Length adjustment: 42 Effective length of query: 820 Effective length of database: 831 Effective search space: 681420 Effective search space used: 681420 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 24 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