GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Weissella oryzae SG25

Align alcohol dehydrogenase (EC 1.1.1.1); acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10) (characterized)
to candidate WP_027698995.1 TT13_RS05060 bifunctional acetaldehyde-CoA/alcohol dehydrogenase

Query= BRENDA::C7IV28
         (872 letters)



>NCBI__GCF_000691805.2:WP_027698995.1
          Length = 900

 Score =  721 bits (1862), Expect = 0.0
 Identities = 398/897 (44%), Positives = 558/897 (62%), Gaps = 37/897 (4%)

Query: 7   EKKETKEKTEVKETTDVKKQIDLLVERAKRAQEKFMSYTQEQINEIVKAMALAGIEKHVE 66
           +KK    + +       K+    LV++A+ A ++F +Y+Q Q+++IV AMALAG E  + 
Sbjct: 8   KKKVLTAEEKAARFEAAKEMTSALVDKAEIALKEFSTYSQAQVDKIVAAMALAGSENSLL 67

Query: 67  LAKLAHEETKMGVYEDKITKNLFAVEYVYNYIKDKKTVGILKENLEENYMEVAEPVGVIA 126
           LA  A+ ET  GV EDK TKN FA E VYN IK  KTVG++ E+     +E+A P+G++A
Sbjct: 68  LAHEAYAETGRGVVEDKDTKNRFASESVYNAIKKDKTVGVINEDRVTGKVELAAPLGILA 127

Query: 127 GVTPVTNPTSTTMFKCLIAIKTRNPIIFSFHPKALKCSIEAAKTMYEAALKAGAPEGCIG 186
           G+ P TNPTST +FK ++  KTRN I+F+FHP+A K S  AAK +YEAA+ AGAP+  I 
Sbjct: 128 GIVPTTNPTSTAIFKSMLTAKTRNVIVFAFHPQAQKSSSHAAKIVYEAAVAAGAPKNFIQ 187

Query: 187 WIETPSIEATQLLMTHPDISLILATGGAGMVKAAYSSGKPALGVGPGNVPCYIEKTANIK 246
           WIETPS++ T  L+ +P I+ ILATGG  MV AA  SG P++GVG GN   YI+KTANI 
Sbjct: 188 WIETPSLDGTSALIQNPKIASILATGGPSMVNAALRSGNPSMGVGAGNGAVYIDKTANIN 247

Query: 247 RAVSDLILSKTFDNGTVCASEQAVIIDEEIADEVKKLMREYGCYFLNKEETKKLEEFAID 306
           RAV DL+LSK FDNG +CA+E +V+ID  + DE    ++  G Y   K +  K+  F   
Sbjct: 248 RAVEDLLLSKRFDNGMICATENSVVIDASVYDEFMAKLQAQGAYLTPKRDYDKIANFVFK 307

Query: 307 KNT---GLMNPAVVGQPATKIAQMAGFKVPENTKILVAEYPAVGPEYPLSREKLSPILAL 363
            N    G+  P V G     IA+ AG K+P +  +L+ E         LS EKLSP+L++
Sbjct: 308 PNAEGFGVAGP-VAGMSGQWIAKNAGVKIPADKDVLLFELDKKNIGEALSSEKLSPLLSV 366

Query: 364 YTVKDYKEGIKRCEEMIQFGGLGHSAVIH--SENQQIINEFANRVQASRILVNAPASQGA 421
           Y   D +EGI+  + ++ + G GH+A I   +++   + E+A+ +  +RILVN P S G 
Sbjct: 367 YKAADRQEGIEIVQSLLNYQGAGHNAAIQIGAQDDPFVKEYADAIGVARILVNQPDSIGG 426

Query: 422 IGDIYNTAI-PSLTLGCGTMGGNSTTDNVSIYNLINIKRVFIRKERMKWFRVPPQIYFER 480
           +GDIY  A+ PSLTLG G+ G NS + N+S Y+L+NIK V  R+ R +W R+P  IY+E 
Sbjct: 427 VGDIYTDALRPSLTLGTGSWGKNSLSHNLSTYDLLNIKTVARRRNRPQWVRIPNNIYYES 486

Query: 481 GSLQYLSQVKS-KKAFIVTDPAMVKLGFIDKV--TYQLDKANIKHEIFSEVEPDPSVDTV 537
            ++ YL ++    +AFIV DP MVK GF+DKV   + L +  IK  ++  V+PDP++   
Sbjct: 487 NAITYLQELPGVDRAFIVADPGMVKFGFVDKVLDQFALHETVIKTSLYGTVQPDPTLKQA 546

Query: 538 EKGVKIMKEFQPDLIIAVGGGSPIDAAKGMWLFYEYPDTK---------------FEDLR 582
               + M +FQPD +I +GGGS +DA K     YEY                   F+ + 
Sbjct: 547 IDIARQMAQFQPDTVITIGGGSALDAGKVGRFIYEYAQQPGHEGILDDDRALKELFQQMA 606

Query: 583 LKFMDIRKRTYKFPELGKKALFIAVPTTSGTGSEVTAFAVITDKKRNIKYPLADYELTPD 642
            KFMDIRKR  KF       L +A+PTTSGTGSEVT FAVITD + ++KYPLADYELTP 
Sbjct: 607 QKFMDIRKRIVKFDHQVLTQL-VAIPTTSGTGSEVTPFAVITDDETHVKYPLADYELTPQ 665

Query: 643 IAIIDPDLTMTIPPSVTADTGMDALTHAIEAYVSVMASDYTDALAEKAIKLIFEYLPKAY 702
           +AI+DP+  MT+P    A +G+DAL+HA+E+YVSVM+S +T   A +AIK IF+ L  +Y
Sbjct: 666 VAIVDPEFVMTVPKRTVAFSGLDALSHALESYVSVMSSQFTRPWALQAIKCIFDNLETSY 725

Query: 703 --------KNGQDKVAREKMHNASCIAGMAFTNAFLGINHSMAHILGAKFHLPHGRANAI 754
                   K GQ  +AR K+H A+ +AGM+F NAFLG+NHS+AH +G +F LPHG A  I
Sbjct: 726 HYDPAHPTKEGQ--IARAKVHYAATLAGMSFANAFLGLNHSLAHKIGGEFGLPHGLAITI 783

Query: 755 LLPYVIEYNAELPK-KFAAFPQYEYPKAAEKYAEIAKMLGLPASTVEEGVKSLIEAIKNL 813
            + +VI++NA     K   FP+YE   A + YA+IA+ +GL        V +L++ IK+L
Sbjct: 784 AMSHVIKFNAVTGNVKRTPFPRYETYTAQKDYADIARHIGLEGKDDAALVDALLKKIKDL 843

Query: 814 MKELNLPLTLKEAGINKEEFEKQIMEMSDIAFNDQCTGSNPRMPLVSEIAEIYRKAY 870
              L++  TL   G+ K+     I +++D+ ++DQCT  NPR P +SEI E+    Y
Sbjct: 844 AAALDVNTTLSGNGVTKDALTNSIDKLTDLVYDDQCTPGNPRQPRLSEIKELLNDLY 900


Lambda     K      H
   0.316    0.133    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: 1800
Number of extensions: 77
Number of successful extensions: 10
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: 872
Length of database: 900
Length adjustment: 43
Effective length of query: 829
Effective length of database: 857
Effective search space:   710453
Effective search space used:   710453
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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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