Alignments for a candidate for ald-dh-CoA in Lactobacillus oryzae SG293

GapMind for catabolism of small carbon sources

Alignments for a candidate for ald-dh-CoA in Lactobacillus oryzae SG293

Align acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10) (characterized)
to candidate WP_034529506.1 LOSG293_RS08930 bifunctional acetaldehyde-CoA/alcohol dehydrogenase

Query= BRENDA::A0A1D3TRQ6
         (871 letters)



>NCBI__GCF_000740055.1:WP_034529506.1
          Length = 871

 Score =  926 bits (2392), Expect = 0.0
 Identities = 478/873 (54%), Positives = 623/873 (71%), Gaps = 14/873 (1%)

Query: 1   MEEKKIPTAK----EHVNQLVDN----AQIALKEYLKLDQETVDNIVHQMALAGLAKQQE 52
           ++E K  T K    E V+Q++D     A  AL       QE VD+IVHQMA+AGL    +
Sbjct: 2   LKEIKKTTTKIDQNESVDQMIDRLTSKAHDALCAMDDFTQEQVDHIVHQMAMAGLDNHMK 61

Query: 53  LAKMAVEETGRGIYEDKITKNIFATEYIWHSIKYQKTVGIIEENEEDDFMLVAEPIGIVA 112
           LAK+A EETGRG+ EDK  KNIFATE IW+SIK  +TVGII ++ E   + VAEP+GI+A
Sbjct: 62  LAKIAYEETGRGVIEDKAIKNIFATEEIWNSIKNDRTVGIINDDRERQLITVAEPLGILA 121

Query: 113 GVTPVTNPTSTTMFKAISCAKTRNPIIFGFHPSAQQCSKAAALALRDAAIAAGAPENCIQ 172
           GVTPVTNPTSTT+FK++   KTRNPIIF FHP AQ+ S  AA  +  AAIAAGAPE  IQ
Sbjct: 122 GVTPVTNPTSTTLFKSLIAVKTRNPIIFAFHPQAQKSSVEAAKVVAQAAIAAGAPEGVIQ 181

Query: 173 WIEYPSLEATQELMNHPGVALILATGGSGMVKQAYSSGKPALGVGPGNVPCFIEKTAVLE 232
           WI+ PS+EAT  LMNHP VA +LATGG GMVK AYS+GKPALGVGPGN P ++EKTA ++
Sbjct: 182 WIDKPSIEATSALMNHPMVASVLATGGPGMVKSAYSTGKPALGVGPGNGPAYVEKTAKIK 241

Query: 233 RAVNDLVLSKSFDNGMICASEQAAVIEAPVYDKVVALMKKAGCYFATKEEIKKLEPVVIN 292
           RAVND+VLSK+FDNGM+CASE +A+I+A +Y  V A M+    +F  K + +KL   + +
Sbjct: 242 RAVNDIVLSKTFDNGMVCASENSAIIDADIYKDVKAEMEDRKVFFIKKADHQKLADAMFD 301

Query: 293 LEKGAVNPAIVGKAPYQIAALAGITIPKETKVLCTELAGVGPQYPLSKEKLSPVLAVVKA 352
            ++G V   I G +  +IA LAGI +P++TKVL  E+  VGP+  LS EKLSPVL+V K+
Sbjct: 302 PKRGGVKGPIAGMSAVKIAELAGIDVPEDTKVLAAEITKVGPEDWLSAEKLSPVLSVYKS 361

Query: 353 KNVEDGFDLCEKMLILGGMGHSSVLHSTDNEVINAFSNRMKTGRIIINSPSTHGAIGDLY 412
           K+ +D F L   +L  GG+GH++ +H+ D+++   F  +MK  R+++N+PS  G IG++Y
Sbjct: 362 KDHKDAFRLANDLLHFGGLGHTASIHTEDDDLATEFGIKMKASRVLVNTPSAIGGIGNIY 421

Query: 413 NTNMPSLTLGCGSYGGNSTTRNVSAVDLVNVKRVAKRRNNMQWFKIPDRIYFESGSTAYL 472
           N  +PSLTLG GS+G NS + NVS+ DL+N+K +AKRRNNMQW K+P R+YFE  S  YL
Sbjct: 422 NEMIPSLTLGTGSWGKNSVSHNVSSFDLLNIKTIAKRRNNMQWVKLP-RVYFEKTSVRYL 480

Query: 473 SKMPNITKAFIVTDPSMTQLGYVNKVLYQLRKREQYVHCEIFDQVEPDPSLDTINKGVEA 532
           + MP I K FIV  PSM + GYV+KVL +L++R   +   +F   E DP+ DT+NKG E 
Sbjct: 481 NSMPGIQKVFIVASPSMIEHGYVDKVLGELKRRPNEIEYSLFAVRESDPTTDTVNKGTEQ 540

Query: 533 MKNFNPDVIIALGGGSAIDAAKGMWLFYEHPEADFKNMSLKFLDIRKRAYKFPMLGKKAQ 592
           M+ F PD IIALGGGS +DAAKGMWLFYEHP+A F     KFLDIRKR Y+      KAQ
Sbjct: 541 MRTFQPDTIIALGGGSPMDAAKGMWLFYEHPDASFFGAKQKFLDIRKRTYELEK-PNKAQ 599

Query: 593 FVAIPTTSGTGSEVTSFAVISDKTENKKYPLADYELTPDVAIIDPDFVMSVPKKSTAWTG 652
           F+AIPTTSGTGSEVT FAVI+D   + KYPLADY LTPDVAI+D  FV +VPK + A++G
Sbjct: 600 FIAIPTTSGTGSEVTPFAVITDAKTHVKYPLADYALTPDVAIVDSQFVQTVPKGTVAYSG 659

Query: 653 MDVLTHAFEAYVSIMASDYSDALAVKAIELVFQYLKSSFTNGAKDPTAREKMHNASTIAG 712
           +D L+HA E++V+ MASDY+  L+++AI+LV + L  S+ NG  D TAREKMHNA+T+AG
Sbjct: 660 LDTLSHAIESFVANMASDYTRPLSLQAIKLVMENLTDSY-NG--DATAREKMHNAATLAG 716

Query: 713 MAFTNAFLGINHSLAHKLGGEFHVPHGCANAILLPHVIRYNGAECPTKFTAFPKYEHYIV 772
           MAF NAFLG+NHS+AHKLGGEF +PHG A  I +PHVIRYN  E P K T +PKYE++  
Sbjct: 717 MAFANAFLGVNHSIAHKLGGEFGLPHGLAIMITMPHVIRYNFKE-PKKLTMWPKYEYFRA 775

Query: 773 GDKIFDLAKKLGLNPKNNNDAVEKFAQEVEKLNEYLEIPATLKEFGIEEKAFSNKVDELA 832
            +   ++A+ LGL      + +E   Q+V  L   + +  +LK  G+++  F + VD LA
Sbjct: 776 DEDYAEIARYLGLKGNTKEELMEALVQKVIDLAHSVGVTLSLKANGVDKAHFESAVDHLA 835

Query: 833 DLAFGDQCTTANPRLPLVTELKDLYMIAYYGKG 865
           +LA+ DQCTTANP+ PL++ELK + +  Y GKG
Sbjct: 836 ELAYEDQCTTANPKEPLISELKQIMIDEYDGKG 868


Lambda     K      H
   0.317    0.133    0.385 

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: 1858
Number of extensions: 79
Number of successful extensions: 6
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: 871
Length of database: 871
Length adjustment: 42
Effective length of query: 829
Effective length of database: 829
Effective search space:   687241
Effective search space used:   687241
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources