Alignments for a candidate for aldA in Kocuria turfanensis HO-9042

GapMind for catabolism of small carbon sources

Alignments for a candidate for aldA in Kocuria turfanensis HO-9042

Align Lactaldehyde dehydrogenase (EC 1.2.1.22); Rhamnulose-1-phosphate aldolase (EC 4.1.2.19) (characterized)
to candidate WP_062735672.1 AYX06_RS10185 bifunctional rhamnulose-1-phosphate aldolase/short-chain dehydrogenase

Query= reanno::Cola:Echvi_1572
         (702 letters)



>NCBI__GCF_001580365.1:WP_062735672.1
          Length = 681

 Score =  669 bits (1727), Expect = 0.0
 Identities = 342/678 (50%), Positives = 454/678 (66%), Gaps = 8/678 (1%)

Query: 28  VALLIYRSNILGADLRITNYGGGNTSCKTTEVDPLTKEETEVMWVKGSGGDIGTLKRSGL 87
           V  LI RSN LGAD + TNY GGNTS +    DP+T E+ E++WVKGSGGD+GTL   GL
Sbjct: 9   VEALIERSNRLGADPKNTNYAGGNTSAQGPATDPVTGEDVELLWVKGSGGDLGTLTEQGL 68

Query: 88  AGLYVEKLHSLKNVYRGLEFEDEMVGLFNHCIYDLDSKAPSIDTPLHAFLPFKHIDHLHP 147
           A L +++L +L  VY G+E EDEMV  F++C++     APSIDT +H  +   H+DHLHP
Sbjct: 69  ATLRLDRLRALVEVYPGVEREDEMVAAFDYCLHGKGGAAPSIDTAMHGLVDAAHVDHLHP 128

Query: 148 DAAIAIAASKDGEKITEELFEGQIAWVPWQRPGFDLALQLEKALNENPGIRGIMLGGHGL 207
           D+ IA+A + DG+++T E+F  ++ WVPW+RPGF L L +      +P   G +LGGHG+
Sbjct: 129 DSGIAVATAADGQRLTAEIFGDRVVWVPWRRPGFQLGLDIAAVKEAHPEAIGCILGGHGI 188

Query: 208 FTWGDTAYECYINSLEVIDKASEYLEQNYGKD--RPVFGGQKIESLAPEQRQEQASIIAP 265
             WG+T+ E   NS  +ID A  Y++Q+   +   PV  G   E+L   +R+ +A+ +AP
Sbjct: 189 TAWGETSEEAETNSRWIIDTAEAYIDQHSPDEPFGPVLDG--YEALPEAERRAKAAALAP 246

Query: 266 VLRGLASGYNRMVGHFTDDERVLQFANSHDLEKLAPLGTSCPDHFLRTKIRPLVLDFPAD 325
           V+RGLA      VGHFTDD RVL+F  + +  +LA LGTSCPDHFLRTK++PLVLD  AD
Sbjct: 247 VIRGLAGHDRPQVGHFTDDARVLEFLAAAEHPRLAALGTSCPDHFLRTKVKPLVLDLSAD 306

Query: 326 VDLSKADEIKEKLDKDFEEYRAYYKKYYEDHKRDNSPAMRDPNPVVIIWPGVGMFSYAKN 385
              +   E   +L +  E YRA Y+ YY+ H   +SPA+R  +P +++ PGVGMFS+ K+
Sbjct: 307 ---APVQECVSRLQELHEAYRADYQAYYDRHAGPDSPAIRGADPAIVLVPGVGMFSFGKD 363

Query: 386 KQTARVASEFYINAINVMRGAEAVSEYVALPLQEAFDIEYWLLEEAKLQRMPKEQPLSRK 445
           KQTARVA EFY+NAINVMRGAE +S Y  +   E F IEYW LEEAKL RMPK +PL+ +
Sbjct: 364 KQTARVAGEFYLNAINVMRGAEGISSYAPIDEAEKFRIEYWALEEAKLARMPKPKPLATR 423

Query: 446 VALVTGGAGGIGKAIADKLASEGACVFITDINQERLDGAVATY-SKDVGGGAVMDVTKGD 504
           +ALVTG A GIGKAIA +LA+EGACV I D++ E+   A A     DV  G  ++V    
Sbjct: 424 IALVTGAASGIGKAIAARLAAEGACVVIADLDLEKARAAAAELGGPDVAVGVAVNVADEA 483

Query: 505 DIIKAYKAAALKFGGVDIIVNCAGLAISKPIEQTSEQDWDLLQDILVKGQFAVSKAGVET 564
            +  A  AA L FGG+D++VN AGL++SKP+ +T+E DWDL  D++ KG F VSK     
Sbjct: 484 AVQAAIDAAVLGFGGLDLVVNNAGLSLSKPLLETTEADWDLQHDVMAKGSFLVSKNAARV 543

Query: 565 LRAQNLGGDIINIASKNALVSGPNNVGYGTAKAAQVHMSRLLAAELGKDKIRVNVVNPDA 624
           L AQ++GGDI+ I+SKN++ +GPNN+ Y   KA Q H  RLLAAELG+ +IRVN +NPD 
Sbjct: 544 LIAQDMGGDIVYISSKNSVFAGPNNIAYSATKADQAHQVRLLAAELGEHQIRVNGINPDG 603

Query: 625 VIEGSKIWEGEWAKGRAKAYGITVEELPAFYAKRTILNEIIGVDDIANGVFAFVGGHLSK 684
           V+ GS I+ G W   RA  YG+  EEL  FYA+RT+L   +  + +AN VFA   G LS 
Sbjct: 604 VVRGSGIFAGGWGAKRAAVYGVPEEELGKFYAQRTLLKREVLPEHVANAVFALTAGDLSH 663

Query: 685 CTGNILNVDGGVAAAFVR 702
            TG  + VD GVAAAF+R
Sbjct: 664 TTGLHVPVDAGVAAAFLR 681


Lambda     K      H
   0.317    0.136    0.401 

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: 1208
Number of extensions: 49
Number of successful extensions: 4
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: 702
Length of database: 681
Length adjustment: 39
Effective length of query: 663
Effective length of database: 642
Effective search space:   425646
Effective search space used:   425646
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: 54 (25.4 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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 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