GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rhaD 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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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