GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Verminephrobacter eiseniae EF01-2

Align rhamnulose-1-phosphate aldolase (EC 4.1.2.19) / lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_011809870.1 VEIS_RS10335 bifunctional rhamnulose-1-phosphate aldolase/short-chain dehydrogenase

Query= reanno::Smeli:SMc02322
         (699 letters)



>NCBI__GCF_000015565.1:WP_011809870.1
          Length = 702

 Score =  857 bits (2214), Expect = 0.0
 Identities = 428/690 (62%), Positives = 522/690 (75%), Gaps = 4/690 (0%)

Query: 14  WDDGKAAGMTEPEKLLYRSNLLGSDKRITNYGGGNTSAKVMEKDPLTGEIVEVLWVKGSG 73
           WD   AA +     LLYRSNLLGSD RITNYGGGNTSAK+ + DPLTG+ V+VLWVKGSG
Sbjct: 13  WDANHAATLDAARLLLYRSNLLGSDLRITNYGGGNTSAKIWQADPLTGQQVQVLWVKGSG 72

Query: 74  GDVGTIKMDGFSTLYMDKLRALKGIYRGVEFEDEMVGYLPHCTFNLNPRAASIDTPLHAY 133
           GD+G++ +DGFSTLYMDKL AL+ IYRG   EDEMVGYLPHCTFNLNPR ASIDTPLHAY
Sbjct: 73  GDLGSMALDGFSTLYMDKLLALQAIYRGPGHEDEMVGYLPHCTFNLNPRVASIDTPLHAY 132

Query: 134 VPKPHVDHMHPDAIIAIAASKNSRELTSKIFGDEIGWLPWKRPGYELGLWLEKFCQENPD 193
           +P  HVDHMHPDA+IAIAA  +S +LT +IF   +GWLPW+RPG+ELGL L+++   +P 
Sbjct: 133 LPFAHVDHMHPDAVIAIAAMADSEKLTQQIFAGTVGWLPWRRPGFELGLMLQRYQAAHPG 192

Query: 194 ARGVVLESHGLFTWGDTAKEAYETTIEIINRAIAWFETENTG---PAFGGRSKPVLAAAD 250
            RG+VL  HGLF+WGD A+  Y+ T+ +I  A  W + E      P+FGG ++  L+  +
Sbjct: 193 QRGLVLAGHGLFSWGDDARACYDNTVGLIASAQNWLDRERVVRQVPSFGGPARQALSQDE 252

Query: 251 RAAIAKKLMPVIRGLISAGESKVGHFDDSQAVLDFVTSTSLEPLAALGTSCPDHFLRTKI 310
           + A   +++PV+RGL S    K+ H +   AVL+FV S  L PLAALGTSCPDHFLRTKI
Sbjct: 253 QDATLARVLPVLRGLASKTGPKLLHVERQAAVLEFVNSRDLAPLAALGTSCPDHFLRTKI 312

Query: 311 RPLVVDFDPAQPDVGNTLAGLPEAIATYRADYAAYYERCKRADSPAMRDPNAVVYLVPGV 370
           RPL+++              L E +A YRADY AYY+RC+RADSPA+RD N V+ L+PG+
Sbjct: 313 RPLILEPAVYMLQGAALAQALQERLAAYRADYGAYYQRCRRADSPALRDANPVIVLLPGI 372

Query: 371 GMITFAKDKATARISAEFYVNAINVMRGASGVSTYVGLPEQEAFDIEYWLLEEAKLQRMP 430
           GM+  AKDKATARI+AEFYVNAINVMR A  +  YVGLPEQEAFDIEYW LEEAKLQR P
Sbjct: 373 GMVAMAKDKATARIAAEFYVNAINVMREAHAIDRYVGLPEQEAFDIEYWWLEEAKLQRSP 432

Query: 431 KPKSLAGRIALVTGGAGGIGKATANRLMQEGACVVLADIDETALEAAQTELSTRYGKDFV 490
            PK LAG++ALVTGGAGGIG+A A R++ EGACVVL DID+ AL     EL+  +G D V
Sbjct: 433 PPKPLAGKVALVTGGAGGIGRAIARRVLAEGACVVLVDIDQGALATVTAELAQAHGPDHV 492

Query: 491 RSVNMNVTSEAAVESGFGDALLAFGGLDILVSNAGLATSAAVEDTTLALWNKNMDILATG 550
           R +  +VTSEA+V + F  A L FGGLDI VSNAG+A +A +EDT++ LWN +  +LATG
Sbjct: 493 RGLQCDVTSEASVIAAFRHAALEFGGLDIAVSNAGIAAAAPLEDTSIELWNHSQGVLATG 552

Query: 551 YFLVSREAFRIFRNQKAGGNVVFVASKNGLAASPGASAYCTAKAAEIHLARCLALEGASA 610
           YFLV REAFR+ + Q AGG++V +ASKNG+ ASP ASAYC AKAAEI L+R  ALEGA  
Sbjct: 553 YFLVGREAFRLMKAQGAGGSIVVIASKNGMVASPQASAYCAAKAAEIQLSRSFALEGAPW 612

Query: 611 QIRVNVVNPDAVLRGSKIWTGEWKEQRAAAYKMDVDELEAHYRERSMLKLSVFPEDIAEA 670
            IR NVVNPDAV+RGS+IW+G+W  +RAAA K+   +LEA YR+RSMLK SV PEDIAEA
Sbjct: 613 GIRSNVVNPDAVIRGSRIWSGKWSAERAAANKIAEQDLEAFYRDRSMLKRSVLPEDIAEA 672

Query: 671 IYFLASD-MSAKSTGNIVNVDAGNAQSFTR 699
            YF A++ +SAKSTGNI+NVDAGN  +FTR
Sbjct: 673 AYFFAAERLSAKSTGNILNVDAGNLAAFTR 702


Lambda     K      H
   0.317    0.133    0.393 

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: 1231
Number of extensions: 36
Number of successful extensions: 5
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: 699
Length of database: 702
Length adjustment: 39
Effective length of query: 660
Effective length of database: 663
Effective search space:   437580
Effective search space used:   437580
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 (21.7 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