GapMind for catabolism of small carbon sources

 

Alignments for a candidate for eda in Collinsella tanakaei YIT 12063

Align 2-dehydro-3-deoxy-phosphogluconate aldolase; Keto-3-deoxygluconate 6-phosphate aldolase; KDGP aldolase; EC 4.1.2.14 (characterized)
to candidate WP_009140812.1 HMPREF9452_RS03910 KDGP aldolase family protein

Query= SwissProt::D0ZLR2
         (247 letters)



>NCBI__GCF_000225705.1:WP_009140812.1
          Length = 245

 Score =  214 bits (546), Expect = 1e-60
 Identities = 120/249 (48%), Positives = 164/249 (65%), Gaps = 6/249 (2%)

Query: 1   MQQINFYRQRVAINVLAKDIANAKAIYEAAEGHAVIGVLSAQFATVEEGVPEVKRWMAEV 60
           M  IN+Y  RV +NVLA  + NA+ IY+AAEGH  +GVL+A +  VE  V ++ ++M  +
Sbjct: 1   MTNINYYNDRVCLNVLAGCLENARDIYKAAEGHVEVGVLTANYPDVETCVEDMAKYMEVL 60

Query: 61  P-SISVGLGAGDPAQYYKAAMIAAHTHPAHVNQTFTGSGFAAGALAATGGEQTHINALVS 119
             ++SVGLG G+PAQ+   A +A      H NQ F+  G+     A  G +++HINALVS
Sbjct: 61  EGNLSVGLGGGNPAQWRAVADVAKTIKANHFNQVFSAVGWTR---ANVGNDESHINALVS 117

Query: 120 PTGTPGEVVISTG-VSSSQGTPARVSCEAAVRMMQDMGAHAAKFFPMGGEKSLPELYALA 178
           PTGTPG+V ISTG +S     PA VS + A+ M+++MG ++ KFFPMGG K   EL A+A
Sbjct: 118 PTGTPGKVKISTGPLSKDCADPATVSVDTAITMIKEMGGNSLKFFPMGGLKVRDELKAVA 177

Query: 179 TTAARHGMTLIEPTGGISLDNFGIILQTCLEAGVPRVMPHVYSSIIDPQTGNTRPEDIIR 238
              AR    L EPTGGI LDNF  I++  ++AGV R++PHVYSSIID  TG T+ E + +
Sbjct: 178 EACAREDFCL-EPTGGIDLDNFEEIMRIIIDAGVKRIIPHVYSSIIDKSTGCTKIECVEQ 236

Query: 239 LMEIVKALV 247
           L+ +VK LV
Sbjct: 237 LLNMVKTLV 245


Lambda     K      H
   0.317    0.131    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: 189
Number of extensions: 10
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: 247
Length of database: 245
Length adjustment: 24
Effective length of query: 223
Effective length of database: 221
Effective search space:    49283
Effective search space used:    49283
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: 46 (22.3 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