GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdgA in Klebsiella michiganensis M5al

Align 2-dehydro-3-deoxy-phosphogluconate aldolase; Keto-3-deoxygluconate 6-phosphate aldolase; KDGP aldolase; EC 4.1.2.14 (characterized)
to candidate BWI76_RS02895 BWI76_RS02895 hypothetical protein

Query= SwissProt::D0ZLR2
         (247 letters)



>FitnessBrowser__Koxy:BWI76_RS02895
          Length = 246

 Score =  219 bits (559), Expect = 3e-62
 Identities = 120/244 (49%), Positives = 154/244 (63%), Gaps = 5/244 (2%)

Query: 5   NFYRQRVAINVLAKDIANAKAIYEAAEGHAVIGVLSAQFATVEEGVPEVKRWMAEVPS-I 63
           NFYR RV +NVLA    NA  IYEAAEGH ++GVLS  +  V   V +++ +   + + +
Sbjct: 6   NFYRDRVCLNVLAGSKDNASEIYEAAEGHVLVGVLSKNYPDVASAVADMREYALRIDNAL 65

Query: 64  SVGLGAGDPAQYYKAAMIAAHTHPAHVNQTFTGSGFAAGALAATGGEQTHINALVSPTGT 123
           SVGLGAGDP Q    + I+    P HVNQ FTG    A + A  G   T +N LVSPTGT
Sbjct: 66  SVGLGAGDPNQSAMVSEISRQVQPQHVNQVFTG---VATSRALLGQNDTVVNGLVSPTGT 122

Query: 124 PGEVVISTGVSSSQGTPARVSCEAAVRMMQDMGAHAAKFFPMGGEKSLPELYALATTAAR 183
           PG V ISTG  SS      V  E A+ +++DMG  + K+FPMGG K   E  A+A   AR
Sbjct: 123 PGMVKISTGPLSSGAPDGIVPLETAIALLKDMGGSSIKYFPMGGLKHRDEFIAVAEACAR 182

Query: 184 HGMTLIEPTGGISLDNFGIILQTCLEAGVPRVMPHVYSSIIDPQTGNTRPEDIIRLMEIV 243
           +   L EPTGGI L+N+G ILQ  L+AGV +++PH+YSSIID  +GNTRP D+ +L+ I 
Sbjct: 183 YDFWL-EPTGGIDLENYGEILQIALDAGVSKIIPHIYSSIIDKASGNTRPADVRQLLSIT 241

Query: 244 KALV 247
           K LV
Sbjct: 242 KQLV 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: 165
Number of extensions: 9
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: 247
Length of database: 246
Length adjustment: 24
Effective length of query: 223
Effective length of database: 222
Effective search space:    49506
Effective search space used:    49506
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 17 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