GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Escherichia coli BW25113

Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate 15740 b1619 7-alpha-hydroxysteroid dehydrogenase (NCBI)

Query= reanno::pseudo6_N2E2:Pf6N2E2_5967
         (272 letters)



>FitnessBrowser__Keio:15740
          Length = 255

 Score =  131 bits (330), Expect = 1e-35
 Identities = 81/248 (32%), Positives = 131/248 (52%), Gaps = 6/248 (2%)

Query: 18  RLKNKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAEKVETVAAHWRERGADVHALKA 77
           RL  K  ++TGA  GIG+ I   FA+  A +V+SDI A+    V    ++ G    A + 
Sbjct: 8   RLDGKCAIITGAGAGIGKEIAITFATAGASVVVSDINADAANHVVDEIQQLGGQAFACRC 67

Query: 78  DVSNQQDLHAMARHAVERHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYGC 137
           D++++Q+L A+A  A+ + G++D+LVN AG    + P +M   D+RR + +++   ++  
Sbjct: 68  DITSEQELSALADFAISKLGKVDILVNNAGGGGPK-PFDMPMADFRRAYELNVFSFFHLS 126

Query: 138 KAVLPQMIEQGVGSIINIASTHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVNA 197
           + V P+M + G G I+ I S  + +       Y  +K     L R +  +   K +RVN 
Sbjct: 127 QLVAPEMEKNGGGVILTITSMAAENKNINMTSYASSKAAASHLVRNMAFDLGEKNIRVNG 186

Query: 198 IAPGYIETQLNVDYWNGFADPYAERQRALDLHPPRRIGQPIEVAMTAVFLASDEAPFINA 257
           IAPG I T    D       P  E Q+ L   P RR+GQP ++A  A+FL S  A +++ 
Sbjct: 187 IAPGAILT----DALKSVITPEIE-QKMLQHTPIRRLGQPQDIANAALFLCSPAASWVSG 241

Query: 258 SCITIDGG 265
             +T+ GG
Sbjct: 242 QILTVSGG 249


Lambda     K      H
   0.321    0.137    0.419 

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: 133
Number of extensions: 4
Number of successful extensions: 3
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: 272
Length of database: 255
Length adjustment: 25
Effective length of query: 247
Effective length of database: 230
Effective search space:    56810
Effective search space used:    56810
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 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