GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Cupriavidus basilensis 4G11

Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate RR42_RS28045 RR42_RS28045 3-oxoacyl-ACP reductase

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



>FitnessBrowser__Cup4G11:RR42_RS28045
          Length = 249

 Score =  158 bits (399), Expect = 1e-43
 Identities = 92/252 (36%), Positives = 143/252 (56%), Gaps = 11/252 (4%)

Query: 18  RLKNKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAEKVETVAAHWRERGADVHALKA 77
           ++K KV ++TG+A+G+G A     A +  ++VI+DI  E+ E  AA  R  G   H + A
Sbjct: 4   QIKGKVAIVTGSARGLGAATARHLAQEGVKVVITDILREQAEATAAALRADGLQAHCIVA 63

Query: 78  DVSNQQDLHAMARHAVERHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYGC 137
           D++   D+  +    +   G + +LVN AG    +  ++MTEEDW     + L GA+   
Sbjct: 64  DITRGADVQRLVDETIAHFGGVHILVNNAGFPRDKYLVKMTEEDWDLVMEVMLKGAFLAT 123

Query: 138 KAVLPQMIEQGVGSIINIAS-THSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVN 196
           KAV+P++IEQG G +INI+S  H  +  P    Y  AK GL+G+ +AL +E    GV VN
Sbjct: 124 KAVMPRLIEQGWGRVINISSRAHFGN--PTQANYAAAKAGLIGMAKALALEQGRYGVTVN 181

Query: 197 AIAPGYIETQLNVDYWNGFADPYAE--RQRALDLHPPRRIGQPIEVAMTAVFLASDEAPF 254
            +APG++ET++        A P  E  ++RA+   P +R+G+P ++A    FLAS+ A F
Sbjct: 182 CVAPGFMETEMVQ------ALPTYETIKERAVAAQPIKRVGRPGDIADAVAFLASERASF 235

Query: 255 INASCITIDGGR 266
           I    + + GGR
Sbjct: 236 ITGEVLHVTGGR 247


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: 161
Number of extensions: 8
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: 249
Length adjustment: 24
Effective length of query: 248
Effective length of database: 225
Effective search space:    55800
Effective search space used:    55800
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