GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Cupriavidus basilensis 4G11

Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate RR42_RS26090 RR42_RS26090 acetyl-CoA acetyltransferase

Query= SwissProt::P0C7L2
         (401 letters)



>FitnessBrowser__Cup4G11:RR42_RS26090
          Length = 391

 Score =  321 bits (822), Expect = 3e-92
 Identities = 183/404 (45%), Positives = 257/404 (63%), Gaps = 17/404 (4%)

Query: 1   MREAFICDGIRTPIGRYGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQA 60
           M +  I    RT +G++GG+L+ V A +L A  ++ LL R+  L  E +D+V+LG    A
Sbjct: 1   MEDVVIVAAARTAVGKFGGSLAKVPAPELGATVIKALLERSG-LKPEMVDEVLLGQVLTA 59

Query: 61  GEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESM 120
           G   +N AR A + AGLP +V   TI ++CGSGL A+  AA+AIK GD D++IAGG E+M
Sbjct: 60  G-GGQNPARQAAIKAGLPNTVPAMTIGKVCGSGLKAVHLAAQAIKCGDADIVIAGGQENM 118

Query: 121 SRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQ----QFGTDSMPETAENVAELLKI 176
           S +P V+     A SR  +       W+  + ++       F    M  TAENVA+   I
Sbjct: 119 SASPHVL-----AGSRDGQRMGD---WKLTDTMIVDGLWDAFNQYHMGTTAENVAKAYHI 170

Query: 177 SREDQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLR 236
           SRE QD+FA  SQQ+   AQ +G   +EIVPV + +KKG V     DE ++  TT + L 
Sbjct: 171 SREQQDAFAAASQQKAELAQKTGRFKDEIVPVSIVSKKGTVV-FDTDEFIKHGTTADALA 229

Query: 237 GLKAPFRANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMG 296
           GL+  F   G +TAGNASG+NDGAAA+++ S   A   GLTP ARI + A+AG++P +MG
Sbjct: 230 GLRPAFDKAGSVTAGNASGLNDGAAAVLMMSASKARELGLTPLARIASYASAGLDPAIMG 289

Query: 297 LGPVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGGAIALG 356
           +GPVPA++R L +AG SI+D+D++E+NEAFAAQA  V +E+    DA  +N NGGAIA+G
Sbjct: 290 MGPVPASQRCLHKAGWSINDLDLMEINEAFAAQACAVNQEMDW--DASKINVNGGAIAIG 347

Query: 357 HPLGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILER 400
           HP+G SG R+ +   HE+ RR+ R  L ++CIG G G+A+ +ER
Sbjct: 348 HPIGASGCRILVTLLHEMARRDARRGLASLCIGGGMGVALAVER 391


Lambda     K      H
   0.319    0.135    0.384 

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: 443
Number of extensions: 21
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: 401
Length of database: 391
Length adjustment: 31
Effective length of query: 370
Effective length of database: 360
Effective search space:   133200
Effective search space used:   133200
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: 50 (23.9 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