GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Shewanella amazonensis SB2B

Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate 6938035 Sama_2168 3-ketoacyl-CoA thiolase (RefSeq)

Query= SwissProt::P0C7L2
         (401 letters)



>FitnessBrowser__SB2B:6938035
          Length = 436

 Score =  171 bits (434), Expect = 3e-47
 Identities = 138/425 (32%), Positives = 209/425 (49%), Gaps = 38/425 (8%)

Query: 6   ICDGIRTPIGRYGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQAGEDNR 65
           I  G+RTP  +   A   V A D+  + + ELL R+  LD + ++ ++ G   Q      
Sbjct: 17  IVSGLRTPFAKQATAFHGVSALDMGKMVVNELLSRS-ELDPKLVEQLVYGQVVQMPAAP- 74

Query: 66  NVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESMSRAPF 125
           N+AR   L  G+  +    ++ R C +   +    A +I  G+ ++ IAGG +S S  P 
Sbjct: 75  NIAREIVLGTGMNVATDAYSVTRACATSFQSTVNIAESIMTGNIEIGIAGGADSSSVLPI 134

Query: 126 VMGKA----------ASAFSRQAEMFDTTIGWRF---VNPLMAQQFGTDSMPETAENVAE 172
            + K           A  F ++  +F   +G +    V P +A+     SM +TAE +A+
Sbjct: 135 GVSKKLAHALVDLTKARTFGQKLAIF-RRLGIKDLLPVPPAVAEYSTGLSMGQTAEQMAK 193

Query: 173 LLKISREDQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTL 232
              ISR DQD+ A RS    A+  +SG++  E   V++ +       I+ D ++R  + L
Sbjct: 194 THGISRADQDAMAHRSHTLAAQTWASGVMKNE---VMVAHVPPYNQFIEKDNNIRESSDL 250

Query: 233 EQLRGLKAPF-RANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVE 291
                L+  F R +G +TA N++ + DGA+AL++ SE  A A G TP   I + A A ++
Sbjct: 251 ASYAKLRPVFDRKHGSVTAANSTPLTDGASALLLMSEGRAKALGYTPIGYIKSYAFAAID 310

Query: 292 P-RLMGLGPVPATRRVLERAGLSIHDMDVIELNEAFAAQAL----------------GVL 334
               M +GP  AT   L+RAG+ + D+ +IE++EAFAAQAL                G  
Sbjct: 311 VWEDMLMGPSYATPMALKRAGMQLEDLTLIEMHEAFAAQALANMKMFASKKFAEEKLGQN 370

Query: 335 RELGLPDDAPHVNPNGGAIALGHPLGMSGARLALAASHELHRRNGRYALCTMCIGVGQGI 394
           R +G   D    N  GG++A GHP   +GARL     +EL RR G   L T C   G G 
Sbjct: 371 RAIG-EIDMSKFNVLGGSLAYGHPFAATGARLITQMCNELKRRGGGVGLTTACAAGGLGA 429

Query: 395 AMILE 399
           AMILE
Sbjct: 430 AMILE 434


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: 357
Number of extensions: 21
Number of successful extensions: 6
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: 436
Length adjustment: 32
Effective length of query: 369
Effective length of database: 404
Effective search space:   149076
Effective search space used:   149076
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