GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Shewanella loihica PV-4

Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate 5209189 Shew_1667 acetyl-CoA acetyltransferase (RefSeq)

Query= uniprot:A0A2Z5MFE9
         (400 letters)



>FitnessBrowser__PV4:5209189
          Length = 396

 Score =  244 bits (623), Expect = 3e-69
 Identities = 151/393 (38%), Positives = 217/393 (55%), Gaps = 9/393 (2%)

Query: 6   ICDAIRTPIGRYGGALKDVRADDLGAVPIKALIQRNPGVDWRAVDDVIYGCANQAGEDNR 65
           I  A RTP+G + G+L  V +  L A  IK L+    GV    V++V+ GC   AG   +
Sbjct: 12  IVAAKRTPMGGFQGSLSSVPSPTLAATAIKGLMDA-AGVQGGDVNEVLMGCVLPAGL-GQ 69

Query: 66  NVARMSALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVESMTRAPF 125
             AR + L A LP      T+N++CGSGM  V  A   IKAG A ++IAGG+ESM++AP+
Sbjct: 70  APARQATLGADLPLSVGATTVNKVCGSGMKTVMLAHDLIKAGSADVVIAGGMESMSQAPY 129

Query: 126 VMGKAASAFTRQAEIHDTTIGWRFVNPLMKRQYGVDSMPETAENVAEQFGISRADQDAFA 185
           ++ KA          H   +   F++ L +  Y   +M   A+  A+ FGI+R   D FA
Sbjct: 130 LLDKARGGMRMG---HGKVLDHMFLDGL-EDAYTGGAMGTFAQKTADDFGITREAMDNFA 185

Query: 186 LASQQKAARAQRDGTLAQEIVGVEIAQKKGDAIRVTLDEHPRETSLESLARLKGVVRPDG 245
           L+S QKA  A   G    EIV V +A +KGD + V  DE P     E +  L+     DG
Sbjct: 186 LSSLQKANAAIESGAFKAEIVPVTVASRKGDLV-VDTDEQPGNARPEKIPTLRPAFAKDG 244

Query: 246 TVTAGNASGVNDGACALLIASQQAAEQYGLRRRARVVGMATAGVEPRIMGIGPAPATQKL 305
           T+TA N+S ++DGA  L++ S   A + GL   A + G  T   EP +    P  A  KL
Sbjct: 245 TITAANSSSISDGAAVLMMMSADEASKRGLEVLATIKGHTTHSQEPSMFTTAPVGAMNKL 304

Query: 306 LRQLGMTLDQLDVIELNEAFASQGLAVLRMLGLRDDDPRVNPNGGAIALGHPLGASGARL 365
           L ++  + D++D+ E+NEAFA   +  +  LGL  D+ +VN NGGA ALGHP+G SGAR+
Sbjct: 305 LDKVNWSKDEVDLFEINEAFAMVTMLAISELGL--DEAKVNVNGGACALGHPIGCSGARV 362

Query: 366 VTTALHQLERSNGRFALCTMCIGVGQGIALVIE 398
           + T +H L+    +  + ++CIG G+  A+ IE
Sbjct: 363 LVTLIHALKARGLKRGVASLCIGGGEATAMAIE 395


Lambda     K      H
   0.319    0.134    0.386 

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: 373
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: 400
Length of database: 396
Length adjustment: 31
Effective length of query: 369
Effective length of database: 365
Effective search space:   134685
Effective search space used:   134685
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