GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Shewanella amazonensis SB2B

Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate 6935813 Sama_0031 3-ketoacyl-CoA thiolase (RefSeq)

Query= uniprot:A0A2Z5MFE9
         (400 letters)



>FitnessBrowser__SB2B:6935813
          Length = 387

 Score =  311 bits (798), Expect = 2e-89
 Identities = 189/404 (46%), Positives = 246/404 (60%), Gaps = 21/404 (5%)

Query: 1   MNDAYICDAIRTPIGRY-GGALKDVRADDLGAVPIKALIQRNPGVDWRAVDDVIYGCANQ 59
           M  A I D IRTP+GR  GG  ++VRA+ L A  +KAL+ RNPGVD   ++DVI+GC  Q
Sbjct: 1   MKQAVIVDCIRTPMGRSKGGVFRNVRAETLSAELMKALLLRNPGVDPNTIEDVIWGCVQQ 60

Query: 60  AGEDNRNVARMSALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVES 119
             E   N+AR ++LLAG+P  A   T+NRLCGS M+A+  A+RAI  G     I GGVE 
Sbjct: 61  TLEQGFNIARNASLLAGVPKTAGAVTVNRLCGSSMEALHQASRAIMTGMGDTFIIGGVEH 120

Query: 120 MTRAPFVMGKAASAFTRQAEIHDTTIGWRFVNPLMKRQYGVDSMPETAENVAEQFGISRA 179
           M   P   G          + H        +   + +  G+  M  TAE + +  GISR 
Sbjct: 121 MGHVPMNHG---------VDFHPG------LAANVAKASGM--MGLTAEMLGKLHGISRE 163

Query: 180 DQDAFALASQQKAARAQRDGTLAQEIVGVEIAQKKGDAIRVTLDEHPR-ETSLESLARLK 238
            QD FA+ S Q+A  A  +G  A EI  +E     G  I+V  DE  R ET+LESLA L+
Sbjct: 164 MQDQFAVRSHQRAHAASIEGRFANEIYAIEGHDANGALIKVDYDEVIRPETTLESLAGLR 223

Query: 239 GVVRP-DGTVTAGNASGVNDGACALLIASQQAAEQYGLRRRARVVGMATAGVEPRIMGIG 297
            V  P +GTVTAG +S ++DGA A+L+  ++ A   GL  RARV  MA AG +  IMG G
Sbjct: 224 PVFDPANGTVTAGTSSALSDGAAAMLVMEEEKARALGLTIRARVRSMAVAGCDAAIMGYG 283

Query: 298 PAPATQKLLRQLGMTLDQLDVIELNEAFASQGLAVLRMLGLRD-DDPRVNPNGGAIALGH 356
           P PATQK L + G+++  +DVIELNEAFA+Q L  ++ LGL D  + +VN NGGAIALGH
Sbjct: 284 PVPATQKALARAGLSIQDMDVIELNEAFAAQSLPCVKDLGLMDVVEDKVNLNGGAIALGH 343

Query: 357 PLGASGARLVTTALHQLERSNGRFALCTMCIGVGQGIALVIERL 400
           PLG SGAR+ TT ++ +E  +    L TMCIG+GQGIA V ER+
Sbjct: 344 PLGCSGARISTTLINLMEHKDATLGLATMCIGLGQGIATVFERV 387


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: 416
Number of extensions: 20
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: 400
Length of database: 387
Length adjustment: 31
Effective length of query: 369
Effective length of database: 356
Effective search space:   131364
Effective search space used:   131364
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.

Links

Downloads

Related tools

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