GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Klebsiella michiganensis M5al

Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate BWI76_RS01360 BWI76_RS01360 acetyl-CoA C-acyltransferase FadA

Query= uniprot:A0A2Z5MFE9
         (400 letters)



>FitnessBrowser__Koxy:BWI76_RS01360
          Length = 387

 Score =  301 bits (770), Expect = 3e-86
 Identities = 178/406 (43%), Positives = 240/406 (59%), Gaps = 25/406 (6%)

Query: 1   MNDAYICDAIRTPIGRY-GGALKDVRADDLGAVPIKALIQRNPGVDWRAVDDVIYGCANQ 59
           M    I DA+RTP+GR  GGA + VRADDL A  +++L+ RNP ++  A+DD+ +GC  Q
Sbjct: 1   MEQVVIVDAVRTPMGRSKGGAFRHVRADDLSAHLMRSLLSRNPSLEASAIDDIYWGCVQQ 60

Query: 60  AGEDNRNVARMSALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVES 119
             E   N+AR +ALLA +P   P  T+NRLCGS M A+  AAR I  G+A + + GGVE 
Sbjct: 61  TLEQGFNIARNAALLAEIPHSVPATTVNRLCGSSMQALHDAARMIMTGDASVCLIGGVEH 120

Query: 120 MTRAPFVMGKAASAFTRQAEIHDTTIGWRFVNPLMKRQY--GVDSMPETAENVAEQFGIS 177
           M   P   G          + H          P + R        M  TAE +A   GIS
Sbjct: 121 MGHVPMSHG---------VDFH----------PGLSRNVAKAAGMMGLTAEMLARLHGIS 161

Query: 178 RADQDAFALASQQKAARAQRDGTLAQEIVGVEIAQKKGDAIRVTLDEHPR-ETSLESLAR 236
           R  QD FA  S  +A  A + G    EI+        G     + DE  R ET++E+LA 
Sbjct: 162 REMQDQFAARSHARAWAATQSGAFKTEIIPTGGHDADGVLKSYSYDEVIRPETTVEALAA 221

Query: 237 LKGVVRP-DGTVTAGNASGVNDGACALLIASQQAAEQYGLRRRARVVGMATAGVEPRIMG 295
           L+    P  GTVTAG +S ++DGA A+L+ S+  A + GL+ RARV  MA  G +P IMG
Sbjct: 222 LRPAFDPVTGTVTAGTSSALSDGAAAMLLMSESRARELGLKPRARVRSMAVVGCDPSIMG 281

Query: 296 IGPAPATQKLLRQLGMTLDQLDVIELNEAFASQGLAVLRMLGLRDD-DPRVNPNGGAIAL 354
            GP PA++  L++ G++   +DV E+NEAFA+Q L  ++ LGL +  D ++N NGGAIAL
Sbjct: 282 YGPVPASKLALKKAGLSASDIDVFEMNEAFAAQILPCIKDLGLMEQIDEKINLNGGAIAL 341

Query: 355 GHPLGASGARLVTTALHQLERSNGRFALCTMCIGVGQGIALVIERL 400
           GHPLG SGAR+ TT ++Q+ER + +F L TMCIG+GQGIA V ER+
Sbjct: 342 GHPLGCSGARISTTLINQMERKDAQFGLATMCIGLGQGIATVFERV 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: 387
Number of extensions: 19
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: 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.

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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