GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Klebsiella michiganensis M5al

Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate BWI76_RS23710 BWI76_RS23710 acetyl-CoA acetyltransferase

Query= SwissProt::P0C7L2
         (401 letters)



>FitnessBrowser__Koxy:BWI76_RS23710
          Length = 396

 Score =  279 bits (714), Expect = 9e-80
 Identities = 165/396 (41%), Positives = 232/396 (58%), Gaps = 12/396 (3%)

Query: 6   ICDGIRTPIGRYGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQAGEDNR 65
           +  G+RT IG + G+L      DL A  +RE  V    L  + ID+ I+G   Q  E   
Sbjct: 9   VVSGVRTAIGTFNGSLKHTHQHDLGAAVIREA-VNRAGLAPQDIDETIVGNVGQIAESGF 67

Query: 66  NVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESMSRAPF 125
            +AR+  L AG+PQ  +  ++NR CGSGL AL      +++G  ++++A G E+M++ P+
Sbjct: 68  -IARICQLRAGIPQESTAYSVNRQCGSGLQALADGMMQLQSGQAEVVVACGTENMTQLPY 126

Query: 126 VMGKAASAFSR-QAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKISREDQDSF 184
            + KA   +     E+ D  I       ++    G      TAENVA+   I+RE  D F
Sbjct: 127 YLRKARDGYRMGHGELEDGLIS------ILTWPEGPYHNGITAENVAQRFGITREAMDDF 180

Query: 185 ALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGLKAPFRA 244
           A  SQQ+  KA +     E+I+ + + + K        DEH R +T  E+L  L+  F+A
Sbjct: 181 AWSSQQKALKAIAEERFREQILALEVPDGKKATRLFATDEHPR-DTPREKLAALRPAFKA 239

Query: 245 NGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMGLGPVPATR 304
           +GV+TA N+SG+NDGAAAL++ + Q A  +GLTPR RI   A AG    +MG GP PATR
Sbjct: 240 DGVVTAANSSGINDGAAALVMMTRQQAEKRGLTPRMRIRGWAVAGCGAEIMGFGPSPATR 299

Query: 305 RVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGGAIALGHPLGMSGA 364
           R+++R  + +H +D+IELNEAFAAQAL V+ +L L  D   VN NGGAIALGHP+G SGA
Sbjct: 300 RLMDRLNMDVHAIDLIELNEAFAAQALAVMNDLRL--DPARVNVNGGAIALGHPVGASGA 357

Query: 365 RLALAASHELHRRNGRYALCTMCIGVGQGIAMILER 400
            L +   +E+ R   R  L TMCIG GQGI+M+ ER
Sbjct: 358 ILPVKLMYEMARSGARTGLVTMCIGGGQGISMLFER 393


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: 407
Number of extensions: 20
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: 396
Length adjustment: 31
Effective length of query: 370
Effective length of database: 365
Effective search space:   135050
Effective search space used:   135050
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