GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Marinobacter guineae M3B

Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate WP_099618908.1 CLH62_RS14435 acetyl-CoA C-acetyltransferase

Query= SwissProt::P0C7L2
         (401 letters)



>NCBI__GCF_002744735.1:WP_099618908.1
          Length = 402

 Score =  279 bits (713), Expect = 1e-79
 Identities = 173/421 (41%), Positives = 238/421 (56%), Gaps = 44/421 (10%)

Query: 3   EAFICDGIRTPIGR--YGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQA 60
           EA+I D +RTP GR    G+L SV+   L    L  L  RN  LD   +DD+++GC    
Sbjct: 4   EAYIFDAVRTPRGRGKKDGSLHSVKPITLLTTVLHALQERNS-LDTAQVDDIVMGCVTAV 62

Query: 61  GEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESM 120
           G+   ++A+ A L A   + V+G T+NR C SGL+A+  AA  +++G  D+++AGGVE+M
Sbjct: 63  GDQGADIAKTAALAADWDEKVAGVTLNRFCASGLEAVNLAAMKVRSGWEDMVVAGGVEAM 122

Query: 121 SRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKISRED 180
           SR P  MG    A++   E   T +   F    M Q  G D        +A L   SR D
Sbjct: 123 SRVP--MGSDGGAWATDPE---TNLHTGF----MPQGIGADL-------IATLEGFSRMD 166

Query: 181 QDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGLKA 240
            D+FA++SQQ+ A A  +G   + I+PV  +N  GVV  +  DEH+R  TT+E L GL+ 
Sbjct: 167 VDAFAVKSQQKAANAWQNGYFGKSIIPVTDQN--GVVI-LDRDEHVRGNTTVESLSGLRP 223

Query: 241 PF--------------------RANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRA 280
            F                    + N V  AGN+SG+ DGA A++I SE    A GL PRA
Sbjct: 224 SFQMMGEMGFDGVAREKYHYVEKINHVHHAGNSSGIVDGATAMLIGSEAKGKAMGLKPRA 283

Query: 281 RIVAMATAGVEPRLMGLGPVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLP 340
           RIVA A    +P +M  GP PA R+ L +AG++   +D+ E+NEAFA+  +   REL +P
Sbjct: 284 RIVATAVTSTDPTIMLTGPAPAARKALGKAGMTADQIDLFEVNEAFASVVMRFQRELSVP 343

Query: 341 DDAPHVNPNGGAIALGHPLGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILER 400
           D+   VN NGGAIA+GHPLG +GA +      EL RR  R+ L T+C+G G GIA I+ER
Sbjct: 344 DE--KVNVNGGAIAMGHPLGATGAMILGTLLDELERRELRFGLATLCVGGGMGIATIIER 401

Query: 401 V 401
           V
Sbjct: 402 V 402


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: 439
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: 401
Length of database: 402
Length adjustment: 31
Effective length of query: 370
Effective length of database: 371
Effective search space:   137270
Effective search space used:   137270
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 24 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