GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Phyllobacterium brassicacearum STM 196

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_106711729.1 CU102_RS14130 acetyl-CoA C-acetyltransferase

Query= SwissProt::P0C7L2
         (401 letters)



>NCBI__GCF_003010955.1:WP_106711729.1
          Length = 402

 Score =  246 bits (629), Expect = 7e-70
 Identities = 167/426 (39%), Positives = 227/426 (53%), Gaps = 49/426 (11%)

Query: 1   MREAFICDGIRTPIGR--YGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCAN 58
           M EA+I D +RTP GR    G+L  V A  L A  L  L  RN  LD   +DD+I GC +
Sbjct: 1   MTEAYIYDHVRTPRGRGKKDGSLHEVPAVRLGAHVLEALRDRNG-LDTGLVDDIIYGCVD 59

Query: 59  QAGEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVE 118
             GE    + R +   AG      G  I+R C SGLDA+ FAA  I  G  D++IAGGVE
Sbjct: 60  PVGEAGAVIPRSSAFEAGYDFKAPGMQISRFCASGLDAVNFAAAKIVQGADDIVIAGGVE 119

Query: 119 SMSRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPE--TAENVAELLKI 176
           SMSR    MG +  A+       D ++G       +   F    MP+  +A+ +A     
Sbjct: 120 SMSRVG--MGMSGGAW-----YMDPSVG-------LPGYF----MPQGVSADLIATKYGF 161

Query: 177 SREDQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLR 236
           SR+D D++A+ SQ+R  +A   G     ++ +  K++ G+ T + HDEH+RP T ++ L 
Sbjct: 162 SRDDVDAYAVESQKRAGEAWKKGYFKNSVLEI--KDQNGL-TILDHDEHMRPTTDMQALA 218

Query: 237 GLKAPF---------------------RANGVITAGNASGVNDGAAALIIASEQMAAAQG 275
            L   F                       N V  AGN+SG+ DGAA +++ S+    A G
Sbjct: 219 SLNPSFVMPGEMGGFNAVGIQAHPEVETINHVHHAGNSSGIVDGAAGVLLGSKSAGKAIG 278

Query: 276 LTPRARIVAMATAGVEPRLMGLGPVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLR 335
             PRARI A A  G +P LM  GPV  T ++L+RA + I D+D+ ELNEAFAA  L  ++
Sbjct: 279 TKPRARIRAFANIGSDPALMLTGPVDVTEKLLKRAKMKISDIDLFELNEAFAAVVLRYMQ 338

Query: 336 ELGLPDDAPHVNPNGGAIALGHPLGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIA 395
              +P D   +N NGGAIA+GHPLG +GA +      EL RR+   AL T+CIG G G A
Sbjct: 339 AFDIPRD--KINVNGGAIAMGHPLGATGAMILGTVLDELERRDLNVALVTLCIGAGMGTA 396

Query: 396 MILERV 401
            I+ERV
Sbjct: 397 TIIERV 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: 432
Number of extensions: 16
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