GapMind for catabolism of small carbon sources

 

Aligments for a candidate for paaJ1 in Sinorhizobium meliloti 1021

Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate SMc02228 SMc02228 acetyl-CoA acetyltransferase

Query= SwissProt::P0C7L2
         (401 letters)



>lcl|FitnessBrowser__Smeli:SMc02228 SMc02228 acetyl-CoA
           acetyltransferase
          Length = 402

 Score =  248 bits (634), Expect = 2e-70
 Identities = 168/426 (39%), Positives = 225/426 (52%), Gaps = 49/426 (11%)

Query: 1   MREAFICDGIRTPIGR--YGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCAN 58
           M + F+ D +RTP GR    GAL  V +  LAA  L  +  RN  LD   +DDVI+GC +
Sbjct: 1   MTKVFVYDHVRTPRGRGKKDGALHEVPSVRLAAKVLEAVRDRNG-LDTSTVDDVIMGCVD 59

Query: 59  QAGEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVE 118
              +    + + A   AG      G  I+R C SGLDA+ F A  I  G  D++IAGGVE
Sbjct: 60  PVMDAGAVIPKAAAFEAGYSTRAPGMQISRFCASGLDAVNFGAAKIAQGADDIVIAGGVE 119

Query: 119 SMSRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPE--TAENVAELLKI 176
           SMSR    M   A               W F++P +        MP+  +A+ +A     
Sbjct: 120 SMSRVGLGMSGGA---------------W-FMDPSV--NLPAYFMPQGVSADLIATKYGF 161

Query: 177 SREDQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLR 236
           SR+D D++A+ SQ+R A A   G     +VPV  K++ G+V  +  DEH+RP T ++ L 
Sbjct: 162 SRDDVDAYAVESQKRAANAWEKGYFKNSVVPV--KDQNGLVI-LDRDEHMRPGTDMQALA 218

Query: 237 GLKAPF---------------------RANGVITAGNASGVNDGAAALIIASEQMAAAQG 275
            L   F                     R N V  AGN+SG+ DGAAA++I S+    A G
Sbjct: 219 SLNPSFQMPGEMGGFEAVGIQAHPEIERINYVHHAGNSSGIVDGAAAVLIGSKAGGEAMG 278

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

Query: 336 ELGLPDDAPHVNPNGGAIALGHPLGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIA 395
              +P D   +N NGGAIA+GHPLG +GA +      EL RR+   AL T+CIG G G A
Sbjct: 339 AFDIPHD--KINVNGGAIAMGHPLGATGAMILGTVLDELERRDLNTALVTLCIGAGMGTA 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: 423
Number of extensions: 18
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: 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 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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