GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF 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)



>FitnessBrowser__Smeli:SMc02228
          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 (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