GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Sinorhizobium meliloti 1021

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate SMc03895 SMc03895 pyruvate carboxylase

Query= metacyc::MONOMER-13589
         (666 letters)



>FitnessBrowser__Smeli:SMc03895
          Length = 1152

 Score =  384 bits (987), Expect = e-110
 Identities = 198/466 (42%), Positives = 290/466 (62%), Gaps = 19/466 (4%)

Query: 4   KILIANRGEIACRVIKTARKMGIQTVAVYSDADRNALHVSMADEAIHIGPPP-------A 56
           KIL+ANR EIA RV + A ++G++TVA++++ D+ ALH   ADE+  +G  P        
Sbjct: 5   KILVANRSEIAIRVFRAANELGLKTVAIWAEEDKLALHRFKADESYQVGRGPHLPRDLGP 64

Query: 57  NQSYIVIDKIMEAIKASGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPSGAIEAMGDK 116
             SY+ ID+++   K SGA+A+HPGYG LSE  +FA A  A G+ FIGP    +  +G+K
Sbjct: 65  IMSYLSIDEVIRVAKLSGADAIHPGYGLLSESPEFAEACAANGITFIGPKPETMRQLGNK 124

Query: 117 ITSKKLAKEAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSEAE 176
           + ++ LA   GV  VP    L  D +E  +++ EIGYPVM+KAS GGGG+GMR      +
Sbjct: 125 VAARNLAISIGVPVVPATEPLPDDPEEIKRLAEEIGYPVMLKASWGGGGRGMRAIRDPKD 184

Query: 177 VKEGFESSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADKHGNCVYLHERECSIQRRNQ 236
           +      +K EA  +FG D +++EK V + RH+E Q+L D HGN V+L ER+CSIQRRNQ
Sbjct: 185 LIREVTEAKREAKAAFGKDEVYLEKLVERARHVESQILGDTHGNVVHLFERDCSIQRRNQ 244

Query: 237 KVIEEAPSPFLDEATRKAMGEQACALAKAVGYASAGTVEFIVDGQK-NFYFLEMNTRLQV 295
           KV+E AP+P+L++A R+ + + +  +A+A  Y  AGTVE+++D     FYF+E+N R+QV
Sbjct: 245 KVVERAPAPYLNDAQRQELADYSLKIARATNYIGAGTVEYLMDSDTGKFYFIEVNPRIQV 304

Query: 296 EHPVTELITGIDLVEQMIRVAAG------EKLPFQQSDLKINGWAMESRLYAEDPYRNFL 349
           EH VTE++TGID+V+  I +  G      E    +Q D+++NG A++ R+  EDP +NF+
Sbjct: 305 EHTVTEVVTGIDIVKAQIHILDGFAIGAPESGVPRQEDIRLNGHALQCRITTEDPEQNFI 364

Query: 350 PSIGRLTRYRPPVESVTPTSVVRNDTGVYEGGEISMYYDPMIAKLCTWAPTREAAIEEMR 409
           P  GR+T YR      T   +  +    Y G  I+ YYDP++ K+  WAP    AI+ M 
Sbjct: 365 PDYGRITAYR----GATGFGIRLDGGTAYSGAVITRYYDPLLEKVTAWAPNPGEAIQRMI 420

Query: 410 LALDTFEVEGIGHNLPFVGAVMDHPRFVKGDITTAFIAEEYPDGFQ 455
            AL  F + G+  NL F+ A++ HP+F     TT FI +  P+ FQ
Sbjct: 421 RALREFRIRGVATNLTFLEAIISHPKFHDNSYTTRFI-DTTPELFQ 465



 Score = 58.9 bits (141), Expect = 1e-12
 Identities = 40/137 (29%), Positives = 67/137 (48%), Gaps = 12/137 (8%)

Query: 538  PGQPLASLMVDGRPLVM---------KVGKIPMGFRLRLRGADLKVNVRTPRQAELALLM 588
            PG+ L + +  G+ LV+         + G + M F +  +   +KV  R  R A  A+  
Sbjct: 1017 PGEELFADIEKGKTLVILNQAQGEIDEKGMVKMFFEMNGQPRSIKVPDRN-RGASAAVR- 1074

Query: 589  PEKLPPDTSKYLLCPMPGLVVKINVAEGDEVQEGQALATVEAMKMENILRAERRGTVKKI 648
              K     + +L  PMPG++  + VA G  V+ G  L ++EAMKME  L AE+ G + ++
Sbjct: 1075 -RKAEAGNAAHLGAPMPGVISTVAVASGQSVKAGDVLLSIEAMKMETALHAEKDGVISEV 1133

Query: 649  AAAPGASLRVDDVIMEF 665
                G  +   D+++ F
Sbjct: 1134 LVRAGDQIDAKDLLVVF 1150


Lambda     K      H
   0.318    0.134    0.386 

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: 1652
Number of extensions: 78
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 666
Length of database: 1152
Length adjustment: 42
Effective length of query: 624
Effective length of database: 1110
Effective search space:   692640
Effective search space used:   692640
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 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