Alignments for a candidate for pccA in Sinorhizobium meliloti 1021

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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources