Alignments for a candidate for liuB in Rhodococcus qingshengii djl-6-2

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuB in Rhodococcus qingshengii djl-6-2

Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_050656644.1 C1M55_RS12655 pyruvate carboxylase

Query= reanno::pseudo5_N2C3_1:AO356_01595
         (649 letters)



>NCBI__GCF_002893965.1:WP_050656644.1
          Length = 1134

 Score =  371 bits (952), Expect = e-106
 Identities = 218/517 (42%), Positives = 304/517 (58%), Gaps = 12/517 (2%)

Query: 9   LLVANRGEIACRVMRTARAMGLTTVAVHSATDRDARHSREADIRVDLGGS-KAADSYLQI 67
           +LVANRGEIA R  R A  +G  TVAV    DR++ H  +AD    +G       +YL +
Sbjct: 5   VLVANRGEIAIRAFRAAYELGAGTVAVFPYEDRNSIHRLKADESYQIGEKGHPVRAYLSV 64

Query: 68  DKLIAAAKASGAQAIHPGYGFLSENAGFARAIENAGLIFLGPPASAIDAMGSKSAAKTLM 127
           ++++AAAK++GA AI+PGYGFLSEN   + A   AG+ F+GP A  ++  G+K+ A    
Sbjct: 65  EEIVAAAKSAGADAIYPGYGFLSENPDLSAACAEAGIKFVGPSAEILELTGNKARAIAAA 124

Query: 128 ETAGVPLVPGYHGEAQDLETFRDAAERIGYPVLLKATAGGGGKGMKVVEDVSQLAEALAS 187
           + AG+P++      A D++    AAE + +P+ +KA AGGGG+GM+ V + SQL E++ +
Sbjct: 125 KAAGLPVLASSEPSA-DIDELLAAAEDMTFPLFVKAVAGGGGRGMRRVAERSQLKESIEA 183

Query: 188 AQREAQSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVEEAP 247
           A REA+S+FGDS + +E+ ++ PRH+E+Q+ AD+ GN ++L ERDCS+QRRHQKV+E AP
Sbjct: 184 AAREAESAFGDSTVFLEQAVIDPRHIEVQILADEQGNVIHLFERDCSLQRRHQKVIELAP 243

Query: 248 APGLTPQLRRAMGEAAVRAAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPVTEAI 307
           AP L+ +LR  +   AV  A+ IGY  AGTVEFLLD RG   F+EMN R+QVEH VTE +
Sbjct: 244 APNLSEELRAKICADAVAFAKEIGYTCAGTVEFLLDKRGNHVFIEMNPRIQVEHTVTEEV 303

Query: 308 TGLDLVAWQIRVAQGEPLP---ITQAQVPLLGHAIEVRLYAEDPGNDFLPATGRLALYRE 364
           T +DLV  Q+++A G  L    ++Q  + L G A++ R+  EDP N F P TGR+  YR 
Sbjct: 304 TDVDLVQSQLKIASGSTLADLGLSQETIKLRGAALQCRITTEDPANGFRPDTGRITAYR- 362

Query: 365 SAEGPGRRVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDEFVIGGLKTNI 424
           +  G G R+D G   G E+  ++D ML KL   G D E A  R    + EF I G+ TNI
Sbjct: 363 TPGGAGIRLDGGATLGAEVGAYFDSMLVKLTCRGRDLEAAVARARRAVTEFRIRGVSTNI 422

Query: 425 GFLRRIVAHPAFAAAELDTGFIPRYQAQLLPEPSELDDAFWFAAAQGVALSLAPHVRGDD 484
            FL+ ++  P F A  + T FI   + QLL   S  D                PH     
Sbjct: 423 PFLQAVLDDPDFRAGRVTTSFIEE-RPQLLTLRSSADRGTKILTYLADVTVNKPHGERPS 481

Query: 485 AGSPWASTTGMRLGLP-----RETTLHLSCEGQDRAL 516
           A  P      + L  P     R+  L L  EG  +AL
Sbjct: 482 AVYPQDKLPKIDLSTPPPAGSRQRLLELGPEGFAKAL 518



 Score = 50.8 bits (120), Expect = 3e-10
 Identities = 29/79 (36%), Positives = 44/79 (55%), Gaps = 1/79 (1%)

Query: 567  DPLAAAEASHSHQGGLVAPMNGSIVRVLVGVGQTVEAGAQLVVLEAMKMEHSIRAPKAGV 626
            D   A +A  ++ G + AP  G +V + V  GQ +EAG  +  +EAMKME +I +P+AGV
Sbjct: 1047 DVPVAEKADKNNPGHVAAPFAG-VVTLAVKEGQKIEAGDTVATIEAMKMEAAITSPRAGV 1105

Query: 627  IKALYCQEGEMVSEGSALV 645
            +  +     + V  G  LV
Sbjct: 1106 VSRIAISAVQQVEGGDLLV 1124



 Score = 26.2 bits (56), Expect = 0.009
 Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 562  RIDLYDPLAAAEASHSHQGGLVAPMNGSIVRVLVGVGQTVEAGAQLVVL 610
            +I+  D +A  EA    +  + +P  G + R+ +   Q VE G  LVV+
Sbjct: 1079 KIEAGDTVATIEAMKM-EAAITSPRAGVVSRIAISAVQQVEGGDLLVVV 1126


Lambda     K      H
   0.319    0.134    0.390 

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: 1587
Number of extensions: 86
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 649
Length of database: 1134
Length adjustment: 42
Effective length of query: 607
Effective length of database: 1092
Effective search space:   662844
Effective search space used:   662844
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 (21.7 bits)
S2: 56 (26.2 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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