Alignments for a candidate for dddA in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for dddA in Cupriavidus basilensis 4G11

Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate RR42_RS01280 RR42_RS01280 GMC family oxidoreductase

Query= metacyc::MONOMER-15202
         (579 letters)



>FitnessBrowser__Cup4G11:RR42_RS01280
          Length = 559

 Score =  345 bits (886), Expect = 2e-99
 Identities = 219/550 (39%), Positives = 293/550 (53%), Gaps = 29/550 (5%)

Query: 36  FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRT---D 92
           FDY+VVG G+AGC LA RL+   ++ V ++E GG D++  +  P G    +  PR    +
Sbjct: 5   FDYLVVGGGSAGCALAGRLADSGSDSVAVLETGGHDHHVLVSTPAGCAAML--PRAGSHN 62

Query: 93  WRFRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNC 152
           + +RT P PGLNGR    PRG+ LGG SS+N M+Y RG   DYD WA   G D W WD+ 
Sbjct: 63  YGYRTVPQPGLNGRRGYQPRGRGLGGSSSLNAMIYTRGTPADYDRWAS-AGCDGWAWDDV 121

Query: 153 LPDFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRT 212
           LP F R E + R+  G D DP    +HG  G   +   R        F  AA +AG  R 
Sbjct: 122 LPYFRRAECNERV-AGRDDDP----WHGGSGPLHVSDLRTPNPFGQRFIEAAQQAGYRRN 176

Query: 213 RDFNRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQ--------RGNLTVWHSTQVLKLD 264
            DFN  D EG   ++V Q  G RWNA++A+L   +         R NL V   TQVL++ 
Sbjct: 177 DDFNGVDQEGAGWYQVTQHGGERWNAARAYLHRGDAADHASNGGRENLAVMTGTQVLRIA 236

Query: 265 FASGEGSEPRCCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAI 324
           F   EG      GV V   G++ +  AR EV++SAGA GSPQLL +SG+GP + L E  I
Sbjct: 237 F---EGRH--AVGVVVRLDGRETLLRARREVIVSAGAFGSPQLLMVSGVGPASHLRELGI 291

Query: 325 PVVADLPGVGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAP 384
           PVV DLPGVG NLQDHL I    +V  ++                L Y  +R+G ++   
Sbjct: 292 PVVHDLPGVGANLQDHLDIIVHKRVAASELFGVSVGGAFRLLAEILRYRRERTGMLTSNF 351

Query: 385 SQLCIFTRSSKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSG 444
           ++   F +S    + P+L+ H      +   + +      +  VC L P SRG VR+ S 
Sbjct: 352 AEAGAFLKSHAGLDEPDLQLHFVVGMADDHMRRIRLGHGYSCHVCVLRPKSRGEVRLASP 411

Query: 445 NPRQAPAISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPG---VQYQSDED 501
           + R+AP I P +LS   D       +R+ R I +QP  A +  +E            D  
Sbjct: 412 DIREAPMIDPCFLSDPRDLDGLVAGVRIVRRILAQPQLAAFGGKELYSAHLPADGGDDSA 471

Query: 502 LARLAGDIGTTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTN 561
           +  +      TI+HPVGT +MG D+   AVVD  LRVRGV GLRVVDASIMPT+  GNTN
Sbjct: 472 IRAMIRAHADTIYHPVGTCRMGMDE--YAVVDPQLRVRGVEGLRVVDASIMPTLIGGNTN 529

Query: 562 SPTLMIAEKA 571
           +P +MI E+A
Sbjct: 530 APAIMIGERA 539


Lambda     K      H
   0.318    0.135    0.418 

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: 927
Number of extensions: 48
Number of successful extensions: 8
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: 579
Length of database: 559
Length adjustment: 36
Effective length of query: 543
Effective length of database: 523
Effective search space:   283989
Effective search space used:   283989
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: 53 (25.0 bits)

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

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

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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 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