Alignments for a candidate for prpB in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpB in Cupriavidus basilensis 4G11

Align isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate RR42_RS12200 RR42_RS12200 isocitrate lyase

Query= BRENDA::P9WKK7
         (428 letters)



>FitnessBrowser__Cup4G11:RR42_RS12200
          Length = 430

 Score =  605 bits (1559), Expect = e-177
 Identities = 302/419 (72%), Positives = 348/419 (83%), Gaps = 2/419 (0%)

Query: 10  AEQIQQEWDTNPRWKDVTRTYSAEDVVALQGSVVEEHTLARRGAEVLWEQLHDLEWVNAL 69
           A  +Q+EWDTNPRWK V R Y+A+DVV L+GSV  EHTLARRGAE LW  L+   +VN L
Sbjct: 7   ARNLQKEWDTNPRWKGVARHYTADDVVRLRGSVQIEHTLARRGAEKLWHLLNTEPFVNTL 66

Query: 70  GALTGNMAVQQVRAGLKAIYLSGWQVAGDANLSGHTYPDQSLYPANSVPQVVRRINNALQ 129
           GALTGN A+QQV+AGLKAIYLSGWQVAGDANL+G  YPDQSLYPANSVPQVVRRINN  Q
Sbjct: 67  GALTGNQAMQQVKAGLKAIYLSGWQVAGDANLAGEMYPDQSLYPANSVPQVVRRINNTFQ 126

Query: 130 RADQIAKIEGDTSVENWLAPIVADGEAGFGGALNVYELQKALIAAGVAGSHWEDQLASEK 189
           RADQI   EG    + + APIVAD EAGFGG LN +EL K++I AG AG H+EDQLAS K
Sbjct: 127 RADQIQWSEGKGDTD-FFAPIVADAEAGFGGVLNAFELMKSMIDAGAAGVHFEDQLASVK 185

Query: 190 KCGHLGGKVLIPTQQHIRTLTSARLAADVADVPTVVIARTDAEAATLITSDVDERDQPFI 249
           KCGH+GGKVL+PT++ +  LT+ARLAADV+ VPT+VIARTDAEAA L+TSDVDERD+PF 
Sbjct: 186 KCGHMGGKVLVPTREAVAKLTAARLAADVSGVPTLVIARTDAEAADLLTSDVDERDRPFC 245

Query: 250 TGERTREGFYRTKNGIEPCIARAKAYAPFADLIWMETGTPDLEAARQFSEAVKAEYPDQM 309
           TGERT EGFYR K GIE  I+RA AYA  ADL+W ETG PDLE A++F+EAV A++P +M
Sbjct: 246 TGERTVEGFYRVKPGIEQSISRALAYAEVADLVWCETGKPDLEFAKKFAEAVHAKFPGKM 305

Query: 310 LAYNCSPSFNWKKHLDDATIAKFQKELAAMGFKFQFITLAGFHALNYSMFDLAYGYAQNQ 369
           LAYNCSPSFNWKK+LDDATIAKFQKEL AMG+KFQFITLAGFH+LNYSMF+LAYGYA+N 
Sbjct: 306 LAYNCSPSFNWKKNLDDATIAKFQKELGAMGYKFQFITLAGFHSLNYSMFNLAYGYARNH 365

Query: 370 MSAYVELQEREFAAEERGYTATKHQREVGAGYFDRIATTVD-PNSSTTALTGSTEEGQF 427
           MSA+VELQE EF A E+G+TA KHQREVG GYFD +  T++   SSTTAL GSTE+ QF
Sbjct: 366 MSAFVELQENEFTAAEKGFTAVKHQREVGTGYFDAVTQTIEGGQSSTTALKGSTEDEQF 424


Lambda     K      H
   0.316    0.130    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: 632
Number of extensions: 19
Number of successful extensions: 3
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: 428
Length of database: 430
Length adjustment: 32
Effective length of query: 396
Effective length of database: 398
Effective search space:   157608
Effective search space used:   157608
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 (21.6 bits)
S2: 51 (24.3 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