Alignments for a candidate for iolA in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for iolA in Cupriavidus basilensis 4G11

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate RR42_RS25635 RR42_RS25635 methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::Q02252
         (535 letters)



>FitnessBrowser__Cup4G11:RR42_RS25635
          Length = 507

 Score =  620 bits (1599), Expect = 0.0
 Identities = 291/483 (60%), Positives = 376/483 (77%)

Query: 37  VPTVKLFIGGKFVESKSDKWIDIHNPATNEVIGRVPQATKAEMDAAIASCKRAFPAWADT 96
           +PT KL I GKFVES S++W ++ NPAT +VIGRVP AT  E+DAAIAS +RAF AW +T
Sbjct: 12  LPTAKLLIDGKFVESDSNQWGNVVNPATQQVIGRVPFATVEEVDAAIASAQRAFLAWRNT 71

Query: 97  SVLSRQQVLLRYQQLIKENLKEIAKLITLEQGKTLADAEGDVFRGLQVVEHACSVTSLMM 156
            + +R +V+L++Q L++ N++ IA+ +T EQGKTL DA+GD+FRGL+VVEHACSV +L M
Sbjct: 72  PLGARLRVMLKFQDLVRRNMERIARTLTAEQGKTLPDAQGDIFRGLEVVEHACSVGTLQM 131

Query: 157 GETMPSITKDMDLYSYRLPLGVCAGIAPFNFPAMIPLWMFPMAMVCGNTFLMKPSERVPG 216
           GE   ++   +D Y+ R P+GVCAGI PFNFP MIPLWMFPMA+VCGNTF++KPSE+ P 
Sbjct: 132 GEFAENVAGGVDTYTLRQPIGVCAGITPFNFPGMIPLWMFPMAIVCGNTFVLKPSEQDPL 191

Query: 217 ATMLLAKLLQDSGAPDGTLNIIHGQHEAVNFICDHPDIKAISFVGSNKAGEYIFERGSRH 276
           +TM L +L  ++G P G LN++HG    V+ +C HPD+KAISFVGS   G +++  GS+H
Sbjct: 192 STMELVELAMEAGVPPGVLNVVHGGKTVVDMLCTHPDVKAISFVGSTHVGTHVYNLGSKH 251

Query: 277 GKRVQANMGAKNHGVVMPDANKENTLNQLVGAAFGAAGQRCMALSTAVLVGEAKKWLPEL 336
           GKRVQ+ MGAKNH VV+PDAN++ TLN LVGA FGAAGQRCMA S  VLVG+++ WLPEL
Sbjct: 252 GKRVQSMMGAKNHAVVLPDANRQQTLNALVGAGFGAAGQRCMATSVVVLVGQSRDWLPEL 311

Query: 337 VEHAKNLRVNAGDQPGADLGPLITPQAKERVCNLIDSGTKEGASILLDGRKIKVKGYENG 396
           V  AK L+VNAG +PG D+GP+++  A  R+  LI+ G + GA++LLDGR +KV GYENG
Sbjct: 312 VAKAKLLKVNAGHEPGTDVGPVMSKAAHARITGLIEEGVQAGAALLLDGRNVKVPGYENG 371

Query: 397 NFVGPTIISNVKPNMTCYKEEIFGPVLVVLETETLDEAIQIVNNNPYGNGTAIFTTNGAT 456
           NFVGPTI S V P+M+ Y +EIFGPV+VVLE +TLDEAI +VN NP GNG  +FT +GA 
Sbjct: 372 NFVGPTIFSGVSPDMSIYTQEIFGPVVVVLEVDTLDEAIALVNRNPMGNGVGLFTQSGAA 431

Query: 457 ARKYAHLVDVGQVGVNVPIPVPLPMFSFTGSRSSFRGDTNFYGKQGIQFYTQLKTITSQW 516
           ARK+   +DVGQVG+N+PIPVP+P FSFTGSR S  GD   YGKQ +QFYTQ KT+T++W
Sbjct: 432 ARKFQSEIDVGQVGINIPIPVPVPYFSFTGSRGSKLGDLGPYGKQVVQFYTQTKTVTARW 491

Query: 517 KEE 519
            ++
Sbjct: 492 FDD 494


Lambda     K      H
   0.318    0.133    0.391 

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: 715
Number of extensions: 26
Number of successful extensions: 2
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: 535
Length of database: 507
Length adjustment: 35
Effective length of query: 500
Effective length of database: 472
Effective search space:   236000
Effective search space used:   236000
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: 52 (24.6 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