Alignments for a candidate for liuB in Rhodobacter ovatus JA234

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuB in Rhodobacter ovatus JA234

Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_097029448.1 CRO07_RS04350 pyruvate carboxylase

Query= reanno::SB2B:6937189
         (673 letters)



>NCBI__GCF_900207575.1:WP_097029448.1
          Length = 1154

 Score =  391 bits (1004), Expect = e-112
 Identities = 203/451 (45%), Positives = 298/451 (66%), Gaps = 13/451 (2%)

Query: 2   FNKLLIANRGEIACRVIRTARDMGIKTVAVYSDADRDARHVALADESFYLGES-APASSY 60
           F K+LIANRGEIA RV+R A +MG KTVAVY++ D+ + H   ADE++ +GE  +P  +Y
Sbjct: 4   FRKILIANRGEIAIRVMRAANEMGKKTVAVYAEEDKLSLHRFKADEAYRIGEGLSPVGAY 63

Query: 61  LRGELIIDIAKKCGAEAIHPGYGFLSENAAFARACEASGIAFVGPGSDAIDAMGSKSAAK 120
           L    II +AK  GA+AIHPGYG LSEN  F  AC+A+GIAF+GP ++ + A+G K++A+
Sbjct: 64  LSIPEIIRVAKMSGADAIHPGYGLLSENPDFVEACDAAGIAFIGPRAETMRALGDKASAR 123

Query: 121 LIMEKAGVPLVPGYH--GDDQSDATLLAEAKKIGYPLLIKAAYGGGGKGMRIVESESELK 178
            +   AGVP++P     GDD  +     +A ++GYPL++KA++GGGG+GMR + SE+EL 
Sbjct: 124 RVAMAAGVPVIPATEVLGDDMDEVK--RQAAEVGYPLMLKASWGGGGRGMRPIPSEAELA 181

Query: 179 AAIDSARREAASSFGNDKLLMERYLRQPRHVEVQVFADSQGNCVYLSDRDCSIQRRHQKV 238
             +   RREA ++FGN +  +E+ + + RHVEVQ+  D QGN  +L +RDC++QRR+QKV
Sbjct: 182 DKVREGRREAEAAFGNGEGYLEKMILRARHVEVQILGDKQGNIYHLYERDCTVQRRNQKV 241

Query: 239 VEEAPAPGLPDSLRKQMGEAAVAAAKAIDYRGAGTVEFLLDVD-MSFFFMEMNTRLQVEH 297
           VE APAP L D  R ++ E        ++Y  AGTVEFL+D+D   F+F+E+N R+QVEH
Sbjct: 242 VERAPAPYLTDDQRAEVCELGRRICAHVNYECAGTVEFLMDMDSQQFYFIEVNPRVQVEH 301

Query: 298 PVTEMVTGQDLVKWQLLVAAGAQLP-----LEQHEIQIHGHAFEVRIYAEDPNNEFLPAS 352
            VTE VTG D+V+ Q+ +A GA L        Q +I + GHA + R+  EDP N F+P  
Sbjct: 302 TVTEEVTGIDIVQAQIRIAEGATLAEATGVARQEDITLSGHALQCRVTTEDPQNNFIPDY 361

Query: 353 GKLTFLREPEPSRHVRIDSGVR-ENDVISNYYDPMIAKLIVWDESRPRALARLTRALGDY 411
           G+LT  R       +R+D G      VI+ YYD ++ K+  W ++  +A++R+ RAL ++
Sbjct: 362 GRLTAYRS-ATGMGIRLDGGTAYAGGVITRYYDSLLVKVTAWAQTPEKAISRMDRALREF 420

Query: 412 RVGGLKHNIEFLSNIAEHPAFAQANFSTDFI 442
           R+ G+  NI F+ N+ +HP+F   +++T FI
Sbjct: 421 RIRGVATNIAFVENLLKHPSFLDYSYTTKFI 451



 Score = 45.1 bits (105), Expect = 2e-08
 Identities = 27/65 (41%), Positives = 32/65 (49%)

Query: 596  APMNGTVVTHLVAAGDKVSAGQGLLVMEAMKMEYTIEAPFDGVVSEFFFAPGELVSDGTL 655
            APM G+V    V  G KV  G  LL +EAMKME  + A     V     APG  +    L
Sbjct: 1089 APMPGSVAAVAVTVGQKVKPGDLLLTIEAMKMETGLHADRAATVKAVHVAPGAQIEAKDL 1148

Query: 656  LLALE 660
            L+ LE
Sbjct: 1149 LIELE 1153


Lambda     K      H
   0.317    0.134    0.380 

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: 1753
Number of extensions: 69
Number of successful extensions: 7
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: 673
Length of database: 1154
Length adjustment: 43
Effective length of query: 630
Effective length of database: 1111
Effective search space:   699930
Effective search space used:   699930
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 Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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