Alignments for a candidate for liuB in Ochrobactrum thiophenivorans DSM 7216

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuB in Ochrobactrum thiophenivorans DSM 7216

Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_094508694.1 CEV31_RS16810 ATP-grasp domain-containing protein

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



>NCBI__GCF_002252445.1:WP_094508694.1
          Length = 569

 Score =  392 bits (1007), Expect = e-113
 Identities = 214/443 (48%), Positives = 280/443 (63%), Gaps = 11/443 (2%)

Query: 4   KLLIANRGEIACRVIRTARDMGIKTVAVYSDADRDARHVALADESFYLGESAPASSYLRG 63
           KLLIANRGEIA R+IR A D G+K+VA+YSDAD ++ H   ADE++ LG   P  +YL  
Sbjct: 3   KLLIANRGEIAIRIIRAAADYGVKSVAIYSDADANSLHAEFADEAYGLGAGRPNDTYLNI 62

Query: 64  ELIIDIAKKCGAEAIHPGYGFLSENAAFARACEASGIAFVGPGSDAIDAMGSKSAAKLIM 123
             I+DIAK+ GA+A+HPGYGFLSE A FA+A   +G+ +VGP  + I A+G K AA+ I 
Sbjct: 63  AKILDIAKRAGADAVHPGYGFLSERAEFAKAVIDAGLMWVGPSPEVITALGDKVAARRIA 122

Query: 124 EKAGVPLVPGYHGDDQSDATLLAEAKKIGYPLLIKAAYGGGGKGMRIVESESELKAAIDS 183
           E+ G PLV G  G  +S A  +A A++ G PL IKAA+GGGG+GM++     E+    DS
Sbjct: 123 EQVGAPLVRGSDGPLESAAEAVAFAREAGLPLAIKAAFGGGGRGMKVAYHLEEVGELFDS 182

Query: 184 ARREAASSFGNDKLLMERYLRQPRHVEVQVFADSQGNCVYLSDRDCSIQRRHQKVVEEAP 243
           A REA  +FG  +   E++L +PRH+E QV AD+ GN V L  RDCS+QRR+QK+VEEAP
Sbjct: 183 AVREAVEAFGRGECYAEQFLEKPRHIEAQVIADTHGNTVVLGTRDCSLQRRNQKLVEEAP 242

Query: 244 APGLPDSLRKQMGEAAVAAAKAIDYRGAGTVEFLLDVDMSFFFMEMNTRLQVEHPVTEMV 303
           AP +    R ++ E+A A   A  Y GAGTVEFLL  + +  F+E+NTRLQVEHP+TE  
Sbjct: 243 APFITQDQRNRIHESARAICAAAGYTGAGTVEFLLSQNGTISFLEVNTRLQVEHPITEET 302

Query: 304 TGQDLVKWQLLVAAGAQLPLEQHEIQIHGHAFEVRIYAEDPNNEFLPASGKLTFLREPEP 363
           TG D+V  QL +A G +L + +   +  GHAFE RI AEDP   FLP  G +T  R P  
Sbjct: 303 TGVDIVIEQLRIADGKKLSVTETP-EPRGHAFEFRINAEDPGRGFLPTPGLITRFRAPS- 360

Query: 364 SRHVRIDSGVRENDVISNYYDPMIAKLIVWDESRPRALARLTRALGDYRVGGLKHNIEFL 423
              VR+D+GV     I   YD M+AKLIVW  +R  AL R  RAL ++ + G+   + F 
Sbjct: 361 GPGVRLDTGVESGSEIPGLYDSMMAKLIVWGATREEALIRARRALAEFHIEGVASVLPFH 420

Query: 424 SNIAEHPAFAQANFSTDFIGRYG 446
             + E           DFIG  G
Sbjct: 421 RAVVE---------DKDFIGEDG 434



 Score = 40.0 bits (92), Expect = 3e-07
 Identities = 28/72 (38%), Positives = 39/72 (54%), Gaps = 1/72 (1%)

Query: 589 SSEDKLKAPMNGTVVTHLVAAGDKVSAGQGLLVMEAMKMEYTIEAPFDGVVSEFFFAPGE 648
           ++E  + AP+ GT    LV  G  VS G+ + ++EAMKME  I AP  G +S      G+
Sbjct: 499 ATEGAVTAPIPGTFQQWLVEDGAMVSEGEIVAIIEAMKMETRIGAPKSGKIS-LRAEAGK 557

Query: 649 LVSDGTLLLALE 660
            VS G  L  +E
Sbjct: 558 SVSLGAELAIIE 569


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: 914
Number of extensions: 40
Number of successful extensions: 5
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: 569
Length adjustment: 37
Effective length of query: 636
Effective length of database: 532
Effective search space:   338352
Effective search space used:   338352
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 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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