GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Rhizobium etli CFN 42

Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_011423856.1 RHE_RS02425 long-chain fatty acid--CoA ligase

Query= metacyc::MONOMER-20125
         (556 letters)



>NCBI__GCF_000092045.1:WP_011423856.1
          Length = 566

 Score =  148 bits (374), Expect = 5e-40
 Identities = 157/568 (27%), Positives = 249/568 (43%), Gaps = 65/568 (11%)

Query: 8   PASSSPLTPLGF---LERAATVYGDCTSVVYDAVSYTWSQTHRRCLCLASSIASLGIENG 64
           PA   PL        LE++   Y D T       S ++     +   +A+ + S+G+E G
Sbjct: 26  PAELPPLEHASLAELLEKSCARYADRTVFSSMGKSMSYRDLESQTRKVAAWLQSIGLEKG 85

Query: 65  HVVSVLAPNVPQMYELHFAVPMAGAILNAVNLRLDARTISILLHHSESKLIFV-DHLSRD 123
             V+V+ PNV Q     +A+  AG ++  VN     R +   L  S +K IFV ++ +R 
Sbjct: 86  DRVAVMMPNVLQNPVATYAILRAGLVVVNVNPLYTPRELEHQLRDSGAKAIFVLENFART 145

Query: 124 L------------ILEAIA--LFPKQAPVPRLVFMADESESGNSSELGKEFFCSYKDLID 169
           +            ++ ++   L PK   V  +V    +     S    K    S+  ++ 
Sbjct: 146 VEQVLNKTDLRHVVVTSLGEMLGPKGLMVNFVVRKVKKLVPSWSIPQHK----SFSQVLR 201

Query: 170 RGDPDFKWVMPKSEWDPMILNYTSGTTSSPKGVVHCHRGIFIMTVDSLI----DWGVPKQ 225
            G       +  +      L YT GTT   KG V  H+ +    +   +     +   KQ
Sbjct: 202 EGAKKSLQPVTLAGGHIAFLQYTGGTTGVAKGAVLTHQNLLANKLQLSLWLRSAFQRKKQ 261

Query: 226 PV---YLWTLPMFHANGWSYPWGMA-AVGGTNICLRKFDSEIIYDMIKRHGVTHMC---G 278
           P    +L  LP++H    +    M  ++G  NI +   +   I  ++K  G +++    G
Sbjct: 262 PEVLNFLCALPLYHIFALTVNSLMGMSLGAHNILIA--NPRDIPGLVKEFGKSNIHIFPG 319

Query: 279 APVVLNMLSNAPGSEPLKTTVQIMTAGA----PPPSAVLFRTESLGFAVSHGYGLTETAG 334
              + N L N      L  +  IM+ G       P A  +  ++ G A++ GYGL+ET+ 
Sbjct: 320 LNTLFNALMNNAEFAKLDFSSLIMSLGGGMAVQRPVAERW-LKTTGTAITEGYGLSETS- 377

Query: 335 LVVSCAWKKEWNHLPATERARLKSRQGVGTV----MQTKIDVVDPVTGAAVKRDGSTLGE 390
                         P     R  S +  G++      T++D+ D   G ++      +GE
Sbjct: 378 --------------PVATANRFDSIEFTGSIGLPIPSTELDIRDE-EGRSLPL--GEIGE 420

Query: 391 VVLRGGSVMLGYLKDPEGTAKSMTADGWFYTGDVGVMHPDGYLEIKDRSKDVIISGGENL 450
           + +RG  VM GY + PE TA+ MTADG+F +GD+G M   GY +I DR KD+I+  G N+
Sbjct: 421 ICIRGPQVMAGYWQKPEETARVMTADGYFRSGDMGFMDERGYTKIVDRKKDMILVSGFNV 480

Query: 451 SSVEVESILYSHPDILEAAVVARPDEFWGETPCAFVSLKKGLTKKPTEKEIVEYCRSKLP 510
              E+E +   H  ILEAA V  PD   GE    FV  K       TE E+  +C + L 
Sbjct: 481 YPNEIEEVAAMHAGILEAAAVGVPDGHSGEAVKLFVVRK---DPNLTEAEVRAHCIANLT 537

Query: 511 RYMVPKTVVFKEELPKTSTGKVQKFILR 538
            Y  P+ + F+ ELPK+  GK+ +  LR
Sbjct: 538 NYKRPRFIEFRTELPKSPVGKILRKDLR 565


Lambda     K      H
   0.319    0.135    0.412 

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: 740
Number of extensions: 42
Number of successful extensions: 6
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: 556
Length of database: 566
Length adjustment: 36
Effective length of query: 520
Effective length of database: 530
Effective search space:   275600
Effective search space used:   275600
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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:

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:

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:

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:

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