GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hcl in Rhizobium etli CFN 42

Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate WP_042117995.1 RHE_RS04635 malonyl-CoA synthase

Query= SwissProt::Q8GQN9
         (527 letters)



>NCBI__GCF_000092045.1:WP_042117995.1
          Length = 504

 Score =  186 bits (473), Expect = 1e-51
 Identities = 146/478 (30%), Positives = 223/478 (46%), Gaps = 11/478 (2%)

Query: 49  SYTYDELALRVNRCGSALRTTLGLQPKDRVLVCVLDGIDFPTTFLGAIKGGVVPIAINTL 108
           ++TY +      R   A+  TLG++P DRV V V    +    +L  ++ G V + +NT 
Sbjct: 27  TWTYGDAFALSGRIAGAM-DTLGIRPGDRVAVQVDKSAEALILYLACVRSGAVYLPLNTA 85

Query: 109 LTESDYEYMLTDSAARVAVVSQELLPLFAPMLGKVPTLEHLVVAGGAGEDSLAALLATGS 168
            T ++ +Y L D+  R+ VV+         +  +   +   + A G+G  SL  L     
Sbjct: 86  YTLAELDYFLGDAEPRLVVVASGAREGVETIAKRHGAIVETLDADGSG--SLLDLARDEP 143

Query: 169 EQFEAAPTRPDDHCFWLYSSGSTGAPKGTVHIHSDLIHTAELYARPILGIREGDVVFSAA 228
             F  A    DD    LY+SG+TG  KG +  H +L+  A L  R    +   D +  A 
Sbjct: 144 ADFVDASRAADDLAAILYTSGTTGRSKGAMLTHGNLLSNA-LTLRDYWRVTADDRLIHAL 202

Query: 229 KLFFAYGLGNGLIFPLAVGATAVLMAERPTPAAVFERLRRHQPDIFYGVPTLYASMLANP 288
            +F  +GL       L  GA+  L+++      +       Q  +  GVPT Y  +L +P
Sbjct: 203 PIFHTHGLFVATNVTLLAGASMFLLSKFDADEVIS---LMPQATMLMGVPTFYVRLLQSP 259

Query: 289 DCPKEGELRLRACTSAGEALPEDVGRRWQARFGVDILDGIGSTEMLHIFLSNRAGDVHYG 348
              KE   ++R   S    L  +    +QAR G  IL+  G TE      +   G    G
Sbjct: 260 RFGKEAAAKIRLFISGSAPLLAETHTEFQARTGHAILERYGMTETNMNTSNPYDGKRIAG 319

Query: 349 TSGKPVPGYRLRLIDEDGAEITTAGVAGELQISGPSSAVMYWNNPEKTAATFMGE-WTRS 407
           T G P+PG  +R+ D    ++      G ++I GP+    YW  PEKTAA F G+ +  S
Sbjct: 320 TVGLPLPGVTVRVTDPATGQVLPPEQTGMIEIKGPNVFKGYWRMPEKTAAEFTGDGFFIS 379

Query: 408 GDKYLVNDEGYYVYAGRSDDMLKVSGIYVSPIEVESALIAHEAVLEAAVVGWEDEDHLIK 467
           GD   ++ +GY    GR  D++   G  + P EVES +   E V+E+AV+G    D    
Sbjct: 380 GDLGKIDSDGYVHIVGRGKDLVISGGYNIYPKEVESEIDQIEGVVESAVIGVPHPDFGEG 439

Query: 468 PKAFIVLKPGYGAGEALRTDLKAHVKNLLAPYKYPRWIEFVDDLPKTATGKIQRFKLR 525
             A +V KPG    E  +T + A +++ LA YK P+ I F +DLP+   GK+Q+  LR
Sbjct: 440 VTAVVVRKPGAALDE--KTIISA-LQDRLARYKQPKRIIFAEDLPRNTMGKVQKNILR 494


Lambda     K      H
   0.319    0.138    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: 681
Number of extensions: 38
Number of successful extensions: 6
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: 527
Length of database: 504
Length adjustment: 35
Effective length of query: 492
Effective length of database: 469
Effective search space:   230748
Effective search space used:   230748
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: 52 (24.6 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