GapMind for Amino acid biosynthesis

 

Alignments for a candidate for prpE in Desulfatibacillum aliphaticivorans DSM 15576

Align 2-methylpropanoate--CoA ligase CCL4; HlCCL4; 2-methylbutanoate--CoA ligase CCL4; Butanoate--CoA ligase CCL3; Propionate--CoA ligase CCL3; EC 6.2.1.-; EC 6.2.1.17 (characterized)
to candidate WP_028315795.1 G491_RS0119705 fatty acid--CoA ligase

Query= SwissProt::M4IQQ5
         (556 letters)



>NCBI__GCF_000429905.1:WP_028315795.1
          Length = 544

 Score =  267 bits (682), Expect = 9e-76
 Identities = 175/540 (32%), Positives = 288/540 (53%), Gaps = 32/540 (5%)

Query: 16  PLGFLERAATVYGDCTSVVY-DAVSYTWSQTHRRCLCLASSIASLGIENGHVVSVLAPNV 74
           PL   +  AT+Y     +VY D ++YT+    +R   LA+++  LGI  G  V+V+  + 
Sbjct: 16  PLLIKQLLATIYEPDQEIVYRDKMTYTYKDMEKRTRKLANALEGLGITQGSTVAVMDWDS 75

Query: 75  PQMYELHFAVPMAGAILNAVNLRLDARTISILLHHSESKLIFVDHLSRDLILEAIALFPK 134
            +  E  FAVPM GA+L+ +N+RL    +   ++H+E  +I V H     +LEA+    +
Sbjct: 76  HRYLECFFAVPMMGAVLHTINIRLSPEQLVYTVNHAEDDIILV-HKDFAPLLEAVK--DQ 132

Query: 135 QAPVPRLVFMADESESGNSSELGKEFFCSYKDLIDRGDPDFKWVMPKSEWDPMI-LNYTS 193
              V + V +AD  ++  +S    EF   Y+DL++    +++W  P  + + M  + YT+
Sbjct: 133 LTTVKKFVLIADYEDAPATS---LEFAGEYEDLVEAAGEEYEW--PDFDENAMATMFYTT 187

Query: 194 GTTSSPKGVVHCHRGIFIMTVDSL-----------IDWGVPKQPVYLWTLPMFHANGWSY 242
           GTT  PKGV   HR + + T   +           ID G     VY+   PMFH + W  
Sbjct: 188 GTTGLPKGVYFSHRQLVLHTFGLMSAANSFRAQLKIDAG----DVYMPLTPMFHVHAWGM 243

Query: 243 PWGMAAVGGTNICLRKFDSEIIYDMIKRHGVTHMCGAPVVLNMLSNAPGSEPLKTTV-QI 301
           P+ M  +G   I   +++ E+I  + + + V+     P +L+ML N+P ++    +  ++
Sbjct: 244 PYSMTVMGAKQIYPGRYEPELILKLYRDYKVSFSHCVPTILHMLLNSPSAKDTDFSGWKM 303

Query: 302 MTAGAPPPSAVLFRTESLGFAVSHGYGLTETAGLVVSCAWKKEWNHLPATERARLKSRQG 361
           +  GA  P  +      LG  +   YG++ET  L+     K     LP  E+   +++ G
Sbjct: 304 IIGGAALPKGMCIEGLKLGINIYSAYGMSETCPLLTQALLKPNMLDLPLEEQVVYRTKTG 363

Query: 362 VGTVMQTKIDVVDPVTGAAVKRDGSTLGEVVLRGGSVMLGYLKDPEGTAKSMTADGWFYT 421
           +      ++ VVDP  G  +  DG T GEVV+R   +  GYL +PE  ++ +   GW +T
Sbjct: 364 L-PCPGVQLRVVDPA-GNPLPHDGKTAGEVVVRAPWLTQGYLNNPE-KSEELWEKGWLHT 420

Query: 422 GDVGVMHPDGYLEIKDRSKDVIISGGENLSSVEVESILYSHPDILEAAVVARPDEFWGET 481
           GDVG++   GYL+I DR KDVI +GGE LSS+E+ESI+  H  + E AVV   D+ WGE 
Sbjct: 421 GDVGIIDELGYLQITDRIKDVIKTGGEWLSSLELESIISQHKGVSEVAVVGVKDDKWGER 480

Query: 482 PCAFVSLKKG--LTKKPTEKEIVEYCRS-KLPRYMVPKTVVFKEELPKTSTGKVQKFILR 538
           P A +  K+G  L+K+  +  +  +  +  +P+Y +P++++F +E+PKTS GK+ K  +R
Sbjct: 481 PMALIVPKEGQELSKEEVQTFMGAWVENGAIPKYGIPESILFVDEIPKTSVGKIDKKEIR 540


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: 800
Number of extensions: 41
Number of successful extensions: 8
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: 556
Length of database: 544
Length adjustment: 36
Effective length of query: 520
Effective length of database: 508
Effective search space:   264160
Effective search space used:   264160
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 Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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:

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