GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acs in Desulfovibrio vulgaris Hildenborough

Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate 206897 DVU1453 long-chain-fatty-acid--CoA ligase

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



>lcl|MicrobesOnline__882:206897 DVU1453 long-chain-fatty-acid--CoA
           ligase
          Length = 564

 Score =  177 bits (450), Expect = 7e-49
 Identities = 153/542 (28%), Positives = 246/542 (45%), Gaps = 41/542 (7%)

Query: 19  FLERAATVYGDCTSVVYDAVSYTWSQTHRRCLCLASSIASLGIENGHVVSVLAPNVPQMY 78
           FL+ AA  +   T++++     ++++        A+++ + G+  G  VSV+ PNVPQ  
Sbjct: 25  FLDEAAERHPKQTAIIFRNYKVSYAKLRLLAERFAANLRAQGVLPGDRVSVMLPNVPQAI 84

Query: 79  ELHFAVPMAGAILNAVNLRLDARTISILLHHSESKLIFVDHLSRDLILEAIALFPKQAPV 138
              + +  AG  +   N     + +   +H S ++ +    ++ DL+   I     +  +
Sbjct: 85  IAFWGLLKAGCTVVMTNPLYMEKELVHQIHDSGAEYM----IALDLVWPKIEPLRDRLGI 140

Query: 139 PRLVFMADESESGNSSELGKEFFC----SYKDLIDRGDPDFKW--VMPKSEW------DP 186
            +          G    L   F      +++D+   G+    W  +  K E       +P
Sbjct: 141 RKFFITRISDALGFPLNLLYRFKAKREGTWRDVPFDGETVIPWKTLFKKKEGYSAKVENP 200

Query: 187 M----ILNYTSGTTSSPKGVV--HCHRGIFIMTVDSLIDWGVPKQPVYLWTLPMFHANGW 240
                +L YT GTT   KGV+  H +  + +  + +++      +  +L  +P FH  G 
Sbjct: 201 REALALLQYTGGTTGISKGVMLTHYNLSVNVQQIKAILGESTRMRHTFLGLMPYFHVYGL 260

Query: 241 SYPWGM-AAVGGTNICLRKFDSEIIYDMIKRHGVTHMCGAPVVLNMLSNAP--GSEPLKT 297
           +    +  A+G T I   ++    +   I +H  T   GAP +   L      G   LK+
Sbjct: 261 TTCLTLPTALGATIIPFPRYVPRDVLVGIDKHKPTIFPGAPSIYISLMQQKDVGEFDLKS 320

Query: 298 TVQIMTAGAPPPSAVLFRTESL-GFAVSHGYGLTETAGLVVSCAWKKEWNHLPATERARL 356
               ++  AP P   + R   L G  V  G+GLTE + +           HL      + 
Sbjct: 321 IKYCISGSAPMPLEHIRRFHELTGAQVIEGFGLTEASPVT----------HLNPIHGVQK 370

Query: 357 KSRQGVGTVMQTKIDVVDPVTGAAVKRDGSTLGEVVLRGGSVMLGYLKDPEGTAKSMTAD 416
               GV     T+  VVD   G      G  +GE+++RG  VM GYL  P+ TA ++  +
Sbjct: 371 PGSIGV-PFPDTEARVVDMEVGLVPLPPGK-IGELIIRGPQVMQGYLNRPDETANTLR-N 427

Query: 417 GWFYTGDVGVMHPDGYLEIKDRSKDVIISGGENLSSVEVESILYSHPDILEAAVVARPDE 476
           GW YTGD+  M  DGY  I DR KD+II GG N+   E++ +L+ HP + EA  V  P  
Sbjct: 428 GWLYTGDIATMDEDGYFFIVDRKKDMIIVGGYNVYPREIDEVLHEHPKVKEAVTVGVPHA 487

Query: 477 FWGETPCAFVSLKKGLTKKPTEKEIVEYCRSKLPRYMVPKTVVFKEELPKTSTGKVQKFI 536
             GE   A++  ++G+  K T+ EIV +CR +L  Y VPK V F+ ELPKT  GKV + I
Sbjct: 488 TRGEIIKAYIVPREGV--KLTKAEIVAHCREQLANYKVPKQVEFRNELPKTIVGKVLRRI 545

Query: 537 LR 538
           LR
Sbjct: 546 LR 547


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: 811
Number of extensions: 51
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 556
Length of database: 564
Length adjustment: 36
Effective length of query: 520
Effective length of database: 528
Effective search space:   274560
Effective search space used:   274560
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 Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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