GapMind for catabolism of small carbon sources

 

Alignments 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)



>MicrobesOnline__882:206897
          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 (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