GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Shewanella loihica PV-4

Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate 5209735 Shew_2188 long-chain-fatty-acid--CoA ligase (RefSeq)

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



>FitnessBrowser__PV4:5209735
          Length = 557

 Score =  146 bits (369), Expect = 2e-39
 Identities = 145/553 (26%), Positives = 234/553 (42%), Gaps = 50/553 (9%)

Query: 17  LGFLERAATVYGDCTSVVYDAVSYTWSQTHRRCLCLASSIAS-LGIENGHVVSVLAPNVP 75
           +   E +   Y D  + V    + T+ +   R    A+ + + L ++ G  V+++ PN+ 
Sbjct: 26  IDLFESSVAKYADQPAFVNMGATLTYRKLEERSRAFAAYLQNELKLQKGDRVAIMMPNLL 85

Query: 76  QMYELHFAVPMAGAILNAVNLRLDARTISILLHHSESKLIFVDHLSRDLILEAIALFPKQ 135
           Q     F +  AG ++  VN     R +   L+ S +K I V     + + + +   P +
Sbjct: 86  QYPIALFGILRAGMVVVNVNPLYTPRELKHQLNDSGAKAIVVVSNFANTLEQVVEQTPVK 145

Query: 136 ------------APVPRLVFMADESESGNSSELGKEFFCSYKDLIDRGDPDFKWVMPKSE 183
                       AP   LV    +       +       S +  + +G    ++V P  +
Sbjct: 146 SVILTGLGDLLSAPKRTLVNFVVKYIKKMVPKYHLPHAISMRQSLSKGRR-LQYVKPTIK 204

Query: 184 WDPM-ILNYTSGTTSSPKGVVHCHRGIFIMTVDSLIDWGVPKQPVY-------LWTLPMF 235
            D +  L YT GTT   KG +  H  I    V +L+       P+        +  LP++
Sbjct: 205 GDDIAFLQYTGGTTGVSKGAMLTHGNI----VSNLLQADAAYSPLLADGKEFVVTALPLY 260

Query: 236 HANGWSYPWGMAAVGGTNICL--RKFDSEIIYDMIKRHGVTHMCGAPVVLNMLSNAPGSE 293
           H    +    +    G N  L     D       +K+H  T + G   + N L ++   +
Sbjct: 261 HIFALTVNCLLFLHKGANNLLITNPRDIPAFVSELKKHPFTALTGVNTLFNALVSSEEFK 320

Query: 294 PLKTTVQIMTAGAPPPSAVLFRTESLGFAVSH---GYGLTETAGLVVSCAWKKEWNHLPA 350
            L  +   ++ G           +  G   +    GYGLTE + L+  C +  E  +   
Sbjct: 321 TLDFSNLKLSIGGGMAVQRAVADKWQGITKTRLLEGYGLTEASPLLTCCPYNLEGYN--- 377

Query: 351 TERARLKSRQGVG-TVMQTKIDVVDPVTGAAVKRDGSTLGEVVLRGGSVMLGYLKDPEGT 409
                      +G  V  T + V D      V   G T GE+  +G  VM GY + PE T
Sbjct: 378 ---------GSIGFPVANTDMQVRDEEGN--VLPQGET-GELFAKGPQVMKGYWQRPEET 425

Query: 410 AKSMTADGWFYTGDVGVMHPDGYLEIKDRSKDVIISGGENLSSVEVESILYSHPDILEAA 469
           AK +  DG+  TGD+G M   G+  I DR KD+I+  G N+   EVE ++  HP +LE A
Sbjct: 426 AKVIDKDGYLATGDIGYMDEQGFFFIVDRKKDMILVSGFNVFPNEVEEVVALHPKVLEVA 485

Query: 470 VVARPDEFWGETPCAFVSLKKGLTKKPTEKEIVEYCRSKLPRYMVPKTVVFKEELPKTST 529
            V  P E  GE    FV  K    K  TE++++++CR  L  Y +PK V F++ELPK++ 
Sbjct: 486 AVGVPHEVSGELVKVFVVPK---DKSLTEEQVIKHCRHHLTGYKIPKLVEFRDELPKSNV 542

Query: 530 GKVQKFILRDMAR 542
           GK+ +  LRD A+
Sbjct: 543 GKILRRELRDEAK 555


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: 694
Number of extensions: 33
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 556
Length of database: 557
Length adjustment: 36
Effective length of query: 520
Effective length of database: 521
Effective search space:   270920
Effective search space used:   270920
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