GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Rhodobacter viridis JA737

Align long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211); acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_110804971.1 C8J30_RS06890 3-hydroxyacyl-CoA dehydrogenase

Query= BRENDA::Q64428
         (763 letters)



>NCBI__GCF_003217355.1:WP_110804971.1
          Length = 728

 Score =  328 bits (840), Expect = 8e-94
 Identities = 225/728 (30%), Positives = 363/728 (49%), Gaps = 53/728 (7%)

Query: 49  VAVIRINSPNSKVNTLNKEVQSEFVEVMNEIWANDQIRSAVLISSKPGCFVAGADINMLA 108
           VAVI  +  +  +N ++ E  ++   +++   A+   +  VL S K   F  G D+N++A
Sbjct: 13  VAVITWDVADKSMNVMSLEGFAQLSALVDGCLADPACKGIVLTSGKKD-FAGGMDLNVIA 71

Query: 109 SCTTPQEAA-------------RISQEGQKMFEKLEKSPKPVVAAISGSCLGGGLELAIA 155
                   A             +I + G  M  K  K  KP+   + G+ LG GLEL ++
Sbjct: 72  KMRAGGAEAIFAGVMQMHAVLRKIERAG--MDPKTLKGAKPIACVLPGTALGIGLELPLS 129

Query: 156 CQYRIATKDRKTVLGVPEVLLGILPGAGGTQRLPKMVGVPAAFDMMLTGRNIRADRAKKM 215
           C    A ++ K  +G+PE+++GI PGAGGT RL + +G   A   +L G+      AK  
Sbjct: 130 CHRIFAAENPKAKIGLPEIMVGIFPGAGGTTRLVRKMGAMMAAPFLLEGKLSDPKAAKAA 189

Query: 216 GLVDQL-VDPLGPG----IKSPEERTIEYLEEVAVNFAKGLADRKVSAKQSKGLMEKLTS 270
           G++D++  DP+       +K+ +   ++  +      AKG      +     G M  + +
Sbjct: 190 GIIDEVCADPMAAARDWVLKATDADLVKPWD------AKGYKMPGGAPYHPAGFMTYVGA 243

Query: 271 YAMTIPFVRQQVYKTVEEKVKKQTKGLYPAPLKIIDAVKTGLEQGNDAGYLAESEKFGEL 330
            AM                V  +T G+YPA   ++ AV  G     D     E+  F ++
Sbjct: 244 SAM----------------VHGKTMGVYPAAKALLSAVYEGALVPFDQALRIEARWFTKV 287

Query: 331 ALTKESKALMG--LYNGQVLCK-KNKFGAPQKTVQQLAILGAGLMGAGIAQVSVDKGLKT 387
            +   S A++     N + L K  N+     ++V +L +LGAG+MGAGIA V+ + G++ 
Sbjct: 288 LMNPSSGAMIRSLFINKEALEKGANRPKVADQSVTKLGVLGAGMMGAGIAYVAANAGIEV 347

Query: 388 LLKDTTVTGLGRGQQQVFKGLNDKVKKKALTSFERDSIFSNLIGQLDYKGFEKADMVIEA 447
           +L D +     RG+      L+  ++++ +T  ++  +   +    DY      D+V+EA
Sbjct: 348 VLIDASQEAADRGKSYSTGILDKGIQRRKVTEAKKAEVLDRITATTDYAALAGCDLVVEA 407

Query: 448 VFEDLAVKHKVLKEVESVTPEHCIFASNTSALPINQIAAVSQRPEKVIGMHYFSPVDKMQ 507
           VFED  VK +V  + E+V     IFA+NTS LPI+ +A  SQRP   IG+H+FSPVDKM 
Sbjct: 408 VFEDPKVKAEVTAKAEAVIGAGAIFATNTSTLPISGLAKASQRPANFIGIHFFSPVDKMN 467

Query: 508 LLEIITTDKTSKDTTASAVAVGLKQGKVIIVVKDGPGFYTTRCLAPMMSEVIRILQEGVD 567
           L+EII    T +   A A+       K  IVV D   FY  RC+ P ++E IR++ EGV+
Sbjct: 468 LVEIIRGKDTGEVAVAKALDFVRAIRKTPIVVNDARFFYANRCIIPYINEGIRMVAEGVN 527

Query: 568 PKKLDALTTGFGFPVGAATLADEVGIDVAQHVAEDLGKAFGERFGGGSV-ELLKLMVSKG 626
           P  ++      G P+G   L DE  ID+   +A+    A G+ +  G+V E++  M  +G
Sbjct: 528 PVLVENAAKLVGMPLGPLQLVDETSIDLGVKIAKATKAAMGDAYPDGAVDEVVFWMAEQG 587

Query: 627 FLGRKSGKGFYIYQSGSKNKNLNSEIDNILVNLRLPAKPEVSSDEDIQYRVITRFVNEAV 686
            LG+K+  GFY Y +G +    +       ++ + P   +      +Q+R++   V EAV
Sbjct: 588 RLGKKADAGFYTYDAGKRGGMWDG------LSAQYPRAADQPDLTHVQHRLLMVQVLEAV 641

Query: 687 LCLQEGILATPEEGDIGAVFGLGFPPCLGGPFRFVDLYGAQKVVDRLRKYESAYGTQFTP 746
              ++G+L    EGD+GA+ G GF P  GGPF ++D+ GA + V+      + YG +F P
Sbjct: 642 RAFEQGVLTDIREGDVGAILGWGFAPWSGGPFAWLDILGAARAVEICDGLAAQYGARFEP 701

Query: 747 CQLLRDLA 754
             LLRD+A
Sbjct: 702 PALLRDIA 709


Lambda     K      H
   0.317    0.135    0.380 

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: 1111
Number of extensions: 63
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 763
Length of database: 728
Length adjustment: 40
Effective length of query: 723
Effective length of database: 688
Effective search space:   497424
Effective search space used:   497424
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Sep 24 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