Alignments for a candidate for fadA in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Dyella japonica UNC79MFTsu3.2

Align long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211); acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate N515DRAFT_0416 N515DRAFT_0416 3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase / 3-hydroxybutyryl-CoA epimerase

Query= BRENDA::Q64428
         (763 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0416
          Length = 686

 Score =  338 bits (866), Expect = 7e-97
 Identities = 224/704 (31%), Positives = 350/704 (49%), Gaps = 53/704 (7%)

Query: 49  VAVIRINSPNSKVNTLNKEVQSEFVEVMNEIWANDQIRSAVLISSKPGCFVAGADINMLA 108
           +  + ++  NS VN L++EV  E  +++  + + ++    ++ S+KPG F  GADI    
Sbjct: 19  IVTLTLDRANSSVNALSREVLDELGQIVERL-SIEKPAGVLIHSAKPGGFAVGADIKEFV 77

Query: 109 SCTTPQEAARISQEGQKMFEKLEKSPKPVVAAISGSCLGGGLELAIACQYRIATKDRKTV 168
                    +  + GQ++FE L + P P VAAI G+C+GGG EL +AC+ RIA  D KT 
Sbjct: 78  EYARDGTVLQNIENGQRVFESLARLPCPTVAAIHGACMGGGTELVLACRQRIAADDEKTR 137

Query: 169 LGVPEVLLGILPGAGGTQRLPKMVGVPAAFDMMLTGRNIRADRAKKMGLVDQLVDPLGPG 228
           +G+PEV+LGI PG GGT RLP+++G   A  +MLTG+ + A RA  +G+VD+L  P    
Sbjct: 138 IGLPEVMLGIHPGWGGTARLPRLIGALDALPVMLTGKALSARRAAALGVVDRLAPP---- 193

Query: 229 IKSPEERTIEYLEEVAVNFAKGLADRKVSAKQSKGLMEKLTSYAMTIPFVRQQVYKTVEE 288
                    E L E     A+ L  R  +   ++ L    T+       +   V K    
Sbjct: 194 --------NELLAE-----ARALLRRPHARPAARRLKAWATNTWPARQILAPMVLKQTAA 240

Query: 289 KVKKQTKGLYPAPLKIIDAVKTGLEQGNDAGYLAESEKFGELALTKESKALMGLYNGQVL 348
           KV+K+    YPAP  +I+  + G         L E+    +LA T  ++ L+ ++  Q  
Sbjct: 241 KVRKEH---YPAPFALINVWQRGGSSIQQRLKL-EARSVAKLAETSTARNLIRIFLLQER 296

Query: 349 CKKNKFGAPQKTVQQLAILGAGLMGAGIAQVSVDKGLKTLLKDTTVTGLGRGQQQVFKGL 408
            K    G  +  ++ + ++GAG+MG  IA  +  KG +  L+D  +  +    Q      
Sbjct: 297 LKGQGSGV-EHGIEHVHVVGAGVMGGDIAAWAAFKGFQVTLQDREMKFI----QPALDRA 351

Query: 409 NDKVKKKALTSFERDSIFSNLIGQLDYKGFEKADMVIEAVFEDLAVKHKVLKEVESVTPE 468
               +KK  T  + +     L   ++ KG   AD+ IEA+FE+   K  +   +E     
Sbjct: 352 RALYEKKLKTPEKVEETARRLRADVEGKGVAAADLAIEAIFENAEAKQALYASIEPQFQA 411

Query: 469 HCIFASNTSALPINQIAAVSQRPEKVIGMHYFSPVDKMQLLEIITTDKTSKDTTASAVAV 528
             I A+NTS++P++++    + P++ +G+H+F+PV +M L+E++  D    +    A+A 
Sbjct: 412 DEILATNTSSIPLDELRRGLKAPQRFLGLHFFNPVAQMPLVEVVRHDGLDPEVEKRALAF 471

Query: 529 GLKQGKVIIVVKDGPGFYTTRCLAPMMSEVIRILQEGVDPKKLDALTTGFGFPVGAATLA 588
               GK+ + VK  PGF   R L P + E IR+  EGV    LD     FG P+G   LA
Sbjct: 472 CKAIGKLPVAVKGTPGFLVNRILMPYLLEAIRLYNEGVPGPVLDKEAKKFGMPMGPIELA 531

Query: 589 DEVGIDVAQHVAEDLGKAFGERFGGGSVELLKLMVSKGFLGRKSGKGFYIYQSGSKNKNL 648
           D VG+DV   V ++L    G     G  + L    + G  G+K G+GFY++Q G      
Sbjct: 532 DTVGLDVCASVGKELAPFLGLELPPGIEDKL----AAGKRGKKDGQGFYVWQEGK----- 582

Query: 649 NSEIDNILVNLRLPAKPEVSSD----EDIQYRVITRFVNEAVLCLQEGILATPEEGDIGA 704
                        P KPEV  D     D+Q R++   VNEAV CL +G++   +  D G 
Sbjct: 583 -------------PQKPEVDPDYAVPADLQERMLLPMVNEAVACLADGVVDDADLLDAGV 629

Query: 705 VFGLGFPPCLGGPFRFVDLYGAQKVVDRLRKYESAYGTQFTPCQ 748
           +FG GF P  GGP ++V   GA  +  +L +    +G +FTP Q
Sbjct: 630 IFGTGFAPFRGGPIQYVRSEGAAVIKGKLERLAQRHGERFTPKQ 673


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: 1160
Number of extensions: 65
Number of successful extensions: 6
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: 763
Length of database: 686
Length adjustment: 40
Effective length of query: 723
Effective length of database: 646
Effective search space:   467058
Effective search space used:   467058
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 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources