Alignments for a candidate for fadA in Methylocapsa acidiphila B2

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Methylocapsa acidiphila B2

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_026606470.1 METAC_RS0106925 3-hydroxyacyl-CoA dehydrogenase

Query= BRENDA::Q64428
         (763 letters)



>NCBI__GCF_000427445.1:WP_026606470.1
          Length = 736

 Score =  326 bits (836), Expect = 2e-93
 Identities = 229/729 (31%), Positives = 348/729 (47%), Gaps = 48/729 (6%)

Query: 49  VAVIRINSPNSKVNTLNKEVQSEFVEVMNEIWANDQIRSAVLISSKPGCFVAGADINMLA 108
           VA++  + P   +N +  +V  E  +V+  + A+  I+  V+ S K   F  GAD++ML 
Sbjct: 15  VALLTWDMPGRSMNVITPDVIDELEKVVEHVAADAAIKGCVITSGKE-TFSGGADLSMLQ 73

Query: 109 SCTTP----------QEAARISQEGQK----MFEKLEKSPKPVVAAISGSCLGGGLELAI 154
                          +EAAR+  E  +    ++ KLE   KP  AAI+G CLGG  ELA+
Sbjct: 74  VAAAEYRKALRDKGEEEAARLFFEASRRLSLVYRKLETCGKPFAAAINGLCLGGAFELAL 133

Query: 155 ACQYRIATKDRKTVLGVPEVLLGILPGAGGTQRLPKMVGVPAAFDMMLTGRNIRADRAKK 214
           AC YR+     K  +G+PE+ +G+ PGAGGTQR+ +++    A  M+  G  IR   AK 
Sbjct: 134 ACHYRVVADVDKARVGLPEIKVGLFPGAGGTQRVARLMHTGDALQMLFKGEQIRPKAAKT 193

Query: 215 MGLVDQLVDPLGPGIKSPEERTIEYLEEVAVNFAKGLADRKVSAKQSKGLMEKLTSYAMT 274
           M LV +          +P    +   +       KG+A    S         KL S  + 
Sbjct: 194 MNLVHEA---------APAGEILARAKSFIAGGGKGVAPWDESTF-------KLPSGKVF 237

Query: 275 IPFVRQQVYKTVEEKVKKQTKGLYPAPLKIIDAVKTGLEQGNDAGYLAESEKFGELALTK 334
            P     V+       +++T   YPA   I+ +V  GL+   D     ES  F ++  + 
Sbjct: 238 SP-QGMMVWPAANAIYRRETHDNYPAAKAILHSVYEGLQLPMDLALRVESRWFAKILRSP 296

Query: 335 ESKAL-------MGLYNGQVLCKKNKFGAPQKTVQQLAILGAGLMGAGIAQVSVDKGLKT 387
           E+ A+       MG  N      +    AP   ++++ ++GAG MGAGIA V+   G+  
Sbjct: 297 EAAAMIRTLFVSMGELNKGA---RRPAHAPAAPIKKVGVIGAGFMGAGIAYVTAGAGMDV 353

Query: 388 LLKDTTVTGLGRGQQQVFKGLNDKVKKKALTSFERDSIFSNLIGQLDYKGFEKADMVIEA 447
           +L D       +G+    + ++ +V K    + E++++   +    DY+    AD+VIEA
Sbjct: 354 VLIDRDQAAADKGKSVCDQLISGQVLKGRAKTAEKEALLGRIKPSADYEDLAGADLVIEA 413

Query: 448 VFEDLAVKHKVLKEVESVTPEHCIFASNTSALPINQIAAVSQRPEKVIGMHYFSPVDKMQ 507
           VFED A+K  V ++       + +FASNTS LPI  +A     PE+ IG+H+FSPV+KM 
Sbjct: 414 VFEDRAIKADVTRKARLALGPNAVFASNTSTLPIGSLAEAYAEPEQFIGIHFFSPVEKMA 473

Query: 508 LLEIITTDKTSKDTTASAVAVGLKQGKVIIVVKDGPGFYTTRCLAPMMSEVIRILQEGVD 567
           L+E+I  +KT     A A+       K  IVV D  GF+  RC+   + E   +L EG  
Sbjct: 474 LVEVILGEKTGDRALAVALDFIRAIKKTPIVVNDSRGFFANRCVGNYIREGHLMLLEGAP 533

Query: 568 PKKLDALTTGFGFPVGAATLADEVGIDVAQHVAEDLGKAFGERFGGGSVE-LLKLMV-SK 625
           P  ++ +    G PVG   L DEV +D+A  + E   +  GE       E LL+ MV   
Sbjct: 534 PALIENVAKMAGMPVGPLALNDEVALDLALKILEATKQDLGEAAVDADQEALLRAMVKGH 593

Query: 626 GFLGRKSGKGFYIYQSGSKNKNLNSEIDNILVNLRLPAKPEVSSDEDIQYRVITRFVNEA 685
           G LGRK+GKGFY Y +           D     L     P+     + + R +     EA
Sbjct: 594 GRLGRKNGKGFYDYPAQGPKFLWPGLADFQKAKL----DPDRIDIAEFKRRFLVAQALEA 649

Query: 686 VLCLQEGILATPEEGDIGAVFGLGFPPCLGGPFRFVDLYGAQKVVDRLRKYESAYGTQFT 745
              ++EG++  P E D+G++ G GF P  GG   ++D  GA   V    +    YG +FT
Sbjct: 650 ARAIEEGVVTDPREADVGSIIGFGFAPFTGGVLSYIDGMGAANFVVLCDELRRKYGPRFT 709

Query: 746 PCQLLRDLA 754
           P Q+L D+A
Sbjct: 710 PPQILIDMA 718


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: 1166
Number of extensions: 52
Number of successful extensions: 5
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: 736
Length adjustment: 40
Effective length of query: 723
Effective length of database: 696
Effective search space:   503208
Effective search space used:   503208
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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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