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_026606700.1 METAC_RS0108535 fatty acid oxidation complex subunit alpha FadB

Query= BRENDA::Q64428
         (763 letters)



>NCBI__GCF_000427445.1:WP_026606700.1
          Length = 716

 Score =  336 bits (862), Expect = 2e-96
 Identities = 222/719 (30%), Positives = 366/719 (50%), Gaps = 43/719 (5%)

Query: 52  IRINSPNSKVNTLNKEVQSEFVEVMNEIWANDQIRSAVLISSKPGCFVAGADINMLASC- 110
           +R    +  VN L+K    E    ++ + A   I+ A++ S K   F+ GADI    +  
Sbjct: 20  LRFARGDEPVNKLDKLAFDELRRAIDILAAAPGIKGALITSGKDA-FIVGADIFEFTALF 78

Query: 111 -TTPQEAARISQEGQKMFEKLEKSPKPVVAAISGSCLGGGLELAIACQYRIATKDRKTVL 169
             T +  +    +   +   L + P P VA I+G  LGGG ELA+A  YR+ +   K  +
Sbjct: 79  KETREAISAFVAQNSAILTALGELPFPTVAEINGFALGGGFELALAADYRVMSTAAK--I 136

Query: 170 GVPEVLLGILPGAGGTQRLPKMVGVPAAFDMMLTGRNIRADRAKKMGLVDQLVDPLGPGI 229
           GVPE+ LGI PG GGT RLP+++G+ A  D +++G    A+ A ++  VD +  P     
Sbjct: 137 GVPEIHLGIFPGYGGTARLPRLIGLGAGADWIISGAQQTAETALRLEAVDAMATP----- 191

Query: 230 KSPEERTIEYLEEVAV----NFAKGLAD---RKVSAKQSKGLMEKLTSYAMTIPFVRQQV 282
                   + L  +A+        G AD   R++  K   G     T  A  +   +   
Sbjct: 192 --------DILRPIALAKLGQAVSGEADWRRRRLGLKSPLG--HSKTEAAELLATAKSHA 241

Query: 283 YKTVEEKVKKQTKGLYPAPLKIIDAVKTGLEQGNDAGYLAESEKFGELALTKESKALMGL 342
              +            PA    ++ ++       DA    E+E FGE A T+ + +L+ +
Sbjct: 242 ANALPH---------LPAAHLAVELLEEAAGLDRDAALALEAEAFGEAAKTQAAVSLVRI 292

Query: 343 Y-NGQVLCKKNK-FGAPQKTVQQLAILGAGLMGAGIAQVSVDKGLKTLLKDTTVTGLGRG 400
           + N Q L K  K +      V++ A +GAG+MG GIA  S  +G+  ++KD   + L  G
Sbjct: 293 FINEQALKKTAKSYAKTALPVRKAAAVGAGVMGGGIAYQSALRGVPIIMKDIAESALDLG 352

Query: 401 QQQVFKGLNDKVKKKALTSFERDSIFSNLIGQLDYKGFEKADMVIEAVFEDLAVKHKVLK 460
             +  K L  +V++  L   + D++ +++   L Y+GF++ ++VIEAV E L+VK  VL+
Sbjct: 353 MAEARKLLARQVEQGRLAQDKADAVLASITPTLAYEGFDQVNVVIEAVVEILSVKKTVLR 412

Query: 461 EVESVTPEHCIFASNTSALPINQIAAVSQRPEKVIGMHYFSPVDKMQLLEIITTDKTSKD 520
           ++E++     + +SNTS+L I  +A    RPE  IGMH+F+PV +M L+E++   KTS+ 
Sbjct: 413 DIEALVGAQAVISSNTSSLRIGDLAESLNRPENFIGMHFFNPVPRMALVEVVRGPKTSEQ 472

Query: 521 TTASAVAVGLKQGKVIIVVKDGPGFYTTRCLAPMMSEVIRILQEGVDPKKLDALTTGFGF 580
             A+ V      GK  IVV+D PGF   R L P +   ++++++G D   +D    GFG+
Sbjct: 473 AIATIVGYASAMGKTPIVVQDCPGFVVNRALTPYLIAFLQLVRDGADFAAIDRAMEGFGW 532

Query: 581 PVGAATLADEVGIDVAQHVAEDLGKAFGERFGGGSVELLKLMVSKGFLGRKSGKGFYIYQ 640
           P+G A L D +G+D++ HV E +   F +R    +   + +++ +  LG+K+G+GFY Y 
Sbjct: 533 PMGPAYLIDVIGMDISHHVVEIVSAGFPDRMQAPASSAIDVLLREKRLGQKNGRGFYTYS 592

Query: 641 SGSK---NKNLNSEIDNILVNLRLPAKPEVSSDEDIQYRVITRFVNEAVLCLQEGILATP 697
             SK    K  + E + +L   +   K ++   E ++ R++   + EA  C+++G++A P
Sbjct: 593 RDSKGRPRKEPDPETERLLAEAQPNGKRDIGEAEIVE-RMMLPLIFEAARCVEDGVVAAP 651

Query: 698 EEGDIGAVFGLGFPPCLGGPFRFVDLYGAQKVVDRLRKYESAYGTQFTPCQLLRDLANN 756
            E D+  + GLG P  LGG   + D  G   V  R + +ES +G  + P   LR LA N
Sbjct: 652 GEADMCLILGLGLPRYLGGALAYADYLGLANVAARAKAWES-FGAIYRPGASLRALAAN 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: 1034
Number of extensions: 47
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: 2
Length of query: 763
Length of database: 716
Length adjustment: 40
Effective length of query: 723
Effective length of database: 676
Effective search space:   488748
Effective search space used:   488748
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:

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