Alignments for a candidate for ech in Rhodopseudomonas palustris CGA009

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Rhodopseudomonas palustris CGA009

Align fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized)
to candidate WP_011156385.1 TX73_RS04220 3-hydroxyacyl-CoA dehydrogenase

Query= CharProtDB::CH_003230
         (714 letters)



>NCBI__GCF_000195775.1:WP_011156385.1
          Length = 738

 Score =  413 bits (1062), Expect = e-119
 Identities = 256/734 (34%), Positives = 390/734 (53%), Gaps = 30/734 (4%)

Query: 7   FTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKPDNFI 66
           F +    D IA++T D+PG+ MN L A    ++ AI +   ++  ++GVV  SAK D F 
Sbjct: 6   FKVETDADGIALVTWDLPGKSMNVLDAATIEELGAIAEATTKDAAVKGVVITSAK-DAFC 64

Query: 67  AGADINMIGNC----------KTAQEAEAL----ARQGQQLMAEIHALPIQVIAAIHGAC 112
           AGAD++M+ +           K  + A+ +    +R+  Q++  I       +AAI+G  
Sbjct: 65  AGADLSMLESMNQQFAQIRKDKGEEAAQKMLFDESRKLSQILRGIETCGKPWVAAINGLA 124

Query: 113 LGGGLELALACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGK 172
           LGGG E+ LACH RV  D+PKT LGLPE+++GL PG GGTQR+PR++    A+ ++L G 
Sbjct: 125 LGGGFEVTLACHYRVAADNPKTRLGLPEIKVGLFPGGGGTQRIPRIVDPQNAMTILLKGD 184

Query: 173 QLRAKQALKLGLVDDVVPHSILLEAAVELAKKERPSSRPLPVRERILAGPLGRA------ 226
           Q++  +A  L LVD VVP + L++ A +  K    +  P   +   L G  G+       
Sbjct: 185 QIKLDKAKALKLVDAVVPAADLIKTAKDWIKNGGKAVAPWDEKGFKLPG--GQVFSKQGM 242

Query: 227 LLFKMVGKKTEHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQAL- 285
           ++F         +T  NYPA   I+  V  GL          E+R F  +  T ++ A+ 
Sbjct: 243 MMFPAGNAIYRRETYDNYPAARAIMSCVYEGLLVPIDVALRIESRYFAHVLQTKEAAAMI 302

Query: 286 RSIFFASTDVKKDPG--SDAPPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQ 343
           RS+F +  ++ K        PP  +  + I+G G MG  + YV+A KAGI V + D + +
Sbjct: 303 RSLFLSMQELNKGARRPQGVPPTKVKKLAIIGAGFMGASVGYVSA-KAGIEVVLIDRDQE 361

Query: 344 GINHALKYSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELK 403
             +    +    ++G +++   K ++RD  ++ I+ T D+   +  DL+IEAVFE+ ++K
Sbjct: 362 SADKGKAHCQSVIDGLIKKGRAKEADRDALMSRITATPDFNAISDCDLVIEAVFEDRKVK 421

Query: 404 QQMVAEVEQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHA 463
            +  A+ +       IFASNTS+LPI  +A       + IG+HFFSPVEKM LVE+I   
Sbjct: 422 AETYAKAQPLLKEGAIFASNTSTLPINSLAEEFKDQSKFIGIHFFSPVEKMMLVEVILGN 481

Query: 464 GTSAQTIATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAAL 523
            TS  T+AT +   ++ GKTPIVV D  GF+ NR +  +  E + ML +G     I+ A 
Sbjct: 482 NTSDVTLATALDYTRQIGKTPIVVNDSRGFFANRCVLRFTAEGLEMLMEGVPAPMIETAA 541

Query: 524 VKFGFPVGPIQLLDEVGIDTGTKIIPVLEAAYGERF---SAPANVVSSILNDDRKGRKNG 580
              G PVGP+ L DEV +D   KI+   EA  GE+         +V  +    R GRKNG
Sbjct: 542 KMAGMPVGPLSLADEVALDLILKIMKATEADLGEQAVDQQQKKLMVELVEKQGRFGRKNG 601

Query: 581 RGFYLYGQKGRKSKKQVDPAIYPLIGTQGQGRISAPQVAERCVMLMLNEAVRCVDEQVIR 640
           +GFY+Y +KG+  K   D              I   ++ +R + +   EA R V++ VI 
Sbjct: 602 KGFYVYPEKGKGQKSLWDGIAALQPKHLDPDTIDVEELKQRFLAVQAVEAARTVEDNVIV 661

Query: 641 SVRDGDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMGA 700
             R+ D+G++ G GF PF GG   YID +G  E VA+  +L  ++GSRFTP + L +M  
Sbjct: 662 DPREADVGSILGFGFAPFTGGTLSYIDFMGTKEFVALCHKLEGKFGSRFTPPKLLEDMAK 721

Query: 701 RGESFWKTTATDLQ 714
            G++F+   A   Q
Sbjct: 722 TGDTFYHRFAPKKQ 735


Lambda     K      H
   0.319    0.137    0.393 

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: 983
Number of extensions: 42
Number of successful extensions: 7
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: 714
Length of database: 738
Length adjustment: 40
Effective length of query: 674
Effective length of database: 698
Effective search space:   470452
Effective search space used:   470452
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 (21.8 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