GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Rhodococcus qingshengii djl-6-2

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_076948712.1 C1M55_RS02160 3-hydroxyacyl-CoA dehydrogenase

Query= CharProtDB::CH_003230
         (714 letters)



>NCBI__GCF_002893965.1:WP_076948712.1
          Length = 713

 Score =  340 bits (872), Expect = 1e-97
 Identities = 250/707 (35%), Positives = 357/707 (50%), Gaps = 42/707 (5%)

Query: 14  DNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKE-LRGVVFVSAKPDNFIAGADI- 71
           D I V+TI+ P +  NT+   + + ++A + +L   K+ + G V  S K   F AG D+ 
Sbjct: 14  DGIVVLTINDPNQGANTMNDAYIASMKATVDRLVAEKDSVTGAVITSGKK-TFFAGGDLK 72

Query: 72  NMIGNCKTAQEAEALARQGQQLMAEIHALPI---QVIAAIHGACLGGGLELALACHGRVC 128
           NMI      ++AE +     ++ A++  L      V+AAI+GA LGGGLE+ALA H R+ 
Sbjct: 73  NMIK--VGPEQAEEIYNHSVEIKADLRRLETLGKPVVAAINGAALGGGLEIALATHHRIA 130

Query: 129 TDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALE-MILTGKQLRAKQALKLGLVDD 187
            D     +GLPEV LGLLPG GG  R  R++G+  AL  ++L G+Q    QA ++GL+D+
Sbjct: 131 ADVKGVKIGLPEVTLGLLPGGGGVVRTVRMLGLQNALMGVLLQGQQRGPVQAKEVGLIDE 190

Query: 188 VVPHSILLEAAVELAKKERPSS--RPLPVRERILAG-----PLGRALLFKMVGKKTEHKT 240
           VV     L  A +   K  P    +P  V+   + G     P   A L        +   
Sbjct: 191 VVGSVEELVPAAKAWIKANPEGGVQPWDVKGYKIPGGTPSTPAFAANLPAFPANLRKQLK 250

Query: 241 QGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQALRSIFFASTDVKKDPG 300
               PA   I+     G      +    EAR F  L     ++ +   FF   D++   G
Sbjct: 251 GAPMPAPRAIMAAAVEGSQVDIDNALLIEARYFTSLVTGRVAKNMIQAFFF--DLQSING 308

Query: 301 SDAPPA-----PLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHALKYSWDQ 355
             + PA      +  VG+LG G+MG GIAYV+A KAG  V +KD++ +  N    Y+ + 
Sbjct: 309 GGSRPAGIEKSTIKKVGVLGAGMMGAGIAYVSA-KAGFDVVLKDVSIEAANKGKAYA-EG 366

Query: 356 LEGKVRRRHLKASER-DKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQMVAEVEQNC 414
           +E K   R     E+ D  LA I+ T D   FA  D +IEAVFE+ ELK ++  E+E   
Sbjct: 367 IEAKALSRGKTTQEKSDALLAKITPTADPADFAGVDFVIEAVFESQELKHKVFQEIEDIV 426

Query: 415 AAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQTIATTV 474
               +  SNTS+LPI  +A    R E  IG+HFFSPV+KMPLVEII    TS +T+A   
Sbjct: 427 DPKALLGSNTSTLPITGLATGVKRQEDFIGIHFFSPVDKMPLVEIIRGEKTSDETLARVF 486

Query: 475 KLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKFGFPVGPIQ 534
              +   KTPIVV D  GF+ +R++  +INEAI ML +G     I+ A ++ G+P  P+Q
Sbjct: 487 DYVQAIRKTPIVVNDSRGFFTSRVIGTFINEAIGMLAEGVEPATIEQAGMQAGYPAAPLQ 546

Query: 535 LLDEVGIDTGTKI-IPVLEAAYGERFSAPANVVSSILND-----DRKGRKNGRGFYLYGQ 588
           L DE+ +    KI     +AA  E    PA+    ++N      DRKG+  G GFY Y +
Sbjct: 547 LSDELNLTLMQKIRKESADAAKAEGKELPADPAGEVINTLVEKFDRKGKLGGAGFYDYAE 606

Query: 589 KGRKSKKQVDPAIYPLIGTQGQGRISAP--QVAERCVMLMLNEAVRCVDEQVIRSVRDGD 646
             R            L      G   AP   + +R + +   E  +C DE V+ +  D +
Sbjct: 607 GKRTGLWS------GLRENFNSGTSDAPIQDLIDRMLFIEAIETQKCFDENVLITTADAN 660

Query: 647 IGAVFGIGFPPFLGGPFRYIDSL--GAGEVVAIMQRLATQYGSRFTP 691
           IG++ GIGFP + GG  ++I     G    VA  + LA QYG RFTP
Sbjct: 661 IGSIMGIGFPAWTGGVHQFIVGYEGGTAGFVARAKELAAQYGPRFTP 707


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: 1045
Number of extensions: 45
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 714
Length of database: 713
Length adjustment: 39
Effective length of query: 675
Effective length of database: 674
Effective search space:   454950
Effective search space used:   454950
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:

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