GapMind for catabolism of small carbon sources

 

Aligments for a candidate for paaH in Pseudomonas fluorescens FW300-N2E2

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 Pf6N2E2_6000 Enoyl-CoA hydratase [isoleucine degradation] (EC 4.2.1.17) / 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) / 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3)

Query= CharProtDB::CH_003230
         (714 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6000 Enoyl-CoA hydratase
           [isoleucine degradation] (EC 4.2.1.17) /
           3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) /
           3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3)
          Length = 714

 Score =  382 bits (981), Expect = e-110
 Identities = 268/725 (36%), Positives = 373/725 (51%), Gaps = 33/725 (4%)

Query: 3   MTSAFTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKE-LRGVVFVSAK 61
           MT A       D I V+T+D+PG+  NT+ A +   + A + +L+  K+ + GV+  SAK
Sbjct: 1   MTDAIRYETGQDRIVVLTLDMPGQSANTMNAVYREAMAACVARLQAEKDSIAGVIITSAK 60

Query: 62  PDNFIAGADINMIGNCKTAQ-EAEALARQGQQLMAEIHALPI---QVIAAIHGACLGGGL 117
              F AG D+N +   K  + EA+A       L A++  L      V+AAI+GA LGGG 
Sbjct: 61  -HTFFAGGDLNEL--IKVGKPEAKAFYDMVLLLKAQLRTLETLGKPVVAAINGAALGGGW 117

Query: 118 ELALACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAK 177
           E+ LACH RV  D P   LGLPEV LGLLPG GG  R+ RL+G+  AL  +L GK++ A+
Sbjct: 118 EICLACHHRVALDLPSVQLGLPEVTLGLLPGGGGVVRMVRLLGLEKALPYLLEGKKVNAQ 177

Query: 178 QALKLGLVDDVVPHSILLEAAVELAKKERPSS-RPLPVRERILAGPLGR----ALLFKMV 232
           QAL  GL+D++      L A         PS  +P   +   L G        A +  + 
Sbjct: 178 QALLAGLIDELAKDRNELLAKSRAWILANPSVIQPWDAKGYRLPGGTPSDPKVAQMLAIA 237

Query: 233 GKKTEHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQALRSIFFAS 292
                +KTQG  PA E+IL     G      + +  E R F EL     ++ L   F+  
Sbjct: 238 PSILRNKTQGCLPAPEKILCAAVEGAQVDFDTAHLIETRYFTELTTGQVAKNLIGTFWFQ 297

Query: 293 TDVKKDPGS---DAPPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHAL 349
            +  K  GS      P     VG+LG G+MG GIAYV+A  AGI V +KD++        
Sbjct: 298 LNEIKAGGSRPQGLAPYLTKKVGVLGAGMMGAGIAYVSAV-AGIAVVLKDVDLAAAEKGK 356

Query: 350 KYSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQMVAE 409
             S   L+ K+ R  L A +R+  LA I  T      A  DL+IEAVFE+  +K  + A 
Sbjct: 357 ARSAALLDKKIARGQLTAEQREATLARIHPTDSNADLAGCDLVIEAVFEDRAVKASVSAA 416

Query: 410 VEQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQT 469
            +       + ASNTS+LPI  +A     P + IGLHFFSPVEKMPLVEII  A TS +T
Sbjct: 417 AQAVVGDDAVIASNTSTLPITGLAMAVPDPTKFIGLHFFSPVEKMPLVEIIKGARTSDET 476

Query: 470 IATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKFGFP 529
           +A       +  KTPIVV D  GF+ +R+   + NE I ML +G     I+    K G P
Sbjct: 477 LARGFDFVLQINKTPIVVNDSRGFFTSRVFGTFTNEGIAMLGEGVSAPMIETEARKAGMP 536

Query: 530 VGPIQLLDEVGIDTGTKI----IPVLEAAYGERFSAPA-NVVSSILND-DRKGRKNGRGF 583
           VGP+ + DEV +   + I       L A        PA  V+  +LN+  R G+  G GF
Sbjct: 537 VGPLAVSDEVSLSLMSHIRAQTAKDLHAEGKMPIEHPAFAVIDLLLNEYKRPGKAAGAGF 596

Query: 584 YLYGQKGRKSKKQVDPAIYPLIGTQGQ---GRISAPQVAERCVMLMLNEAVRCVDEQVIR 640
           Y Y   G+K        ++P + ++ +   G+IS   + +R + +   E VRC++E V+ 
Sbjct: 597 YEYPANGQK-------YLWPQLKSRFEKTDGQISPQDIRDRLLFIQALETVRCIEEGVLT 649

Query: 641 SVRDGDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMGA 700
           S  D +IG++FGIGF  + GG  ++I+  G  + V   Q LA QYG RF+P   L+E  A
Sbjct: 650 STADANIGSIFGIGFAAWTGGALQFINQYGLQDFVGRAQYLAEQYGERFSPPALLLEKAA 709

Query: 701 RGESF 705
           R E F
Sbjct: 710 RHELF 714


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: 984
Number of extensions: 39
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: 714
Length adjustment: 39
Effective length of query: 675
Effective length of database: 675
Effective search space:   455625
Effective search space used:   455625
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 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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