GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fadB in Pseudomonas fluorescens FW300-N2E3

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 AO353_01155 AO353_01155 3-hydroxyacyl-CoA dehydrogenase

Query= CharProtDB::CH_003230
         (714 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_01155 AO353_01155
           3-hydroxyacyl-CoA dehydrogenase
          Length = 714

 Score =  388 bits (996), Expect = e-112
 Identities = 267/724 (36%), Positives = 376/724 (51%), Gaps = 31/724 (4%)

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

Query: 62  PDNFIAGADINMIGNCKTAQEAEALARQGQQLMAEIHALPI---QVIAAIHGACLGGGLE 118
              F AG D+N +     +Q A+A       L A++  L      V+AAI+GA LGGG E
Sbjct: 61  K-TFFAGGDLNELIKVGKSQ-AKAFYDMVLLLKAQLRTLETLGKPVVAAINGAALGGGWE 118

Query: 119 LALACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAKQ 178
           + LACH RV  D+P   +GLPEV LGLLPG GG  R+ RL+G+  AL  +L GK++R++Q
Sbjct: 119 ICLACHHRVALDNPSVQIGLPEVTLGLLPGGGGVVRMVRLLGLEKALPYLLEGKKVRSQQ 178

Query: 179 ALKLGLVDDVVPHSILLEAAVELAKKERPS-SRPLPVRERILAGPLGR----ALLFKMVG 233
           AL+ GLVD++      L A         P+  +P  +    + G        A +  +  
Sbjct: 179 ALQAGLVDELAADRDELLAKARAWIATNPTVKQPWDMSGYQIPGGTPSSPKVAQMLAIAP 238

Query: 234 KKTEHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQALRSIFFAST 293
                KTQG  PA E+IL     G      +    E R F EL     ++ +   F+   
Sbjct: 239 SILRSKTQGCLPAPEKILCAAVEGAQVDFDTAQLIETRYFTELTTGQVAKNMIGTFWFQL 298

Query: 294 DVKKDPGSDAP---PAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHALK 350
           +     GS      P     +G+LG G+MG GIAYV+A  AGI V +KDIN         
Sbjct: 299 NEINAGGSRPAGFAPHATKKLGVLGAGMMGAGIAYVSAV-AGIDVVLKDINLAAAEKGKA 357

Query: 351 YSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQMVAEV 410
           +S   L+ KV R  L A++RD  LA I  +      A  DLIIEAVFE+ ELK ++ +  
Sbjct: 358 HSAALLDKKVARGQLSAAQRDATLARIKTSEQGADLAGCDLIIEAVFEDRELKARVSSAA 417

Query: 411 EQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQTI 470
           ++   A  + ASNTS+LPI  +A       + IGLHFFSPV+KMPLVEII    TS +T+
Sbjct: 418 QKVVGADAVIASNTSTLPISGLATAVPDQSKFIGLHFFSPVDKMPLVEIIKGVNTSDETL 477

Query: 471 ATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKFGFPV 530
           A       +  KTPIVV D  GF+ +R+   + NE I ML +G     I+    K G P+
Sbjct: 478 ARGFDFVLQIKKTPIVVNDSRGFFTSRVFGTFTNEGIAMLGEGISAPMIETEARKAGMPI 537

Query: 531 GPIQLLDEVGIDTGTKI-IPVLEAAYGERFSAPAN----VVSSILND-DRKGRKNGRGFY 584
           GP+ + DEV +   + I     +    E    PA+    V+  +LN+  R G+  G GFY
Sbjct: 538 GPLAISDEVSLSLMSHIRQQAAKDLQAEGKPLPAHPAFAVIDLLLNECQRPGKAAGGGFY 597

Query: 585 LYGQKGRKSKKQVDPAIYPLIGT---QGQGRISAPQVAERCVMLMLNEAVRCVDEQVIRS 641
            Y   G+K        ++P + T   +  G+IS   V +R + +   E VRCV+E V+ S
Sbjct: 598 EYPAGGQKH-------LWPELKTRFEKADGQISPQDVRDRLLFVQAIETVRCVEEGVLLS 650

Query: 642 VRDGDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMGAR 701
             D +IG++FGIGF  + GG  ++I+  G  + VA  Q LA QYG RFTP   L+E  A+
Sbjct: 651 TADANIGSIFGIGFAAWTGGALQFINQYGVKDFVARAQYLAEQYGERFTPPALLLEKAAK 710

Query: 702 GESF 705
           G  F
Sbjct: 711 GALF 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: 992
Number of extensions: 41
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 preprint 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