GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo3_N2E3:AO353_01155
          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:

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