Alignments for a candidate for fadB in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadB in Pseudomonas fluorescens GW456-L13

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 PfGW456L13_4146 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)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4146
          Length = 714

 Score =  386 bits (992), Expect = e-111
 Identities = 268/724 (37%), Positives = 371/724 (51%), Gaps = 31/724 (4%)

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

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

Query: 119 LALACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAKQ 178
           + LACH RV  D P   LGLPEV LGLLPG GG  R+ R++G+  AL  +L GK++R  Q
Sbjct: 119 ICLACHHRVALDHPSVQLGLPEVTLGLLPGGGGVVRMVRMLGLEKALPYLLEGKKVRPPQ 178

Query: 179 ALKLGLVDDVVP-HSILLEAAVELAKKERPSSRPLPVRERILAGPLGR----ALLFKMVG 233
           AL+ GL+D +   H  LL  A         + +   V+   + G        A +  +  
Sbjct: 179 ALQAGLIDALATDHEDLLAKARTWILANPAAVQRWDVKGYQIPGGTPSNPKVAQMLAIAP 238

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

Query: 294 DVKKDPGSDAP---PAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHALK 350
           +     GS      P     VG+LG G+MG GIA+V+A  AGI V +KDIN         
Sbjct: 299 NEINAGGSRPQGFAPYVTRKVGVLGAGMMGAGIAFVSA-SAGIDVVLKDINLAAAQKGKA 357

Query: 351 YSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQMVAEV 410
           +S   L+ KV R  +   +RD  L+ I  +      A  DLIIEAVFE+ +LK ++    
Sbjct: 358 HSAALLDKKVARGQISIEQRDTVLSRIQTSESDADLAGCDLIIEAVFEDRDLKAKVSLAA 417

Query: 411 EQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQTI 470
           ++   A  + ASNTS+LPI  +A       + IGLHFFSPVEKMPLVEII  A TS +T+
Sbjct: 418 QKVVGADAVIASNTSTLPISGLACAVPDQSKFIGLHFFSPVEKMPLVEIIKGANTSDETL 477

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

Query: 531 GPIQLLDEVGIDTGTKI----IPVLEAAYGERFSAPA-NVVSSILND-DRKGRKNGRGFY 584
           GP+ + DEV +     I       L+A        PA  V+  +LN+  R G+  G GFY
Sbjct: 538 GPLAISDEVSLSLMNHIRLQTAKDLQAEGKPLTEHPAFTVIDLLLNEFKRPGKAGGGGFY 597

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

Query: 642 VRDGDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMGAR 701
             D ++G++FGIGF  + GG  ++I+  G  + VA  Q LATQYG RF P   L+E  A+
Sbjct: 651 TADANVGSIFGIGFAAWTGGALQFINQYGVQDFVARAQYLATQYGERFAPPALLLEKAAK 710

Query: 702 GESF 705
           GE+F
Sbjct: 711 GEAF 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: 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: 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:

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, 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

GapMind for catabolism of small carbon sources