Alignments for a candidate for paaH in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaH in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_3796 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__pseudo1_N1B4:Pf1N1B4_3796
          Length = 714

 Score =  377 bits (969), Expect = e-109
 Identities = 270/733 (36%), Positives = 374/733 (51%), Gaps = 49/733 (6%)

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

Query: 62  PDNFIAGADINMIGNCKTAQ-EAEA-----LARQGQQLMAEIHALPIQVIAAIHGACLGG 115
              F AG D+N +   K  + EA+A     L  +GQ    E    P  V+AAI+GA LGG
Sbjct: 61  K-TFFAGGDLNEL--IKVGKPEAKAFYDMVLILKGQLRTLETLGKP--VVAAINGAALGG 115

Query: 116 GLELALACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLR 175
           G E+ LACH RV  DDP  +LGLPEV LGLLPG GG  R+ R++G+  AL  +L GK++R
Sbjct: 116 GWEICLACHHRVVLDDPSVLLGLPEVTLGLLPGGGGVVRMVRMLGIEKALPYLLEGKKIR 175

Query: 176 AKQALKLGLVDDVVPHSILLEAAVELAKKERP--SSRPLPVRERILAG---PLGR----- 225
            +QAL+  L+D+      L     EL  K R      P+ V+   + G   P G      
Sbjct: 176 PQQALQARLIDE------LAADRDELMAKARAWIVDHPVAVQRWDVKGYQIPGGTPSDPK 229

Query: 226 -ALLFKMVGKKTEHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQA 284
            A +  +       KTQG  PA E+IL     G      + +  E R F EL     S+ 
Sbjct: 230 LAPMLAITPSILRSKTQGCLPAPEKILCAAVEGAQVDFDTAHLIETRYFTELTTGQVSKN 289

Query: 285 LRSIFFASTDVKKDPGS---DAPPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDIN 341
           L   F+   +     GS      P     VG+LG G+MG GIA+V+A  AGI V +KDIN
Sbjct: 290 LIGTFWFQLNEINAGGSRPQGIAPYVTKKVGVLGAGMMGAGIAFVSAL-AGIDVVLKDIN 348

Query: 342 PQGINHALKYSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLE 401
                    +S   L+ KV R  L   +R++ LA I  T +    A  DL+IEAVFE+ E
Sbjct: 349 LAAAEKGKAHSAALLDKKVARGQLTREQREEILARIHATENDADLAGCDLVIEAVFEDRE 408

Query: 402 LKQQMVAEVEQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIP 461
           LK ++ +  +       + ASNTS+LPI  +A       + IGLHFFSPVEKMPLVEII 
Sbjct: 409 LKTKVSSAAQAVVGPDAVIASNTSTLPISGLAIAVPDQTKFIGLHFFSPVEKMPLVEIIK 468

Query: 462 HAGTSAQTIATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDA 521
              TS +T+A       +  KTPIVV D  GF+ +R+   + NE I ML +G     I+ 
Sbjct: 469 GVHTSDETLARGFDFVLQIKKTPIVVNDSRGFFTSRVFGTFTNEGIAMLGEGVSAPMIET 528

Query: 522 ALVKFGFPVGPIQLLDEVGIDTGTKI----IPVLEAAYGERFSAPANVVSSILNDD--RK 575
              K G PVGP+ + DEV +   + I       L A        PA  V  +L  +  R 
Sbjct: 529 EARKAGMPVGPLAISDEVSLSLMSHIREQTAKDLRAEGKTLIEHPAFAVIDLLLKEYKRP 588

Query: 576 GRKNGRGFYLYGQKGRKSKKQVDPAIYPLIGT---QGQGRISAPQVAERCVMLMLNEAVR 632
           G+  G GFY Y   G+K        ++P + +   +  G+IS   + +R + +   E VR
Sbjct: 589 GKAAGGGFYDYPATGQKH-------LWPELKSRFEKADGQISPQDIRDRLLFVQAIETVR 641

Query: 633 CVDEQVIRSVRDGDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPC 692
           C++E V+ S  D ++G++FGIGF  + GG  ++I+  G  + VA  Q LA QYG RFTP 
Sbjct: 642 CMEEGVLTSTADANVGSIFGIGFAAWTGGALQFINQYGVKDFVARAQYLAEQYGERFTPP 701

Query: 693 ERLVEMGARGESF 705
             L+E  A+   F
Sbjct: 702 ALLLEKAAKNALF 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: 1011
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