Alignments for a candidate for fadB in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadB in Pseudomonas simiae WCS417

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 GFF4142 PS417_21215 3-hydroxyacyl-CoA dehydrogenase

Query= CharProtDB::CH_003230
         (714 letters)



>FitnessBrowser__WCS417:GFF4142
          Length = 715

 Score =  388 bits (996), Expect = e-112
 Identities = 266/725 (36%), Positives = 376/725 (51%), Gaps = 33/725 (4%)

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

Query: 62  PDNFIAGADINMIGNCKTAQEAEAL--ARQGQQLMAEIHALPIQVIAAIHGACLGGGLEL 119
              F AG D+N +     A   +     R+ +  +  +  L   V+AAI+GA LGGG E+
Sbjct: 61  K-TFFAGGDLNELIKVDKAHAKDFYDSVRELKAQLRRLETLGKPVVAAINGAALGGGWEI 119

Query: 120 ALACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAKQA 179
            LACH RV  DD    LGLPEV LGLLPG GG  R+ R++G+  AL  +L GK++R +QA
Sbjct: 120 CLACHYRVALDDKSVQLGLPEVTLGLLPGGGGVVRMVRMLGLEKALPYLLEGKKVRPQQA 179

Query: 180 LKLGLVDDVVPHSILLEAAVELAKKERPSSRPLPVRERILAGPLGR------ALLFKMVG 233
           L+ GLV+++      L A         P ++  P   +    P G       A +  +  
Sbjct: 180 LQAGLVNELAADRDELLAKSRAWILANPDAKQ-PWDNKGYQIPGGTPSSPKVAQMLAIAP 238

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

Query: 294 DVKKDPGSDAP----PAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHAL 349
           + + + GS  P    P     VG+LG G+MG GIAYV+A  AGI V +KDIN        
Sbjct: 299 N-EINAGSSRPQGFAPYVTRKVGVLGAGMMGAGIAYVSA-SAGIEVVLKDINLAAAEKGK 356

Query: 350 KYSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQMVAE 409
            +S   L+ KV R  L A +R+  LA I  T      A  DLIIEAVFE+ ELK ++ A 
Sbjct: 357 AHSAALLDKKVSRGQLTAEQRETFLARIHPTATDEDLAGCDLIIEAVFEDRELKAKVSAA 416

Query: 410 VEQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQT 469
            +    A  + ASNTS+LPI  +A       + IGLHFFSPV+KMPLVEII  A TS +T
Sbjct: 417 AQSVVGADAVIASNTSTLPISGLATAVPDQTRFIGLHFFSPVDKMPLVEIIKGARTSDET 476

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

Query: 530 VGPIQLLDEVGIDTGTKI----IPVLEAAYGERFSAPANVVSSILNDD--RKGRKNGRGF 583
           VGP+ + DEV +     I       L+A      + PA  V  +L ++  R G+  G GF
Sbjct: 537 VGPLAVSDEVSLSLMNHIRQQTAKDLQAEGKAVPTHPATAVIDLLVNEYQRMGKAAGGGF 596

Query: 584 YLYGQKGRKSKKQVDPAIYPLIGTQGQ---GRISAPQVAERCVMLMLNEAVRCVDEQVIR 640
           Y Y   G K        ++P + ++ +    RIS   V +R + +   E VRCV+E V+ 
Sbjct: 597 YDYPSGGHK-------YLWPELKSRFERPDQRISPQDVRDRLLFIQAIETVRCVEEGVLM 649

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

Query: 701 RGESF 705
           +G+ F
Sbjct: 710 QGDVF 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: 1005
Number of extensions: 40
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: 715
Length adjustment: 39
Effective length of query: 675
Effective length of database: 676
Effective search space:   456300
Effective search space used:   456300
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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Protein sequences (fasta format)
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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