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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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