GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Halioglobus japonicus S1-36

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 WP_084198499.1 C0029_RS14200 3-hydroxyacyl-CoA dehydrogenase

Query= CharProtDB::CH_003230
         (714 letters)



>NCBI__GCF_002869505.1:WP_084198499.1
          Length = 718

 Score =  361 bits (927), Expect = e-104
 Identities = 239/714 (33%), Positives = 363/714 (50%), Gaps = 29/714 (4%)

Query: 14  DNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRE-NKELRGVVFVSAKPDNFIAGADIN 72
           D I  +  D  G+ +N +  E+A  +   + +L     EL+G+   S KP  F AG DI 
Sbjct: 11  DGIVDLIFDQEGKSVNVMGEEYAEAMPKALDELEAMGDELKGLYIRSGKPGQFFAGGDIT 70

Query: 73  MIGNCK---TAQEAEALAR---QGQQLMAEIHALPIQVIAAIHGACLGGGLELALACHGR 126
           M+       + +E E + R     ++ +A I  L + V   I+G  LGGG E+ALACH R
Sbjct: 71  MMLEMDLNPSQEEREEMHRGLLDAKEPLARIERLGVPVAVGINGPALGGGYEIALACHYR 130

Query: 127 VCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAKQALKLGLVD 186
           +  D PK  +GLPE  LGLLPG+GG  R+ R++G+  AL +I  GKQL A +AL+ GL+ 
Sbjct: 131 IAMDSPKVKVGLPEAMLGLLPGAGGIVRMTRMLGMQEALGLISQGKQLVAAKALEKGLIH 190

Query: 187 DVVPHSILLEAAVELAKKERPSSRP---LPVRERILAGPLGRAL--LFKMVGKKTEHKTQ 241
           ++      + A  +   K  P +R     P       GP   A   L         ++T+
Sbjct: 191 ELAADEEAMAAQAKAWIKANPDARQPWEQPGYSIPGGGPQDEATQGLTYFGPVNVMNQTK 250

Query: 242 GNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQALRSIFFASTDVKKDPGS 301
           GN  A + I+  V        ++ +  EAR F  L +   S+ + + FF   +   D G+
Sbjct: 251 GNMTAPQVIIAAVIDTARVDYATAHKIEARYFQRLLLDQVSRNMMTTFFIQMNAL-DAGA 309

Query: 302 DAPPA----PLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHALKYSWDQLE 357
             P       +  +GILG G+MG GIA+  A K G+ V +KD+  +  +    Y+    E
Sbjct: 310 SRPEGIAKTEVKKLGILGAGVMGAGIAF-NAAKVGMNVVLKDLTQENADKGKAYAASACE 368

Query: 358 GKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQMVAEVEQNCAAH 417
              + R +   + ++ L  I  T D    A  DL+IEAVFEN ++K  +  E E      
Sbjct: 369 ---KSRRIDEQQAEEILGRIQPTADVADLADCDLVIEAVFENRDVKAAVTRETEAVLGEQ 425

Query: 418 TIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQTIATTVKLA 477
            +FASNTS+LPI ++A  + RP+  IG+HFFSP E+MPLVEII    TS + +A    LA
Sbjct: 426 AVFASNTSALPITELAQASVRPQNFIGMHFFSPAERMPLVEIITGEQTSDECLAWAFDLA 485

Query: 478 KKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKFGFPVGPIQLLD 537
           +K GK PIVV+D  GF+  R++   I +  RML +G     I+      G P+GP++ LD
Sbjct: 486 QKMGKKPIVVKDAPGFFTTRVIGQTITQGQRMLAEGVNPALIENGAAFNGSPMGPLETLD 545

Query: 538 EVGIDTGTKII---PVLEAAYGERF--SAPANVVSSILND-DRKGRKNGRGFYLYGQKGR 591
            + ++T         V   A GE+   SA + V+  ++ + +R G+  G GFY Y   G+
Sbjct: 546 TISLETAYHAANQQRVDAEARGEQVEPSAESEVIRIMVEEAERVGQAKGAGFYDYDDNGK 605

Query: 592 KSKKQVDPAIYPLIGTQGQGRISAPQVAERCVMLMLNEAVRCVDEQVIRSVRDGDIGAVF 651
           K        +  L    G   +    V +R +   + EA+R ++E V+ SV DG+IG++ 
Sbjct: 606 KVATWA--GLKALFAKDGYKDVPYQDVKDRLLFSQVLEAIRIMEEGVLTSVGDGNIGSIM 663

Query: 652 GIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMGARGESF 705
           GIGFPP  GG ++ +++ G        + LA  YG  F P + L++M A G +F
Sbjct: 664 GIGFPPHTGGVYQCVNAYGVQAFADRAKELAAAYGEAFEPPQLLLDMAADGRTF 717


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: 1070
Number of extensions: 50
Number of successful extensions: 6
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: 718
Length adjustment: 40
Effective length of query: 674
Effective length of database: 678
Effective search space:   456972
Effective search space used:   456972
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 24 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