GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaH in Jannaschia aquimarina GSW-M26

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_043916947.1 jaqu_RS00375 enoyl-CoA hydratase/isomerase family protein

Query= CharProtDB::CH_003230
         (714 letters)



>NCBI__GCF_000877395.1:WP_043916947.1
          Length = 727

 Score =  416 bits (1069), Expect = e-120
 Identities = 268/732 (36%), Positives = 380/732 (51%), Gaps = 40/732 (5%)

Query: 7   FTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKPDNFI 66
           FT+    D +AVIT DVPG+ MN +  E   +  A+I     ++ ++G+V  S KPD+F 
Sbjct: 4   FTMEKGADGVAVITWDVPGKSMNVMSMEAWPEFEALIDDALADEAVKGIVVTSGKPDSFA 63

Query: 67  AGADINMIGNCKTAQEAEA-----------------LARQGQQLMAEIHALPIQVIAAIH 109
            G D+N+I   K +   +                  L R G          P  V AA+ 
Sbjct: 64  GGMDLNVIAKMKESAGDDPARGLFEGLMGAHGILRKLERAGMDPKTSKGGKP--VAAALP 121

Query: 110 GACLGGGLELALACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMIL 169
           G  LG GLE+ LACH   C D+PK  +GLPE+ +G+ PG GGT RL R +G   A   +L
Sbjct: 122 GTALGIGLEIPLACHRIFCADNPKAKIGLPEIMVGIFPGMGGTTRLVRKMGAMAASPYLL 181

Query: 170 TGKQLRAKQALKLGLVDDVVPHSILLEAAVELAKKERPSSRPLPVRERILAG-----PLG 224
            GK +   +A   GL+D+VV     L AA E    E    +P   +   + G     P G
Sbjct: 182 EGKMMAPAKAKSAGLIDEVVDDP--LAAAKEWVLSEPKIVKPWDEKGYKMPGGAPYHPSG 239

Query: 225 RALLFKMVGKKTEHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQA 284
             L F         KT+G YPA + +L  V  G      +    EAR F  + M P S A
Sbjct: 240 -FLTFVGASAMVNGKTKGVYPAAKALLSAVYEGALVPFDTALKVEARWFTHVLMNPSSAA 298

Query: 285 L-RSIFFASTDVKKDPGSDAPPAP---LNSVGILGGGLMGGGIAYVTACKAGIPVRIKDI 340
           + RS+F     ++K  G++ P AP   +  VGILG G+MG GIAYV+A  AGI V + D 
Sbjct: 299 MIRSLFINKEALEK--GANRPEAPDQKVRKVGILGAGMMGAGIAYVSA-NAGIEVVLIDR 355

Query: 341 NPQGINHALKYSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENL 400
                N    YS   L+  + R+ +   ++ + L  I+ TTD       DLI+EAVFE++
Sbjct: 356 EQAAANKGKSYSEGLLDKGISRKKVTEEKKAEVLGRITATTDLGALEGCDLIVEAVFEDV 415

Query: 401 ELKQQMVAEVEQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEII 460
            +K +M  +VE       IFA+NTS+LPI ++A  + RPEQ IG+HFFSPV+KM LVEII
Sbjct: 416 GVKAEMTKKVEAVVGEDCIFATNTSTLPITELAKASERPEQFIGIHFFSPVDKMLLVEII 475

Query: 461 PHAGTSAQTIATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHID 520
             A T  + +A  +   ++  KTPIVV D   FY NR + PYINE IRM+ +G     I+
Sbjct: 476 KGAKTGDRAVAKALDFVRQIRKTPIVVNDARFFYANRCIIPYINEGIRMVKEGVEPALIE 535

Query: 521 AALVKFGFPVGPIQLLDEVGIDTGTKIIPVLEAAYGERFSAPANVVSSILNDD-RKGRKN 579
            A    G P+GP+QL DE  +D G KI    +AA G+ +    + V   + +  R GRK+
Sbjct: 536 NAAKLLGMPLGPLQLTDETSVDLGVKIAKATKAAMGDAYDDTTDEVLFFMEEQGRLGRKS 595

Query: 580 GRGFYLYGQKGRKSKKQVD-PAIYPLIGTQGQGRISAPQVAERCVMLMLNEAVRCVDEQV 638
             GFY Y +KG++          +P+  TQ        +V  R +   + EAVR ++E V
Sbjct: 596 NAGFYEYDEKGKRQLLWDGLSERFPVADTQP----DLHEVQNRLMFAQVLEAVRALEEDV 651

Query: 639 IRSVRDGDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEM 698
           +  +R+GD+GA+ G GF P+ GGPF ++D +GA   V     L  ++G+RF   + L EM
Sbjct: 652 LLDIREGDVGAILGWGFAPWSGGPFGWLDIVGAAWAVDKTAELTEKFGARFETPKTLTEM 711

Query: 699 GARGESFWKTTA 710
              G +F+   A
Sbjct: 712 AKSGATFYGDAA 723


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: 1046
Number of extensions: 50
Number of successful extensions: 8
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: 727
Length adjustment: 40
Effective length of query: 674
Effective length of database: 687
Effective search space:   463038
Effective search space used:   463038
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