GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaH in Rhodobacter maris JA276

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_097069274.1 CRO22_RS06210 3-hydroxyacyl-CoA dehydrogenase

Query= CharProtDB::CH_003230
         (714 letters)



>NCBI__GCF_900217815.1:WP_097069274.1
          Length = 728

 Score =  383 bits (984), Expect = e-110
 Identities = 255/722 (35%), Positives = 367/722 (50%), Gaps = 31/722 (4%)

Query: 7   FTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKPDNFI 66
           FT  +  D +AVIT DV  + MN +  E  + +   I Q   ++  +GV+  S K D F 
Sbjct: 4   FTYALGDDGVAVITWDVAAKSMNVMSMEGFALLDGFIDQALADEACKGVIITSGKKD-FA 62

Query: 67  AGADINMIGNCKT--AQEAEALARQGQQLMAEIHALPIQ---------VIAAIHGACLGG 115
            G D+N+I   +   AQ       Q  +++ +I    +          +   + G  LG 
Sbjct: 63  GGMDLNVIAKMRAGGAQTIFEGVMQMHRVLRKIERAGMDPKTLKGGKPIACVLPGTALGI 122

Query: 116 GLELALACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLR 175
           GLEL L+ H     ++PK  +GLPE+ +G+ PG GGT RL R +G   A   +L GK   
Sbjct: 123 GLELPLSTHRIFAANNPKAKIGLPEIMVGIFPGGGGTTRLVRKLGAMMAAPFLLEGKLSD 182

Query: 176 AKQALKLGLVDDVVPHSILLEAAVELAKKERPSSRPLPVRERILAG-----PLGRALLFK 230
            K A   GL+D+V    +       L  K+    +P   +   + G     P G  + F 
Sbjct: 183 PKAAKAAGLIDEVSDDPMAAAREWVLNAKDADLVKPWDAKGYKMPGGAPYHPAG-FMTFL 241

Query: 231 MVGKKTEHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQAL-RSIF 289
                   KT G YPA + +L  V  G      +    EAR F  L + P S A+ RS+F
Sbjct: 242 GASAMVHGKTMGVYPAAKALLSAVYEGALVPFDAALKIEARWFTNLLLNPSSSAMIRSLF 301

Query: 290 FASTDVKKDPGSDAPPAP---LNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGIN 346
                ++K  G++ P      +  VGILG G+MG GIAYV+A  AGI V + D   +  +
Sbjct: 302 INKEALEK--GANRPKVEDQSVKKVGILGAGMMGAGIAYVSA-NAGIEVVLIDSTQEAAD 358

Query: 347 HALKYSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQM 406
               YS   L+  + RR +   ++ + LA I+ TTDY   A  DLI+EAVFE+  +K ++
Sbjct: 359 RGKSYSTGILDKGISRRKVTEEKKAEVLARITATTDYAALAGCDLIVEAVFEDPGVKAEV 418

Query: 407 VAEVEQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTS 466
            A+ E       IFA+NTS+LPI  +A  + RPEQ IG+HFFSPV+KM LVEII  A T 
Sbjct: 419 TAKAEAVIPETAIFATNTSTLPISSLAKASKRPEQFIGIHFFSPVDKMLLVEIIKGAQTG 478

Query: 467 AQTIATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKF 526
              +A  +   +   KTPIVV D   FY NR + PYINE IRM+ +G     I+ A    
Sbjct: 479 DVAVAKALDFVRAIRKTPIVVNDARFFYANRCIIPYINEGIRMVAEGVSPVLIENAAKLV 538

Query: 527 GFPVGPIQLLDEVGIDTGTKIIPVLEAAYGERF--SAPANVVSSILNDDRKGRKNGRGFY 584
           G P+GP+QL+DE  ID G KI     AA G+ +   A   VV  + ++ R G+K   GFY
Sbjct: 539 GMPLGPLQLVDETSIDLGVKIAKATRAAMGDAYPDGAVDEVVFWMADEGRLGKKADAGFY 598

Query: 585 LYGQKGRKSKKQVDPAIYPLIGTQGQGRISAPQVAERCVMLMLNEAVRCVDEQVIRSVRD 644
            Y    R    +     YP    Q +      +V  R +M  + EAVR  ++ V+  +R+
Sbjct: 599 TYTAGKRGGLWEGLAEKYPAAEDQPE----LAEVQHRLLMAQVLEAVRAFEQGVLTDIRE 654

Query: 645 GDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMGARGES 704
           GD+GA+ G GF P+ GGPF ++D +GA   V I + L  +YG+RF     L ++ A+G+ 
Sbjct: 655 GDVGAILGWGFAPWSGGPFAWLDIIGAPRAVEICEALEAKYGARFEAPALLRDIAAKGDG 714

Query: 705 FW 706
           F+
Sbjct: 715 FY 716


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: 1064
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: 728
Length adjustment: 40
Effective length of query: 674
Effective length of database: 688
Effective search space:   463712
Effective search space used:   463712
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