Alignments for a candidate for fadB in Rhodobacter maris JA276

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadB 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:

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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