Alignments for a candidate for fadB in Rhizobium etli CFN 42

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadB in Rhizobium etli CFN 42

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_011423928.1 RHE_RS02825 FAD-dependent oxidoreductase

Query= CharProtDB::CH_003230
         (714 letters)



>NCBI__GCF_000092045.1:WP_011423928.1
          Length = 738

 Score =  396 bits (1018), Expect = e-114
 Identities = 255/729 (34%), Positives = 375/729 (51%), Gaps = 27/729 (3%)

Query: 1   MEMTSAFTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSA 60
           M   + FTL    D IA++T D+PG+ MN   AE   ++ AII     +  ++GVVF S 
Sbjct: 1   MSTYTNFTLETDADGIALVTWDMPGKSMNVFTAEVMEELNAIIDATTADASVKGVVFTSG 60

Query: 61  KPDNFIAGADINMIGNC-------------KTAQEAEALARQGQQLMAEIHALPIQVIAA 107
           K  +F  GAD++MI +              K  Q    L  +   L  ++       ++A
Sbjct: 61  K-SSFSGGADLSMIKSMFSSYQEEKAKSPEKAVQTLFGLVGRMSGLFRKLETSGKPWVSA 119

Query: 108 IHGACLGGGLELALACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEM 167
           I+G C+GG  EL+LACHGRV ++     + LPEV++G+ PG+GGTQR+PRL     AL+M
Sbjct: 120 INGTCMGGAFELSLACHGRVASNAKSVKIALPEVKVGIFPGAGGTQRVPRLANAQDALQM 179

Query: 168 ILTGKQLRAKQALKLGLVDDVVPHSILLEAAVELAKKERPSSRPLPVRERILAG----PL 223
           + TG+ L   +A  + LV  VV    L+ AA ++ K       P   +   L G      
Sbjct: 180 MTTGQSLSGSRAKAMNLVHQVVEPDQLIPAAKQMIKDGLKPVAPWDEKGFKLPGGGIWTP 239

Query: 224 GRALLFKMVGKKTEHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQS- 282
             A L+         +T GNYPA   IL+ V  GL     +G   E R F E+  T ++ 
Sbjct: 240 ASAQLWPAAPAILRRETSGNYPAALAILKCVYEGLQVPFDTGLKIEQRYFTEVLQTREAF 299

Query: 283 QALRSIFFASTDVKKDPGSDA--PPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDI 340
             +RS+F +  ++ K     A  P   L  VG++G G MG  IAYVTA  AGI V + D 
Sbjct: 300 SMIRSLFISMQELGKGARRPAGIPKTELKHVGVVGAGFMGASIAYVTAA-AGISVTLIDR 358

Query: 341 NPQGINHALKYSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENL 400
           + +        S   ++  + +  L   E    L+ I+ + DY   A+  L+IEAVFE+ 
Sbjct: 359 DMEAAAKGKAVSEGLVKDAIGKGRLTQDEAAALLSRITPSGDYADLANVGLVIEAVFEDR 418

Query: 401 ELKQQMVAEVEQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEII 460
           E+K+ ++  VE       IFASNTS+LPI  +A ++ RP   IG+HFFSPVEKM L E+I
Sbjct: 419 EVKKAVIDAVEAVLPEGAIFASNTSTLPITGLARNSKRPADFIGIHFFSPVEKMMLTEVI 478

Query: 461 PHAGTSAQTIATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHID 520
               T  + +A  +       KTPIVV D  GF+VNR +  Y++E+  ML +G     I+
Sbjct: 479 LGTETGDRALAVALDYVAAIKKTPIVVNDTRGFFVNRCVLRYMSESYDMLIEGVPPAMIE 538

Query: 521 AALVKFGFPVGPIQLLDEVGIDTGTKIIPVLEAAYGERFSAPAN---VVSSILNDDRKGR 577
            A    G PVGP+ L DEV ID   KI+    A  GE+   P +   +   +  + R GR
Sbjct: 539 NAAKMAGMPVGPLALNDEVAIDLSLKILKAAVADLGEKAIDPRHMELISRMVEKEGRFGR 598

Query: 578 KNGRGFYLYGQKGRKSKKQVDPAIYPLIGTQGQGRISAPQVAERCVMLMLNEAVRCVDEQ 637
           KN +GFY Y  K   +KK + P +      +    +    + +R ++ +  EA R V+E 
Sbjct: 599 KNSKGFYDYPPK--PAKKSLWPDLKSFYPQKKAEEVDVNVLKQRFLVTIALEAARTVEEG 656

Query: 638 VIRSVRDGDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVE 697
           ++   R+ D+G++ G GF P+ GG   YID +GA   V + +RLA  YG  F P   L +
Sbjct: 657 IVTDPREADVGSILGFGFAPYTGGALSYIDGMGAKAFVDLAERLAETYGDHFKPTPLLRD 716

Query: 698 MGARGESFW 706
           + A+GE+F+
Sbjct: 717 LAAKGETFY 725


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: 991
Number of extensions: 48
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: 738
Length adjustment: 40
Effective length of query: 674
Effective length of database: 698
Effective search space:   470452
Effective search space used:   470452
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 Apr 09 2024. 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