Alignments for a candidate for fadB in Saccharomonospora cyanea NA-134

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadB in Saccharomonospora cyanea NA-134

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_005458850.1 SACCYDRAFT_RS19675 3-hydroxyacyl-CoA dehydrogenase

Query= CharProtDB::CH_003230
         (714 letters)



>NCBI__GCF_000244975.1:WP_005458850.1
          Length = 722

 Score =  374 bits (961), Expect = e-108
 Identities = 263/715 (36%), Positives = 368/715 (51%), Gaps = 30/715 (4%)

Query: 14  DNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLR-ENKELRGVVFVSAKPDNFIAGADIN 72
           D I V+T+D P +  NT+ A+F S +R I+ +L  E   + GVV  SAK   F AG D+N
Sbjct: 14  DGIVVLTLDDPNQSANTMNADFRSSLRVIVDRLEAEQDSITGVVLASAKK-TFFAGGDLN 72

Query: 73  MIGNCKTAQEAEALARQGQQLMAEIHALPI---QVIAAIHGACLGGGLELALACHGRVCT 129
            +    T  +AEA+      +  ++  L      V+AAI+GA LGGGLE+ALACH R+  
Sbjct: 73  DLIKA-TPADAEAITEMSNAMKQDLRRLETLGKPVVAAINGAALGGGLEIALACHHRIAA 131

Query: 130 DDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTA-LEMILTGKQLRAKQALKLGLVDDV 188
           D     +GLPEV LGLLPG GG  R  RL+G+  A L +++ G++ R  +AL+LGLV ++
Sbjct: 132 DVKGVQIGLPEVTLGLLPGGGGIVRTVRLLGIQNAVLNVLVQGQRHRPAKALELGLVHEL 191

Query: 189 VPH-SILLEAAVELAKKERPSSRPLPVRERILAG-----PLGRALLFKMVGKKTEHKTQG 242
           V     LL  A E  K    + +P  V+   + G     P   A L        +     
Sbjct: 192 VGSVDELLPKAKEWIKANPEAQQPWDVKGYKIPGGSPSNPKFAANLPAFPATLRKQLKGA 251

Query: 243 NYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQALRSIFFASTDVKKDPGSD 302
             PA   IL     G      +    E R F  L     ++ +   FF         GS 
Sbjct: 252 PMPAPRAILAAAVEGAQVDVDTASLIETRYFVSLVTGQVAKNMTKAFFFDLQHINSGGSR 311

Query: 303 AP---PAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHALKYSWDQLEGK 359
                      VG+LG G+MG GIAYV+A KAGI V +KD++ +       Y+  +LE K
Sbjct: 312 PDGYEKYQARKVGVLGAGMMGAGIAYVSA-KAGIDVVLKDVSKENAEKGKDYA-RKLEKK 369

Query: 360 VRRRHLKASERDKQLA-LISGTTDYRGFAHRDLIIEAVFENLELKQQMVAEVEQNCAAHT 418
              R     E+ K L   I  T D       D +IEAVFEN ELK ++ AE+E    +  
Sbjct: 370 ALARGKTTEEKSKALLDRIVTTGDAADLEGVDFVIEAVFENTELKHKVFAEIENIVESDA 429

Query: 419 IFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQTIATTVKLAK 478
           +  SNTS+LPI  +A    R E  IG+HFFSPV+KMPLVEII    TS  T+A       
Sbjct: 430 VLGSNTSTLPITGLAEGVKRQEDFIGIHFFSPVDKMPLVEIIRGEKTSDATLAKVFDYTL 489

Query: 479 KQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKFGFPVGPIQLLDE 538
           +  KTPIVV D  GF+ +R++  ++NEA+  + +G     I+ A  + G+P  P+QL+DE
Sbjct: 490 QIKKTPIVVNDSRGFFTSRVIGTFLNEAVAAVGEGVEPATIEQAGAQAGYPAPPLQLMDE 549

Query: 539 VGIDTGTKI----IPVLEAAYGERFSAPANVVSSILND--DRKGRKNGRGFYLYGQKGRK 592
           + +    KI       +EAA G     P+  V   + D  DRKGR  G GFY Y  +G++
Sbjct: 550 LTLTLPRKIRAETKAAVEAAGGTWTPHPSEAVIDRMLDEFDRKGRSAGAGFYEYDSEGKR 609

Query: 593 SKKQVDPAIYPLIGTQGQGRISAPQVAERCVMLMLNEAVRCVDEQVIRSVRDGDIGAVFG 652
           +   + P +    G+ G G +    + ER +     E V+C DE V+ SV+D +IG++FG
Sbjct: 610 A--GLWPGLREAWGS-GSGDVPFRDLQERMLFAEALETVKCFDEGVLNSVQDANIGSIFG 666

Query: 653 IGFPPFLGGPFRYIDSLGAG--EVVAIMQRLATQYGSRFTPCERLVEMGARGESF 705
           IGFP + GG  +Y++S   G    VA  + LA +YGS F P   LVE   +GE F
Sbjct: 667 IGFPAWTGGVVQYMNSYEGGLKGFVARARELAQRYGSHFEPPASLVERAEKGELF 721


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: 1004
Number of extensions: 43
Number of successful extensions: 7
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: 722
Length adjustment: 40
Effective length of query: 674
Effective length of database: 682
Effective search space:   459668
Effective search space used:   459668
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 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