Alignments for a candidate for ech in Cereibacter sphaeroides ATCC 17029

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Cereibacter sphaeroides ATCC 17029

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_011840656.1 RSPH17029_RS04435 enoyl-CoA hydratase/isomerase family protein

Query= CharProtDB::CH_003230
         (714 letters)



>NCBI__GCF_000015985.1:WP_011840656.1
          Length = 733

 Score =  418 bits (1075), Expect = e-121
 Identities = 267/731 (36%), Positives = 394/731 (53%), Gaps = 42/731 (5%)

Query: 7   FTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKPDNFI 66
           FT     D +  IT DVPG+ MN +     +++  +I    ++  ++GV+  S K D F 
Sbjct: 4   FTSRTDADGVCTITWDVPGKSMNVMSMAGFAELDGLIAAALDDPSVKGVILTSGKKD-FA 62

Query: 67  AGADINMIGNCKTAQEAEALARQGQQLMAEIHALPIQV----------------IAAIHG 110
           AG D+N+I   K  +  +  AR   + + E+HA+  ++                +AA+ G
Sbjct: 63  AGMDLNVIARMKE-EGGDDPARAVFEGVMEMHAVLRRIERAGMDPKTLKGGKPIVAALPG 121

Query: 111 ACLGGGLELALACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILT 170
             LG GLEL LACH  +  D+PK  +GLPE+ +G+ PG GGT RL R +G   A  ++L 
Sbjct: 122 TALGLGLELPLACHRIIAADNPKAKIGLPEIMVGIFPGGGGTTRLVRRLGAMMAAPLLLE 181

Query: 171 GKQLRAKQALKLGLVDDVVPHSILLEAAVE--LAKKERPSSRPLPVRERILAG--PLGRA 226
           GK    K A  +G+VD+VVP   LL  A E  L  K+    +P   +   + G  P   A
Sbjct: 182 GKLNDPKGAKAMGVVDEVVPADQLLARAKEWVLGAKDADLVKPWDAKGYKMPGGAPYHPA 241

Query: 227 LLFKMVGKKT--EHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQA 284
                VG       KT G YPA + +L  V  G      +    EAR F  + M P S A
Sbjct: 242 GFMTFVGASAMVTGKTMGVYPAAKGLLAAVYEGALVPFDTALKIEARWFTHVLMNPSSSA 301

Query: 285 L-RSIFFASTDVKKDPGSDAPPAPLNSV---GILGGGLMGGGIAYVTACKAGIPVRIKDI 340
           + RS+F     ++K  G+  P  P  SV   G++G G+MG GIA+V A  AGI V + D 
Sbjct: 302 MIRSLFINKEALEK--GAVRPALPDQSVRKLGVIGAGMMGAGIAHVAA-NAGIEVVLIDA 358

Query: 341 NPQGINHALKYSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENL 400
             +  +    +S   L+  ++R  + A ++ + L  I+ TTDY   +  DLI+EAVFE+ 
Sbjct: 359 TQEAADRGKAHSEGLLDKGMKRGKVSAEKKAEVLGRIAATTDYAALSGCDLIVEAVFEDP 418

Query: 401 ELKQQMVAEVEQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEII 460
            +K ++  +VE       IFA+NTS+LPI  +A  +  P Q IG+HFFSPV+KM LVEII
Sbjct: 419 AVKAEVTQKVEAAVGPDCIFATNTSTLPISGLAKASRDPAQFIGIHFFSPVDKMMLVEII 478

Query: 461 PHAGTSAQTIATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHID 520
               T  + +A  +   ++  KTPIVV D   FY NR + PY+NE IRM+ +G     I+
Sbjct: 479 RGKATGDRAVAKALDFVRQIRKTPIVVHDARFFYANRCIIPYLNEGIRMVAEGVAPALIE 538

Query: 521 AALVKFGFPVGPIQLLDEVGIDTGTKIIPVLEAAYGERF--SAPANVVSSILNDDRKGRK 578
            A    G P+GP+QL+DE  ID G KI    +AA GE +  +A   V+  + ++ R GRK
Sbjct: 539 NAAKLVGMPLGPLQLVDETSIDLGVKIAKATKAALGEAYPDAAVDAVIFPLADEGRLGRK 598

Query: 579 NGRGFYLYGQKGRKSKKQVDPAIYPLIGTQGQGRISAPQVAE---RCVMLMLNEAVRCVD 635
            G GFY Y   G++        ++P +  +     + P++AE   R +   + EAVR ++
Sbjct: 599 AGAGFYAYDAAGKRD------GLWPGLADRWPLAETQPELAEVQHRLLFAQVLEAVRALE 652

Query: 636 EQVIRSVRDGDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERL 695
           E V+  +R+GD+GA+ G GF P+ GGPF ++D +GA   V I + LA ++G+RF P + L
Sbjct: 653 EGVLTDIREGDVGAILGWGFAPWSGGPFSWLDMIGAPRAVEICEGLAERHGTRFAPPKLL 712

Query: 696 VEMGARGESFW 706
           VEM  +GESF+
Sbjct: 713 VEMAGKGESFY 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: 1127
Number of extensions: 52
Number of successful extensions: 9
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: 733
Length adjustment: 40
Effective length of query: 674
Effective length of database: 693
Effective search space:   467082
Effective search space used:   467082
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 10 2024. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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