Alignments for a candidate for ech in Methylobacterium sp. 4-46

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Methylobacterium sp. 4-46

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_012333086.1 M446_RS15720 3-hydroxyacyl-CoA dehydrogenase

Query= CharProtDB::CH_003230
         (714 letters)



>NCBI__GCF_000019365.1:WP_012333086.1
          Length = 733

 Score =  414 bits (1064), Expect = e-120
 Identities = 267/735 (36%), Positives = 389/735 (52%), Gaps = 39/735 (5%)

Query: 1   MEMTSAFTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSA 60
           M++T  F      D IA+ T D PG  MN +  E  +++  II  +  +  ++G V  S 
Sbjct: 1   MDLTH-FRFETDQDGIALATWDSPGRSMNVITPEVMAELDRIIDAVAGDAAVKGCVITSG 59

Query: 61  KPDNFIAGADINMIGNC--------KTAQEAEAL------ARQGQQLMAEIHALPIQVIA 106
           K + F  GAD+ M+           +   E EA+       R+   L  ++        A
Sbjct: 60  K-EAFSGGADLTMLQGLGAEYARLSRERGEEEAMRFFFEETRRLSLLYRKLETCGKPFAA 118

Query: 107 AIHGACLGGGLELALACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALE 166
           AIHG CLGG  ELALACH RV +DD KT +GLPE+++GL PG+GGTQR+ RL+    AL+
Sbjct: 119 AIHGTCLGGAFELALACHHRVVSDDDKTRVGLPEIKVGLFPGAGGTQRVARLMQTGDALQ 178

Query: 167 MILTGKQLRAKQALKLGLVDDVVPH-SILLEA-------AVELAKKERPSSRPLPVRERI 218
           M+  G Q+R   A  +GLV  V    S++ EA          LA  ++P  +    +   
Sbjct: 179 MLFKGDQIRPLMARNMGLVHAVAKRDSVVAEAKAWIRGGGAALAPWDQPKFKAPSGKVYS 238

Query: 219 LAGPLGRALLFKMVGKKTEHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAM 278
            AG     + +         +T  NYPA + IL+ V  GL          E+R F ++  
Sbjct: 239 PAG----MMTWPPANAIYRRETHDNYPAAKAILQSVYEGLQLPMDLALKVESRYFAKILR 294

Query: 279 TPQSQAL-RSIFFASTDVKKDPGSDAP--PAPLNSVGILGGGLMGGGIAYVTACKAGIPV 335
           +P++ A+ RS+F +  ++ K     A   P  L  VG++G G MG GIAYVTA +AGI V
Sbjct: 295 SPEAAAMIRSLFVSMGELNKGARRPAAIGPVSLKRVGVVGAGFMGAGIAYVTA-QAGIEV 353

Query: 336 RIKDINPQGINHALKYSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEA 395
            + D + +       YS   +  ++ +   K ++RD  LA I+ T DY   +  DL+IEA
Sbjct: 354 VLIDQSAEAAEKGKAYSHKLVSDQIMKGRAKTADRDALLARITATADYAALSDCDLVIEA 413

Query: 396 VFENLELKQQMVAEVEQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMP 455
           VFE+ ++K +++A+VE +    TIFASNTS+LPI  +A  + RP+Q IG+HFFSPVEKM 
Sbjct: 414 VFEDPKVKAEVIAKVEASIRPETIFASNTSTLPISGLADGSARPDQFIGIHFFSPVEKML 473

Query: 456 LVEIIPHAGTSAQTIATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGER 515
           LVEII    +  + +A  +   +   KTPIVV D  GF+ NR +  YI E   ML +G  
Sbjct: 474 LVEIIKGRQSGERALAAALDYVRAIRKTPIVVNDARGFFANRCVGAYILEGHLMLAEGVP 533

Query: 516 VEHIDAALVKFGFPVGPIQLLDEVGIDTGTKIIPVLEAAYGERFSAPAN---VVSSILND 572
              I+ A  + G PVGP+ L DEVG+D G KI+   +A  GE    P     +V+ +  +
Sbjct: 534 AAMIENAGRQAGMPVGPLSLNDEVGVDLGLKILKATKAQAGEGAVNPLQERLLVALVEGE 593

Query: 573 DRKGRKNGRGFYLYGQKGRKSKKQVDPAIYPLIGT-QGQGRISAPQVAERCVMLMLNEAV 631
            R GRKN +GFY Y + G    K++ P +  L GT Q    +   ++  R ++    EA 
Sbjct: 594 GRLGRKNRKGFYDYPENG---PKRLWPGLAALAGTRQDPDAVDFQELKHRLLVAQAVEAA 650

Query: 632 RCVDEQVIRSVRDGDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTP 691
           R   E V+   R+ D+G++ G GF PF GG   YID +GA   V + +RL  ++G+RF P
Sbjct: 651 RVYGEGVVTDPREADVGSILGFGFAPFTGGVLSYIDGMGARRFVELCRRLEAKHGARFAP 710

Query: 692 CERLVEMGARGESFW 706
              L+ M   GE F+
Sbjct: 711 PANLLAMAETGERFY 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: 1016
Number of extensions: 46
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: 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 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