Alignments for a candidate for ech in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Sinorhizobium meliloti 1021

Align 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157); 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); short-chain-enoyl-CoA hydratase (EC 4.2.1.150) (characterized)
to candidate SMc02227 SMc02227 fatty oxidation complex enoyl-COA hydratase/3-hydroxyacyl-COA dehydrogenase/3-hydroxybutyryl-COA epimerase

Query= BRENDA::A4YDS4
         (651 letters)



>FitnessBrowser__Smeli:SMc02227
          Length = 737

 Score =  171 bits (432), Expect = 1e-46
 Identities = 128/399 (32%), Positives = 202/399 (50%), Gaps = 28/399 (7%)

Query: 2   KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSL-KEGV 60
           KV V+G+G MG  IA + A  G  V + D   E  ++     +  +      G L KE  
Sbjct: 328 KVGVVGAGFMGASIAYVTAAGGIPVTLIDRDMEAAEKGKTHSEGLVKDAIGKGRLTKEEG 387

Query: 61  EQVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPI 120
           E +L+RI P  D    L+ +  VIEAV ED ++K+ +    EA  +  A+ A+NTS+LPI
Sbjct: 388 EALLSRITPSADYGD-LRDAGLVIEAVFEDRQVKKDVIEKVEAVIAEDAIFASNTSTLPI 446

Query: 121 SEIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKD 180
           + +A   K P R +G+HFF+P   M L E++ GK+T D  +    +   ++ K  IVV D
Sbjct: 447 TGLARNSKRPDRFIGIHFFSPVEKMMLTEVILGKETGDRALAAALDYVAAIRKTPIVVND 506

Query: 181 VPGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSV 240
             GF+VNR + R +     ++ +G+     +  +A +  G P+G   L D   +D+   +
Sbjct: 507 TRGFYVNRCVFRYIHEAYDMLIEGVP--PAMIENAAKMAGMPVGPLSLNDEVAIDLSQKI 564

Query: 241 WKAVTA-RGFKAFP---CSSTEKLVSQ-GKLGVKSGSGYYQYPS--------PG-KFVRP 286
            KA  A  G KA      +  +K+V +  + G K+G G+Y+YP+        PG K + P
Sbjct: 565 LKAAVADLGDKAVDLRHMALIDKMVDELDRRGRKNGKGFYEYPAKPARKYLWPGLKELYP 624

Query: 287 TLPSTSKKLG----RYLISPAVNEVSYLLREGIV-GKDDAEKGCVLGLGLPK---GILSY 338
              +   ++G    R L++ A+ E +  + EGIV    +A+ G +LG G      G LSY
Sbjct: 625 QKDAGEIEVGVLKQRLLVTIAL-EAARTIEEGIVTDPREADVGSILGFGFAPYTGGTLSY 683

Query: 339 ADEIGIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVKEGK 377
            D +G    V   E++    G DH+ P PLL  M ++G+
Sbjct: 684 IDGMGAKAFVELCEKLAADHG-DHFRPTPLLKEMAEKGE 721



 Score = 84.3 bits (207), Expect = 2e-20
 Identities = 55/195 (28%), Positives = 101/195 (51%), Gaps = 18/195 (9%)

Query: 419 NAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAGADVTEFGSLTPVKAMI----- 473
           N    ++++E++  +D       V+ + IT     FS GAD++   S+   +A       
Sbjct: 28  NVFTEEVMKELDAIIDQTTADPAVKGVVITSGKSSFSGGADLSMIKSMFTFQAEERKKDP 87

Query: 474 --ASRKFHEV-------FMKIQFLTKPVIAVINGLALGGGMELALSADFRVAS--KTAEM 522
             A+RK  ++       F K++   KP ++ ING  +GG  E++L+   RVAS  K+ ++
Sbjct: 88  DNAARKLFDLVGRMTGLFRKLETSGKPWVSAINGTCMGGAFEMSLACHGRVASNAKSVKI 147

Query: 523 GQPEINLGLIPGGGGTQRLSRLSG-RKGLELVLTGRRVKAEEAYRLGIVEFLAEPEEL-E 580
             PE+ +G+ PG GGTQR+ RL+  +  L+++ TG  +    A  +G+V  + +P++L E
Sbjct: 148 ALPEVKVGIFPGAGGTQRVPRLTNTQDALQMMTTGSSLTPARAKAMGLVHEVVDPDKLIE 207

Query: 581 SEVRKLANAIAEKSP 595
           +    + N +    P
Sbjct: 208 AAKAMIKNGLKPVQP 222



 Score = 31.6 bits (70), Expect = 1e-04
 Identities = 24/72 (33%), Positives = 37/72 (51%), Gaps = 9/72 (12%)

Query: 330 GLPKGILSYADEIGIDVVVNTLEEMRQTSG-----MDHYSPDPLLLSMVKE-GKLGRKSG 383
           G+P G LS  DE+ ID+    L+      G     + H +   L+  MV E  + GRK+G
Sbjct: 544 GMPVGPLSLNDEVAIDLSQKILKAAVADLGDKAVDLRHMA---LIDKMVDELDRRGRKNG 600

Query: 384 QGFHTYAHEEAK 395
           +GF+ Y  + A+
Sbjct: 601 KGFYEYPAKPAR 612


Lambda     K      H
   0.316    0.134    0.377 

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: 1046
Number of extensions: 44
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 651
Length of database: 737
Length adjustment: 39
Effective length of query: 612
Effective length of database: 698
Effective search space:   427176
Effective search space used:   427176
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (25.4 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