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 Sep 17 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:

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:

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:

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:

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