GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Escherichia coli BW25113

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 16447 b2341 fused enoyl-CoA hydratase and epimerase and isomerase/3-hydroxyacyl-CoA dehydrogenase (NCBI)

Query= BRENDA::A4YDS4
         (651 letters)



>FitnessBrowser__Keio:16447
          Length = 714

 Score =  164 bits (416), Expect = 1e-44
 Identities = 126/398 (31%), Positives = 199/398 (50%), Gaps = 28/398 (7%)

Query: 3   VTVIGSGVMGHGIAELAAI-AGNEVWMNDISTEILQQAMERIKWSL--SKLRESGSLKEG 59
           V ++G G+MG GIA + A  AG  V + DI+ + +  A+ +  W     K+R        
Sbjct: 311 VGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHAL-KYSWDQLEGKVRRRHLKASE 369

Query: 60  VEQVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLP 119
            ++ LA I   TD  +     D +IEAV E+LELK+ +    E + +   + A+NTSSLP
Sbjct: 370 RDKQLALISGTTDY-RGFAHRDLIIEAVFENLELKQQMVAEVEQNCAAHTIFASNTSSLP 428

Query: 120 ISEIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVK 179
           I +IA+    P++V+G+HFF+P   MPLVEI+    TS + + TT ++AK   K  IVV+
Sbjct: 429 IGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQTIATTVKLAKKQGKTPIVVR 488

Query: 180 DVPGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYS 239
           D  GF+VNR+L   +     ++ +G   ++ +D +A+ + GFP+G   L D  G+D G  
Sbjct: 489 DKAGFYVNRILAPYINEAIRMLTQG-ERVEHID-AALVKFGFPVGPIQLLDEVGIDTGTK 546

Query: 240 VWKAVTARGFKAF--PCSSTEKLVSQGKLGVKSGSGYYQYPSPG----KFVRPTLPSTSK 293
           +   + A   + F  P +    +++  + G K+G G+Y Y   G    K V P +     
Sbjct: 547 IIPVLEAAYGERFSAPANVVSSILNDDRKGRKNGRGFYLYGQKGRKSKKQVDPAIYPLIG 606

Query: 294 KLGRYLIS-PAVNE--VSYLLREGIVGKD--------DAEKGCVLGLGLPK---GILSYA 339
             G+  IS P V E  V  +L E +   D        D + G V G+G P    G   Y 
Sbjct: 607 TQGQGRISAPQVAERCVMLMLNEAVRCVDEQVIRSVRDGDIGAVFGIGFPPFLGGPFRYI 666

Query: 340 DEIGIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVKEGK 377
           D +G   VV  ++ +    G   ++P   L+ M   G+
Sbjct: 667 DSLGAGEVVAIMQRLATQYG-SRFTPCERLVEMGARGE 703



 Score =  105 bits (261), Expect = 9e-27
 Identities = 75/218 (34%), Positives = 123/218 (56%), Gaps = 8/218 (3%)

Query: 398 TIVVRVEPPLAWIVLNRP-TRYNAINGDMIREINQALDSLEEREDVR-VIAITGQGRVFS 455
           T+ VR++  +A I ++ P  + N +  +   ++   +  L E +++R V+ ++ +   F 
Sbjct: 8   TLNVRLDN-IAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKPDNFI 66

Query: 456 AGADVTEFGSL-TPVKAMIASRKFHEVFMKIQFLTKPVIAVINGLALGGGMELALSADFR 514
           AGAD+   G+  T  +A   +R+  ++  +I  L   VIA I+G  LGGG+ELAL+   R
Sbjct: 67  AGADINMIGNCKTAQEAEALARQGQQLMAEIHALPIQVIAAIHGACLGGGLELALACHGR 126

Query: 515 VASKTAE--MGQPEINLGLIPGGGGTQRLSRLSG-RKGLELVLTGRRVKAEEAYRLGIVE 571
           V +   +  +G PE+ LGL+PG GGTQRL RL G    LE++LTG++++A++A +LG+V+
Sbjct: 127 VCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAKQALKLGLVD 186

Query: 572 FLAEPEELESEVRKLANAIAEKS-PLAVASAKLAYKLG 608
            +     L     +LA      S PL V    LA  LG
Sbjct: 187 DVVPHSILLEAAVELAKKERPSSRPLPVRERILAGPLG 224



 Score = 46.2 bits (108), Expect = 5e-09
 Identities = 24/97 (24%), Positives = 49/97 (50%), Gaps = 2/97 (2%)

Query: 299 LISPAVNEVSYLLREGIVGKDDAEKGCVLGLGLPKGILSYADEIGIDVVVNTLEEMRQTS 358
           +++P +NE   +L +G   + +     ++  G P G +   DE+GID     +  +    
Sbjct: 498 ILAPYINEAIRMLTQG--ERVEHIDAALVKFGFPVGPIQLLDEVGIDTGTKIIPVLEAAY 555

Query: 359 GMDHYSPDPLLLSMVKEGKLGRKSGQGFHTYAHEEAK 395
           G    +P  ++ S++ + + GRK+G+GF+ Y  +  K
Sbjct: 556 GERFSAPANVVSSILNDDRKGRKNGRGFYLYGQKGRK 592


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: 922
Number of extensions: 38
Number of successful extensions: 7
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: 714
Length adjustment: 39
Effective length of query: 612
Effective length of database: 675
Effective search space:   413100
Effective search space used:   413100
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