GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Keio:16447 b2341 fused enoyl-CoA hydratase and
           epimerase and isomerase/3-hydroxyacyl-CoA dehydrogenase
           (NCBI)
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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