GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Williamsia sterculiae CPCC 203464

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 WP_076475473.1 BW971_RS00105 3-hydroxyacyl-CoA dehydrogenase

Query= BRENDA::A4YDS4
         (651 letters)



>NCBI__GCF_900156495.1:WP_076475473.1
          Length = 724

 Score =  176 bits (445), Expect = 4e-48
 Identities = 131/408 (32%), Positives = 203/408 (49%), Gaps = 38/408 (9%)

Query: 2   KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAME-RIKWSLSKLRESGSLKEGV 60
           KV VIG+G+MG  IA ++A AG +V + D++ E   +  +  +      L+   + +E  
Sbjct: 326 KVGVIGAGMMGAAIAYVSAKAGIDVVLKDVTQEAADKGKQYSVTLEEKALKRGKTTQEKS 385

Query: 61  EQVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPI 120
           +++LARIHP TD+ +  KG DFVIEA  E +E+K  +F   +    P AVL +NTS+LPI
Sbjct: 386 DELLARIHP-TDKPEDFKGVDFVIEAAFESVEVKNQVFGEIQDIVEPDAVLGSNTSTLPI 444

Query: 121 SEIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKD 180
           + +A  +  P+  +G+HFF+P   MPLVEI+RG+ TSD V+    +    + K  IVV D
Sbjct: 445 TGLAKGVNRPEDFIGIHFFSPVDKMPLVEIIRGEKTSDAVLAKVIDYTLQIRKTPIVVHD 504

Query: 181 VPGFFVNRVLLRIMEAGCYLVEKGI--ASIQEVDSSAIEELGFPMGVFLLADYTGLDIGY 238
             GFF +RV+   +      V +G+  A I++  S A    G+P     L+D   L +  
Sbjct: 505 SRGFFTSRVIGTFINEAIAAVGEGVEPARIEQAGSQA----GYPAPPLQLSDELTLTLMQ 560

Query: 239 SVWKAVTARGFKA----FPCSST----EKLVSQGKLGVKSGSGYYQYPSPGK------FV 284
            + KA T  G+KA    FP   +    ++LV  G+   K G G+Y Y   GK       +
Sbjct: 561 KIRKA-TEEGYKAEGKDFPDHGSYEVIDRLVEAGRTSKKDGKGFYDYDDAGKRTGLWPGL 619

Query: 285 RPTLPSTSKKL------GRYLISPAVNEVSYLLREGIVGKDDAEKGCVLGLGLPK---GI 335
           R    S S  +       R L + A+  V       +   +DA  G + G+G P    G+
Sbjct: 620 RDEFKSGSGDVPFIDLQERMLFAEALETVRCFDEGVLTSVEDANIGSIFGIGFPPWTGGV 679

Query: 336 LSYADEI--GIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVKEGKLGRK 381
           + Y ++   G+   V+   E+    G     P     S+V++ K G K
Sbjct: 680 IQYINQYSGGLQGFVDRANELAARYGQQFVPP----TSLVEKAKAGEK 723



 Score = 90.9 bits (224), Expect = 2e-22
 Identities = 59/175 (33%), Positives = 94/175 (53%), Gaps = 14/175 (8%)

Query: 419 NAINGDMIREINQALDSLE-EREDVRVIAITGQGRVFSAGADVTEFGSLT--------PV 469
           N +N   +  I   +D LE E++ +  + IT   + F AG D+ E  +           +
Sbjct: 28  NTMNALFLESIGPIVDRLEAEKDSITGVVITSAKKTFFAGGDLKEMTADQGDRPKEDIAL 87

Query: 470 KAMIASRKFHEVFMKIQFLTKPVIAVINGLALGGGMELALSADFRVAS--KTAEMGQPEI 527
           +   ++    +   +++ L KPV+A +NG ALGGG+ELAL    R+A+  K  ++G PE+
Sbjct: 88  EITNSTNAMKKSLRRLETLGKPVVAAVNGAALGGGLELALHTHHRIAADVKGNQLGLPEV 147

Query: 528 NLGLIPGGGGTQRLSRLSGRKG--LELVLTGRRVKAEEAYRLGIV-EFLAEPEEL 579
            LGL+PGGGG  R  RL G +   + ++L G R K  +A  +G+V E +   EEL
Sbjct: 148 QLGLLPGGGGVTRTVRLLGVQTALMSVLLQGNRFKPAKAKEIGLVDEVVGSVEEL 202



 Score = 27.3 bits (59), Expect = 0.002
 Identities = 26/106 (24%), Positives = 47/106 (44%), Gaps = 16/106 (15%)

Query: 291 TSKKLGRYLISPAVNEVSYLLREGIVGKDDAEKGCVLGLGLPKGILSYADEIGIDV---V 347
           TS+ +G +     +NE    + EG+      + G   G   P   L  +DE+ + +   +
Sbjct: 510 TSRVIGTF-----INEAIAAVGEGVEPARIEQAGSQAGYPAPP--LQLSDELTLTLMQKI 562

Query: 348 VNTLEEMRQTSGMDHYSPD----PLLLSMVKEGKLGRKSGQGFHTY 389
               EE  +  G D   PD     ++  +V+ G+  +K G+GF+ Y
Sbjct: 563 RKATEEGYKAEGKDF--PDHGSYEVIDRLVEAGRTSKKDGKGFYDY 606


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: 1050
Number of extensions: 50
Number of successful extensions: 8
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: 724
Length adjustment: 39
Effective length of query: 612
Effective length of database: 685
Effective search space:   419220
Effective search space used:   419220
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 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:

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