GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ech in Pseudomonas putida KT2440

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 PP_2136 PP_2136 enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase

Query= BRENDA::A4YDS4
         (651 letters)



>lcl|FitnessBrowser__Putida:PP_2136 PP_2136 enoyl-CoA
           hydratase/3-hydroxyacyl-CoA dehydrogenase
          Length = 715

 Score =  188 bits (478), Expect = 6e-52
 Identities = 134/402 (33%), Positives = 194/402 (48%), Gaps = 32/402 (7%)

Query: 2   KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLKEG-V 60
           +  V+G+G+MG GIA  +A+ G  + M DI  E +Q  +      L    E G L    +
Sbjct: 316 QAAVLGAGIMGGGIAYQSAVKGTPILMKDIREEAIQLGLNEASKLLGNRVEKGRLTPAKM 375

Query: 61  EQVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPI 120
            + L  I P           D V+EAV E+ ++K+ +    E      A+LA+NTS++ I
Sbjct: 376 AEALNAIRPTLSYGD-FANVDIVVEAVVENPKVKQAVLAEVEGQVKDDAILASNTSTISI 434

Query: 121 SEIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKD 180
           + +A  LK P+  VGMHFFNP  +MPLVE++RG+ +SD  V TT   AK M K  IVV D
Sbjct: 435 NLLAKALKRPENFVGMHFFNPVHMMPLVEVIRGEKSSDVAVATTVAYAKKMGKNPIVVND 494

Query: 181 VPGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSV 240
            PGF VNRVL         LV  G+  ++ +D   +E+ G+PMG   L D  G+D G+  
Sbjct: 495 CPGFLVNRVLFPYFGGFAKLVSAGVDFVR-ID-KVMEKFGWPMGPAYLMDVVGIDTGHH- 551

Query: 241 WKAVTARGF----KAFPCSSTEKLVSQGKLGVKSGSGYYQYPS-----PGKFVRPTL--- 288
            + V A GF    K    S+ + L    +LG K+G G+Y Y +     P K    T+   
Sbjct: 552 GRDVMAEGFPDRMKDERRSAVDALYEANRLGQKNGKGFYAYETDKRGKPKKVFDATVLDV 611

Query: 289 ---------PSTSKKLGRYLISPAVNEVSYLLREGIV-GKDDAEKGCVLGLGLPK---GI 335
                      T + +  +++ P   E    L +GIV    +A+ G V G+G P    G 
Sbjct: 612 LKPIVFEQREVTDEDIINWMMVPLCLETVRCLEDGIVETAAEADMGLVYGIGFPPFRGGA 671

Query: 336 LSYADEIGIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVKEGK 377
           L Y D IG+   V   ++      +  Y P   L  M K G+
Sbjct: 672 LRYIDSIGVAEFVALADQYADLGPL--YHPTAKLREMAKNGQ 711



 Score =  112 bits (280), Expect = 6e-29
 Identities = 61/165 (36%), Positives = 96/165 (58%), Gaps = 4/165 (2%)

Query: 419 NAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAGADVTEFGS---LTPVKAMIAS 475
           N  N   + E+ QA+D++     V+ + +     VF  GAD+TEF     L   + +  +
Sbjct: 30  NKFNRLTLNELRQAVDAIRADASVKGVIVRSGKDVFIVGADITEFVDNFKLPEAELVAGN 89

Query: 476 RKFHEVFMKIQFLTKPVIAVINGLALGGGMELALSADFRVASKTAEMGQPEINLGLIPGG 535
            + + +F   + L  P +A ING+ALGGG+E+ L+AD+RV S +A +G PE+ LG+ PG 
Sbjct: 90  LEANRIFNAFEDLEVPTVAAINGIALGGGLEMCLAADYRVMSTSARIGLPEVKLGIYPGF 149

Query: 536 GGTQRLSRLSGR-KGLELVLTGRRVKAEEAYRLGIVEFLAEPEEL 579
           GGT RL RL G    +E +  G+  +AE+A ++G V+ +  PE L
Sbjct: 150 GGTVRLPRLIGSDNAIEWIAAGKENRAEDALKVGAVDAVVAPELL 194


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: 1027
Number of extensions: 64
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: 2
Length of query: 651
Length of database: 715
Length adjustment: 39
Effective length of query: 612
Effective length of database: 676
Effective search space:   413712
Effective search space used:   413712
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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