GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Pseudomonas fluorescens GW456-L13

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 PfGW456L13_4041 Enoyl-CoA hydratase (EC 4.2.1.17) / Delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase (EC 5.3.3.8) / 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) / 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3)

Query= BRENDA::A4YDS4
         (651 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4041
          Length = 715

 Score =  179 bits (455), Expect = 3e-49
 Identities = 130/402 (32%), Positives = 198/402 (49%), Gaps = 32/402 (7%)

Query: 2   KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAM-ERIKWSLSKLRESGSLKEGV 60
           +  V+G+G+MG GIA  +A  G  + M DI+   ++Q + E  K  + ++ +       +
Sbjct: 316 QAAVLGAGIMGGGIAYQSASKGTPILMKDINEHGIEQGLAEAAKLLVGRVDKGRMTAAKM 375

Query: 61  EQVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPI 120
            +VL  I P           D V+EAV E+ ++K+ +    E       +LA+NTS++ I
Sbjct: 376 AEVLNGIRPTLSYGD-FGHVDLVVEAVVENPKVKQAVLAEVEDKVKEDTILASNTSTISI 434

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

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

Query: 241 WKAVTARGF----KAFPCSSTEKLVSQGKLGVKSGSGYYQY-------------PSPGKF 283
            + V A GF    K    S+ + L    +LG K+G G+Y Y             PS  + 
Sbjct: 552 GRDVMAEGFPDRMKDDRRSAVDVLYEAKRLGQKNGKGFYAYETDKKGKQKKVADPSVLEV 611

Query: 284 VRPTL----PSTSKKLGRYLISPAVNEVSYLLREGIV-GKDDAEKGCVLGLGLPK---GI 335
           ++P +      T + +  +++ P   E    L +GIV    +A+ G V G+G P    G 
Sbjct: 612 LKPIVYEQREVTDEDIINWMMIPLCLETVRCLEDGIVETAAEADMGLVYGIGFPPFRGGA 671

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



 Score =  115 bits (288), Expect = 7e-30
 Identities = 60/172 (34%), Positives = 102/172 (59%), Gaps = 4/172 (2%)

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

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

Query: 536 GGTQRLSRLSGR-KGLELVLTGRRVKAEEAYRLGIVEFLAEPEELESEVRKL 586
           GGT RL RL G    +E +  G+  + E+A ++G V+ +  PE+L+    +L
Sbjct: 150 GGTVRLPRLIGADNAIEWIAAGKENRPEDALKVGAVDAVVAPEQLQDAALEL 201


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: 1031
Number of extensions: 59
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: 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.

Links

Downloads

Related tools

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