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 17892 b3846 fused 3-hydroxybutyryl-CoA epimerase/delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase/enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase (NCBI)

Query= BRENDA::A4YDS4
         (651 letters)



>FitnessBrowser__Keio:17892
          Length = 729

 Score =  181 bits (458), Expect = 1e-49
 Identities = 125/369 (33%), Positives = 186/369 (50%), Gaps = 31/369 (8%)

Query: 2   KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLKEGVE 61
           +  V+G+G+MG GIA  +A  G  V M DI+ + L   M      L+K  E G + +G++
Sbjct: 315 QAAVLGAGIMGGGIAYQSAWKGVPVVMKDINDKSLTLGMTEAAKLLNKQLERGKI-DGLK 373

Query: 62  Q--VLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLP 119
              V++ IHP  D A      D V+EAV E+ ++K+ +    E       VLA+NTS++P
Sbjct: 374 LAGVISTIHPTLDYA-GFDRVDIVVEAVVENPKVKKAVLAETEQKVRQDTVLASNTSTIP 432

Query: 120 ISEIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVK 179
           ISE+A+ L+ P+   GMHFFNP   MPLVEI+RG+ +SDE +      A  M K  IVV 
Sbjct: 433 ISELANALERPENFCGMHFFNPVHRMPLVEIIRGEKSSDETIAKVVAWASKMGKTPIVVN 492

Query: 180 DVPGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYS 239
           D PGFFVNRVL         L+  G A  +++D    ++ G+PMG   L D  G+D  + 
Sbjct: 493 DCPGFFVNRVLFPYFAGFSQLLRDG-ADFRKIDKVMEKQFGWPMGPAYLLDVVGIDTAHH 551

Query: 240 VWKAVTARGF----KAFPCSSTEKLVSQGKLGVKSGSGYYQYPSPGK------------- 282
             +AV A GF    +     + + L    + G K+G G+++Y    K             
Sbjct: 552 A-QAVMAAGFPQRMQKDYRDAIDALFDANRFGQKNGLGFWRYKEDSKGKPKKEEDAAVED 610

Query: 283 ----FVRPTLPSTSKKLGRYLISPAVNEVSYLLREGIVGKD-DAEKGCVLGLGLPK---G 334
                 +P    + +++   ++ P VNEV   L EGI+    +A+   V GLG P    G
Sbjct: 611 LLAEVSQPKRDFSEEEIIARMMIPMVNEVVRCLEEGIIATPAEADMALVYGLGFPPFHGG 670

Query: 335 ILSYADEIG 343
              + D +G
Sbjct: 671 AFRWLDTLG 679



 Score =  111 bits (278), Expect = 1e-28
 Identities = 61/181 (33%), Positives = 105/181 (58%), Gaps = 4/181 (2%)

Query: 403 VEPPLAWIVLNRPTRYNAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAGADVTE 462
           +E  +A +V + P   N ++   +  + +A+  LE++ D++ + +      F  GAD+TE
Sbjct: 13  LEDGIAELVFDAPGSVNKLDTATVASLGEAIGVLEQQSDLKGLLLRSNKAAFIVGADITE 72

Query: 463 FGSLTPVKAMIASRKFH---EVFMKIQFLTKPVIAVINGLALGGGMELALSADFRVASKT 519
           F SL  V     S+  H    VF +++ L  P IA +NG ALGGG E  L+ D+R+A+  
Sbjct: 73  FLSLFLVPEEQLSQWLHFANSVFNRLEDLPVPTIAAVNGYALGGGCECVLATDYRLATPD 132

Query: 520 AEMGQPEINLGLIPGGGGTQRLSRLSGR-KGLELVLTGRRVKAEEAYRLGIVEFLAEPEE 578
             +G PE  LG++PG GG+ R+ R+ G    LE++  G+ V A++A ++G+V+ + + E+
Sbjct: 133 LRIGLPETKLGIMPGFGGSVRMPRMLGADSALEIIAAGKDVGADQALKIGLVDGVVKAEK 192

Query: 579 L 579
           L
Sbjct: 193 L 193


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: 1038
Number of extensions: 62
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 651
Length of database: 729
Length adjustment: 39
Effective length of query: 612
Effective length of database: 690
Effective search space:   422280
Effective search space used:   422280
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