Alignments for a candidate for ech in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Cupriavidus basilensis 4G11

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 RR42_RS11095 RR42_RS11095 3-hydroxyacyl-CoA dehydrogenase

Query= BRENDA::A4YDS4
         (651 letters)



>FitnessBrowser__Cup4G11:RR42_RS11095
          Length = 693

 Score =  184 bits (468), Expect = 9e-51
 Identities = 129/399 (32%), Positives = 203/399 (50%), Gaps = 26/399 (6%)

Query: 2   KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSL-KEGV 60
           +V VIG+G MG GI      AG  V M +   E L + +  I+ +     + G L +E V
Sbjct: 294 RVAVIGAGTMGGGITMNFLNAGVPVIMLETKQEALDRGVATIRKNYENSAKKGKLTQEKV 353

Query: 61  EQVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPI 120
           EQ +  +   T     +K +D VIEAV E++ +K  +F+  +      A+LA+NTS+L +
Sbjct: 354 EQRMGLL-TTTLSYDEIKDADMVIEAVFEEMGVKEIVFKKLDEVMKQGAILASNTSTLDV 412

Query: 121 SEIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKD 180
           ++IAS  K PQ VVGMHFF+P  +M L+E+VRG+ T  +V+ T  ++AK + K  +V   
Sbjct: 413 NKIASFTKRPQDVVGMHFFSPANVMKLLEVVRGEKTGKDVLATVMQLAKKIKKTAVVSGV 472

Query: 181 VPGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSV 240
             GF  NR++ +      YL+++G  ++ E    AIE+ GF MG F + D  G DIG+++
Sbjct: 473 CDGFIGNRMIEQYSRQAGYLLDEG--ALPEQVDKAIEKFGFAMGPFRMGDLAGNDIGWAI 530

Query: 241 WKAVTARGFKAFPCSSTEKLVSQGKLGVKSGSGYYQY------PSPGKFVRPTLPSTSKK 294
            K       +     + + L   G+ G K+G+G+Y Y      P P + V   +   SK 
Sbjct: 531 RKRRAIDKPEIQYSKTADLLCELGRYGQKTGAGWYDYKAGDRKPYPNQQVNDMIVQHSKD 590

Query: 295 LG------------RYLISPAVNEVSYLLREGIVGK-DDAEKGCVLGLGLP---KGILSY 338
           LG              L+   VNE + +L EGI  K  D +   + G G P    G + Y
Sbjct: 591 LGITRRKISDEEIVERLVFALVNEGAKILEEGIASKASDIDMVYLTGYGFPLFRGGPMLY 650

Query: 339 ADEIGIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVKEGK 377
           AD++G+  V  ++    +    + +   PLL+ +  EGK
Sbjct: 651 ADQVGLFNVAQSMARYAKGYHGEAWQAAPLLVKLAAEGK 689



 Score =  108 bits (269), Expect = 1e-27
 Identities = 70/206 (33%), Positives = 111/206 (53%), Gaps = 20/206 (9%)

Query: 398 TIVVRVEPPLAWIVLNRPTRYNAING-------DMIREINQALDSLEEREDVRVIAITGQ 450
           T   +V+  +A I L+ P     +NG        ++  + +ALD       V+ I ITG 
Sbjct: 2   TAQYQVQDGVAVITLDNPP----VNGLGLSTRLGIVEGMTRALDDAA----VKAIVITGA 53

Query: 451 GRVFSAGADVTEFGSLTPVKAMIASRKFHEVFMKIQFLTKPVIAVINGLALGGGMELALS 510
           G+ FS GAD+ EF   TP      +   H V   ++  +KPV+A I+ +A+GGG+ELAL 
Sbjct: 54  GKAFSGGADIREFN--TPKATQEPT--LHSVIKVVEGSSKPVVAAIHSVAMGGGLELALG 109

Query: 511 ADFRVASKTAEMGQPEINLGLIPGGGGTQRLSRLSG-RKGLELVLTGRRVKAEEAYRLGI 569
            ++RVASK A++  PE+ LGL+PG GGTQRL R+ G    L ++++G  + +E+     +
Sbjct: 110 CNYRVASKGAQIALPEVKLGLLPGAGGTQRLPRVIGLEAALNMIVSGNAIPSEKFAGTKL 169

Query: 570 VEFLAEPEELESEVRKLANAIAEKSP 595
            + + + + L + V     A A   P
Sbjct: 170 FDEIVDGDVLPAAVAFAKTAAANPGP 195


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: 979
Number of extensions: 52
Number of successful extensions: 9
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: 693
Length adjustment: 39
Effective length of query: 612
Effective length of database: 654
Effective search space:   400248
Effective search space used:   400248
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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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources