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 Peroxisomal bifunctional enzyme; PBE; PBFE; EC 4.2.1.17; EC 5.3.3.8; EC 1.1.1.35 (characterized)
to candidate RR42_RS11095 RR42_RS11095 3-hydroxyacyl-CoA dehydrogenase

Query= SwissProt::Q08426
         (723 letters)



>FitnessBrowser__Cup4G11:RR42_RS11095
          Length = 693

 Score =  508 bits (1308), Expect = e-148
 Identities = 301/711 (42%), Positives = 433/711 (60%), Gaps = 32/711 (4%)

Query: 2   AEYTRLHNALALIRLRNPPVNAISTTLLRDIKEGLQKAVIDHTIKAIVICGAEGKFSAGA 61
           A+Y ++ + +A+I L NPPVN +  +    I EG+ +A+ D  +KAIVI GA   FS GA
Sbjct: 3   AQY-QVQDGVAVITLDNPPVNGLGLSTRLGIVEGMTRALDDAAVKAIVITGAGKAFSGGA 61

Query: 62  DIRGFSAPR-TFGLTLGHVVDEIQRNEKPVVAAIQGMAFGGGLELALGCHYRIAHAEAQV 120
           DIR F+ P+ T   TL  V+  ++ + KPVVAAI  +A GGGLELALGC+YR+A   AQ+
Sbjct: 62  DIREFNTPKATQEPTLHSVIKVVEGSSKPVVAAIHSVAMGGGLELALGCNYRVASKGAQI 121

Query: 121 GLPEVTLGLLPGARGTQLLPRLTGVPAALDLITSGRRILADEALKLGILDKVVNSDPVEE 180
            LPEV LGLLPGA GTQ LPR+ G+ AAL++I SG  I +++     + D++V+ D +  
Sbjct: 122 ALPEVKLGLLPGAGGTQRLPRVIGLEAALNMIVSGNAIPSEKFAGTKLFDEIVDGDVLPA 181

Query: 181 AIRFAQRVSDQPLESRRLCNKPI--QSLPNMDSIFSEALLKMRRQHPGCLAQEACVRAVQ 238
           A+ FA+  +  P    ++ +  +  ++     +     +  + +  P  L    CV AV 
Sbjct: 182 AVAFAKTAAANPGPYPKVRDLKVKHENAEGFIAFSRNTVAAVAKNFPAPLK---CVDAVA 238

Query: 239 AAVQYPYEVGIKKEEELFLYLLQSGQARALQYAFFAERKANKW-STPSGASWKTASARPV 297
           A+++ P+E G+K E E F+YL+ + ++RAL++AFF ER A+K    P G +      R +
Sbjct: 239 ASLK-PFEAGLKAEREGFMYLITTPESRALRHAFFGERAASKIPDVPEGTA-----TRKI 292

Query: 298 SSVGVVGLGTMGRGIVISFARARIPVIAVDSDKNQLATANKMITSVLEKEASKMQQSGHP 357
             V V+G GTMG GI ++F  A +PVI +++ +  L      I    E  A K + +   
Sbjct: 293 ERVAVIGAGTMGGGITMNFLNAGVPVIMLETKQEALDRGVATIRKNYENSAKKGKLTQEK 352

Query: 358 WSGPKPRLTSSVK--ELGGVDLVIEAVFEEMSLKKQVFAELSAVCKPEAFLCTNTSALDV 415
                  LT+++   E+   D+VIEAVFEEM +K+ VF +L  V K  A L +NTS LDV
Sbjct: 353 VEQRMGLLTTTLSYDEIKDADMVIEAVFEEMGVKEIVFKKLDEVMKQGAILASNTSTLDV 412

Query: 416 DEIASSTDRPHLVIGTHFFSPAHVMKLLEVIPSQYSSPTTIATVMNLSKKIKKIGVVVGN 475
           ++IAS T RP  V+G HFFSPA+VMKLLEV+  + +    +ATVM L+KKIKK  VV G 
Sbjct: 413 NKIASFTKRPQDVVGMHFFSPANVMKLLEVVRGEKTGKDVLATVMQLAKKIKKTAVVSGV 472

Query: 476 CFGFVGNRMLNPYYNQAYFLLEEGSKPEEVDQVLEEFGFKMGPFRVSDLAGLDVGWKSRK 535
           C GF+GNRM+  Y  QA +LL+EG+ PE+VD+ +E+FGF MGPFR+ DLAG D+GW  RK
Sbjct: 473 CDGFIGNRMIEQYSRQAGYLLDEGALPEQVDKAIEKFGFAMGPFRMGDLAGNDIGWAIRK 532

Query: 536 GQGLTGPTLLPGTPARKRGNRRYCPIPDVLCELGRFGQKTGKGWYQYDKPLGRIHKPDPW 595
            + +  P +            +Y    D+LCELGR+GQKTG GWY Y K   R   P+  
Sbjct: 533 RRAIDKPEI------------QYSKTADLLCELGRYGQKTGAGWYDY-KAGDRKPYPNQQ 579

Query: 596 LSKFLSRYRKTHHIEPRTISQDEILERCLYSLINEAFRILGEGIAASPEHIDVVYLHGYG 655
           ++  + ++ K   I  R IS +EI+ER +++L+NE  +IL EGIA+    ID+VYL GYG
Sbjct: 580 VNDMIVQHSKDLGITRRKISDEEIVERLVFALVNEGAKILEEGIASKASDIDMVYLTGYG 639

Query: 656 WPRHKGGPMFYASTVGLPTVLEKLQKYYR-QNPDIPQLEPSDYLKKLASQG 705
           +P  +GGPM YA  VGL  V + + +Y +  + +  Q  P   L KLA++G
Sbjct: 640 FPLFRGGPMLYADQVGLFNVAQSMARYAKGYHGEAWQAAP--LLVKLAAEG 688


Lambda     K      H
   0.319    0.136    0.405 

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: 1130
Number of extensions: 55
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 723
Length of database: 693
Length adjustment: 39
Effective length of query: 684
Effective length of database: 654
Effective search space:   447336
Effective search space used:   447336
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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