Alignments for a candidate for ech in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Paraburkholderia bryophila 376MFSha3.1

Align Peroxisomal bifunctional enzyme; PBE; PBFE; EC 4.2.1.17; EC 5.3.3.8; EC 1.1.1.35 (characterized)
to candidate H281DRAFT_00916 H281DRAFT_00916 short chain enoyl-CoA hydratase /3-hydroxyacyl-CoA dehydrogenase

Query= SwissProt::Q08426
         (723 letters)



>FitnessBrowser__Burk376:H281DRAFT_00916
          Length = 694

 Score =  521 bits (1341), Expect = e-152
 Identities = 306/709 (43%), Positives = 426/709 (60%), Gaps = 29/709 (4%)

Query: 3   EYTRLHNALALIRLRNPPVNAISTTLLRDIKEGLQKAVIDHTIKAIVICGAEGKFSAGAD 62
           +YT  H+ +A+I L NPPVN +  +    I EG+++A  D  IKAIV+ GA   FS GAD
Sbjct: 4   DYTT-HDGVAVITLNNPPVNGLGLSTRAGIVEGIERAQNDAAIKAIVLTGAGKAFSGGAD 62

Query: 63  IRGFSAPR-TFGLTLGHVVDEIQRNEKPVVAAIQGMAFGGGLELALGCHYRIAHAEAQVG 121
           I  F+ P+ T   TL  V+  ++ + KPVVAAI  +A GGGLELALG HYRIA   AQ+ 
Sbjct: 63  ITEFNTPKATQEPTLATVIKTVEGSPKPVVAAIHSVAMGGGLELALGAHYRIAAPGAQIA 122

Query: 122 LPEVTLGLLPGARGTQLLPRLTGVPAALDLITSGRRILADEALKLGILDKVVNSDPVEEA 181
           LPEV LG+LPGA GTQ LPR  G+ AAL++I SG  +++ +  + G+ D++ + D  E A
Sbjct: 123 LPEVKLGILPGAGGTQRLPRAIGLEAALNMIVSGAPVMSQDLARSGLFDELADGDLTEAA 182

Query: 182 IRFAQRVSDQPLESRRLCNKPIQSLPNMDSIFSEALLKMRRQHPGCLAQEACVRAVQAAV 241
           + FA++V  +     ++  + I+  PN +     A   +        A   C+ AV+A V
Sbjct: 183 LAFARKVGAKEGPHPKVRERKIEH-PNAEGFIQFARNSVATVAKNFPAPLKCIDAVEAGV 241

Query: 242 QYPYEVGIKKEEELFLYLLQSGQARALQYAFFAERKANKWSTPSGASWKTASARPVSSVG 301
           +  ++ G+  E E F+ L+Q+ ++RAL++AFF ER A+K       +      R +  V 
Sbjct: 242 KNGFDKGLAVERECFVALVQTPESRALRHAFFGERAASKIPDVPADT----PVREIRQVA 297

Query: 302 VVGLGTMGRGIVISFARARIPVIAVDSDKNQL----ATANKMITSVLEKEASKMQQSGHP 357
           V+G GTMG GI ++F  A IPV  +++ +  L    AT  K   + ++K   K +     
Sbjct: 298 VIGAGTMGGGIAMNFISAGIPVTLLETKQEALDRGLATIRKNYEATVKKGKLKPEALEER 357

Query: 358 WSGPKPRLTSSVKELGGVDLVIEAVFEEMSLKKQVFAELSAVCKPEAFLCTNTSALDVDE 417
            +   P L  S  +L   DL++EAVFEE+ +K+QVF  L  V K  A L +NTS LDVD+
Sbjct: 358 MALITPTL--SYDDLKNADLIVEAVFEELGVKEQVFKRLDEVAKSGAILASNTSTLDVDK 415

Query: 418 IASSTDRPHLVIGTHFFSPAHVMKLLEVIPSQYSSPTTIATVMNLSKKIKKIGVVVGNCF 477
           IA+ T RP  V+G HFFSPA+VMKLLEV+  + ++   +ATVM L+KKIKK  VV G C 
Sbjct: 416 IAAFTRRPQDVVGMHFFSPANVMKLLEVVRGKETAKDVLATVMKLAKKIKKTAVVSGVCD 475

Query: 478 GFVGNRMLNPYYNQAYFLLEEGSKPEEVDQVLEEFGFKMGPFRVSDLAGLDVGWKSRKGQ 537
           GF+GNRM+  Y  QA F+L+EG+ P +VD+ +E+FGF MGPFR+SDLAG D+GW  RK +
Sbjct: 476 GFIGNRMIEQYIRQALFMLDEGALPAQVDRAIEKFGFAMGPFRMSDLAGNDIGWAIRKRR 535

Query: 538 GLTGPTLLPGTPARKRGNRRYCPIPDVLCELGRFGQKTGKGWYQYDKPLGRIHKPDPWLS 597
               P +             Y  I D LCE GRFGQKTG GWY Y K   R   P   + 
Sbjct: 536 YEEHPEM------------HYSKIADRLCETGRFGQKTGGGWYDY-KAGDRTAHPSKLVD 582

Query: 598 KFLSRYRKTHHIEPRTISQDEILERCLYSLINEAFRILGEGIAASPEHIDVVYLHGYGWP 657
             +  Y    + + R I  DEI+ER +++L+NE  +IL EGIA+ P  ID+VYL GYG+P
Sbjct: 583 DMIVAYSNETNTQRRKIGDDEIVERLVFALVNEGAKILEEGIASKPSDIDMVYLTGYGFP 642

Query: 658 RHKGGPMFYASTVGLPTVLEKLQKYYRQ-NPDIPQLEPSDYLKKLASQG 705
            ++GGPM YA TVGL  V   +++Y  Q N D  QL PS  + +LA+QG
Sbjct: 643 LYRGGPMLYADTVGLYNVERAIRRYASQPNGDAWQLAPS--IAELAAQG 689


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: 1098
Number of extensions: 58
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 723
Length of database: 694
Length adjustment: 39
Effective length of query: 684
Effective length of database: 655
Effective search space:   448020
Effective search space used:   448020
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.

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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