Alignments for a candidate for ech in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Burkholderia phytofirmans PsJN

Align Peroxisomal bifunctional enzyme; PBE; PBFE; EC 4.2.1.17; EC 5.3.3.8; EC 1.1.1.35 (characterized)
to candidate BPHYT_RS09560 BPHYT_RS09560 3-hydroxyacyl-CoA dehydrogenase

Query= SwissProt::Q08426
         (723 letters)



>FitnessBrowser__BFirm:BPHYT_RS09560
          Length = 694

 Score =  519 bits (1337), Expect = e-151
 Identities = 306/700 (43%), Positives = 420/700 (60%), Gaps = 29/700 (4%)

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

Query: 63  IRGFSAPRTFGL-TLGHVVDEIQRNEKPVVAAIQGMAFGGGLELALGCHYRIAHAEAQVG 121
           I  F+ P+     TL  V+  ++ + KPV+AAI  +A GGGLELALG HYRIA   AQ+ 
Sbjct: 63  ITEFNTPKAGQEPTLATVIKIVEGSAKPVIAAIHSVAMGGGLELALGAHYRIAAPGAQIA 122

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

Query: 182 IRFAQRVSDQPLESRRLCNKPIQSLPNMDSIFSEALLKMRRQHPGCLAQEACVRAVQAAV 241
           + FA++VS +     ++ ++ I+  PN       A   +        A   C+ AV+A V
Sbjct: 183 LAFARKVSAKEGPHPKVRDRKIEH-PNAAGFIQFARNTVATMAKNFPAPLKCIDAVEAGV 241

Query: 242 QYPYEVGIKKEEELFLYLLQSGQARALQYAFFAERKANKW-STPSGASWKTASARPVSSV 300
           Q  ++ G+  E E F+ L+Q+ ++ AL++AFF ER A+K    PS         R +  V
Sbjct: 242 QKGFDKGLAFERECFMALVQTPESHALRHAFFGERAASKIPDVPSDTP-----VRDIGQV 296

Query: 301 GVVGLGTMGRGIVISFARARIPVIAVDSDKNQL----ATANKMITSVLEKEASKMQQSGH 356
            V+G GTMG GI ++F  A IPV  +++ +  L    AT  K   + ++K   K +  G 
Sbjct: 297 AVIGAGTMGGGIAMNFINAGIPVTLLETKQEALDRGLATIRKNYEATVKKGKLKPEVLGQ 356

Query: 357 PWSGPKPRLTSSVKELGGVDLVIEAVFEEMSLKKQVFAELSAVCKPEAFLCTNTSALDVD 416
             +   P L  S  +L   DL++EAVFEE+ +K+Q F  L  V K  A L +NTS LDVD
Sbjct: 357 RMALITPTL--SYDDLKNADLIVEAVFEELGVKEQAFKRLDEVAKQGAILASNTSTLDVD 414

Query: 417 EIASSTDRPHLVIGTHFFSPAHVMKLLEVIPSQYSSPTTIATVMNLSKKIKKIGVVVGNC 476
           +IA+ T RP  V+G HFFSPA+VMKLLEV+  + ++   +ATVMNL+KKIKK  VV G C
Sbjct: 415 KIAAFTKRPQDVVGMHFFSPANVMKLLEVVRGKETAKDVLATVMNLAKKIKKTAVVSGVC 474

Query: 477 FGFVGNRMLNPYYNQAYFLLEEGSKPEEVDQVLEEFGFKMGPFRVSDLAGLDVGWKSRKG 536
            GF+GNRM+  Y  QA F+LEEG+ P +VD+ +E+FGF MGPFR+SDLAG D+GW  RK 
Sbjct: 475 DGFIGNRMVEQYIRQALFMLEEGALPAQVDKAIEKFGFAMGPFRMSDLAGNDIGWAIRKR 534

Query: 537 QGLTGPTLLPGTPARKRGNRRYCPIPDVLCELGRFGQKTGKGWYQYDKPLGRIHKPDPWL 596
           + L  P +             Y  I D LCE GRFGQKTG GWY Y K   R   P   +
Sbjct: 535 RYLEHPDM------------HYSKIADRLCETGRFGQKTGGGWYDY-KAGDRTAYPSKVV 581

Query: 597 SKFLSRYRKTHHIEPRTISQDEILERCLYSLINEAFRILGEGIAASPEHIDVVYLHGYGW 656
              +  + K    E R IS +EI+ER +++L+NE  +IL EGIA+    ID+VYL GYG+
Sbjct: 582 DDMIVAFSKETDTERRKISDEEIVERLVFALVNEGAKILEEGIASKASDIDMVYLTGYGF 641

Query: 657 PRHKGGPMFYASTVGLPTVLEKLQKY-YRQNPDIPQLEPS 695
           P ++GGPM YA TVGL  V   +++Y  R N D  QL PS
Sbjct: 642 PLYRGGPMLYADTVGLYNVERAIRRYAARPNGDAWQLAPS 681


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: 1076
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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