Alignments for a candidate for ech in Paraburkholderia phymatum STM815

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Paraburkholderia phymatum STM815

Align Peroxisomal bifunctional enzyme; PBE; PBFE; EC 4.2.1.17; EC 5.3.3.8; EC 1.1.1.35 (characterized)
to candidate WP_012400431.1 BPHY_RS05220 3-hydroxyacyl-CoA dehydrogenase

Query= SwissProt::Q08426
         (723 letters)



>NCBI__GCF_000020045.1:WP_012400431.1
          Length = 694

 Score =  516 bits (1330), Expect = e-150
 Identities = 302/692 (43%), Positives = 424/692 (61%), Gaps = 34/692 (4%)

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

Query: 63  IRGFSAPRTFGL-TLGHVVDEIQRNEKPVVAAIQGMAFGGGLELALGCHYRIAHAEAQVG 121
           I  F+ P+ F   TL  V+  ++ + KPVVAAI  +A GGGLELALG HYR+A   AQ+ 
Sbjct: 63  ITEFNTPKAFQEPTLATVIKAVEGSAKPVVAAIHSVAMGGGLELALGAHYRVAAPGAQIA 122

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

Query: 182 IRFAQRVSDQPLESRRLCNKPIQSLPNMDSIFSEA---LLKMRRQHPGCLAQEACVRAVQ 238
           + FA++V  Q     ++ ++ I   PN       A   +  + +Q+P   A   C+ A++
Sbjct: 183 LAFARKVGAQSGPHPKIRDRNIGH-PNAAGFIQFARNSVAGVAKQYP---APHKCIDAIE 238

Query: 239 AAVQYPYEVGIKKEEELFLYLLQSGQARALQYAFFAERKANKW-STPSGASWKTASARPV 297
           A V   ++ G+K E E FL L+Q+ +++AL++AFF ER A+K    PS        AR +
Sbjct: 239 AGVLKGFDHGVKVERECFLALVQTPESKALRHAFFGERAASKIPDVPSDTP-----ARNI 293

Query: 298 SSVGVVGLGTMGRGIVISFARARIPVIAV----DSDKNQLATANKMITSVLEKEASKMQQ 353
             VGV+G GTMG GI ++F  A +PV  +    D+ +  LAT  K   + ++K    M+ 
Sbjct: 294 DKVGVIGAGTMGGGIAMNFVNAGLPVTLLEMKQDALERGLATIRKNYEATVKKGKLTMEA 353

Query: 354 SGHPWSGPKPRLTSSVKELGGVDLVIEAVFEEMSLKKQVFAELSAVCKPEAFLCTNTSAL 413
                S   P LT   + LG  DL+IEAV+EE+ +K+QVF  L  V KP A L +NTS L
Sbjct: 354 LEQRMSLITPTLT--YEALGDADLIIEAVYEELGVKEQVFTRLDEVAKPGAILASNTSTL 411

Query: 414 DVDEIASSTDRPHLVIGTHFFSPAHVMKLLEVIPSQYSSPTTIATVMNLSKKIKKIGVVV 473
           D+++IA+ T RP  V+G HFFSPA+VMKLLEV+  + ++   +ATVM ++KKI+K  VV 
Sbjct: 412 DLNKIAAFTKRPQDVVGMHFFSPANVMKLLEVVRGKDTAKDVLATVMQVAKKIRKTAVVS 471

Query: 474 GNCFGFVGNRMLNPYYNQAYFLLEEGSKPEEVDQVLEEFGFKMGPFRVSDLAGLDVGWKS 533
           G C GF+GNRM+  Y  QA F+LEEG+ P +VD+ +E+FGF MGPFR+SDLAG D+GW  
Sbjct: 472 GVCDGFIGNRMVEQYVRQALFMLEEGALPAQVDKAIEKFGFAMGPFRMSDLAGNDIGWAI 531

Query: 534 RKGQGLTGPTLLPGTPARKRGNRRYCPIPDVLCELGRFGQKTGKGWYQYDKPLGRIHKPD 593
           RK +    P            + RY  I D LCE GRFGQKTG GWY Y K   R   P 
Sbjct: 532 RKRRYQEEP------------HMRYSKIADRLCEAGRFGQKTGGGWYDY-KAGDRNAYPS 578

Query: 594 PWLSKFLSRYRKTHHIEPRTISQDEILERCLYSLINEAFRILGEGIAASPEHIDVVYLHG 653
             + + +  + K   IE R IS DEI+ER +++L+NE  +IL EGIA+    ID+VYL G
Sbjct: 579 KPIDEMIVAHSKELGIERRKISDDEIVERLVFALVNEGAKILEEGIASKASDIDMVYLTG 638

Query: 654 YGWPRHKGGPMFYASTVGLPTVLEKLQKYYRQ 685
           YG+P  +GGPM YA +VGL  V   +++Y  Q
Sbjct: 639 YGFPLWRGGPMLYADSVGLYNVERAIRRYAAQ 670


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: 1133
Number of extensions: 67
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 24 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)
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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