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_012406378.1 BPHY_RS35840 3-hydroxyacyl-CoA dehydrogenase

Query= SwissProt::Q08426
         (723 letters)



>NCBI__GCF_000020045.1:WP_012406378.1
          Length = 706

 Score =  486 bits (1251), Expect = e-141
 Identities = 290/705 (41%), Positives = 407/705 (57%), Gaps = 28/705 (3%)

Query: 7   LHNALALIRLRNPPVNAISTTLLRDIKEGLQKAVIDHTIKAIVICGAEGKFSAGADIRGF 66
           L   L L+ + NPPVNA+   + R +   ++ A      KA++I GA   F AGADIR F
Sbjct: 14  LRGNLLLVTVDNPPVNALGVEVRRGLVAAIEAAEAYAVAKAVLIVGAGRNFIAGADIREF 73

Query: 67  SAPRTFGLTLGHVVDEIQRNEKPVVAAIQGMAFGGGLELALGCHYRIAHAEAQVGLPEVT 126
             P     TL  V + I+   KPV+ AI G A GGGLE+AL  HYR+A A A++GLPEV 
Sbjct: 74  GKPPQMP-TLPDVCNRIEACSKPVIVAIHGAALGGGLEIALAAHYRLAVAGAKLGLPEVL 132

Query: 127 LGLLPGARGTQLLPRLTGVPAALDLITSGRRILADEALKLGILDKVVNSDPV-EEAIRFA 185
           LGLLPGA GTQ  PRL G  AAL L+ SG+ I A +ALK+G++D+V  SD V  E + +A
Sbjct: 133 LGLLPGAGGTQRAPRLIGAEAALSLMLSGKHIGAQDALKMGLVDRVGQSDDVLTEGLTYA 192

Query: 186 QRVSDQPLESRRLCNKPIQSLPNMDS---IFSEALLKMRRQHPGCLAQEACVRAVQAAVQ 242
           Q++  +    RR   +  Q L + D+     + A     ++  G L+    V  V AA+ 
Sbjct: 193 QQLLSEHAPVRR--TRDAQGLADTDAGAAAIAVARADTAKKSRGLLSPLKIVDCVNAALT 250

Query: 243 YPYEVGIKKEEELFLYLLQSGQARALQYAFFAERKANKWSTPSGASWKTASARPVSSVGV 302
            P+E G++ E   F+  L S Q  AL +AF AER+  K         ++A  RP++S GV
Sbjct: 251 LPFEDGLRFERARFIECLDSPQRAALVHAFQAERQVQK-----APETRSAQPRPIASAGV 305

Query: 303 VGLGTMGRGIVISFARARIPVIAVDSDKNQLATANKMITSVLEKEASKMQQSGHPWSGPK 362
           VG GTMG GI ++   A +PV  ++ D   LA     +  V +   +K + +    +   
Sbjct: 306 VGGGTMGAGIAVALLDAGLPVTMIERDDASLARGRAHVDKVYDGLIAKGRLTHDAKAKKL 365

Query: 363 PRLTSSVK--ELGGVDLVIEAVFEEMSLKKQVFAELSAVCKPEAFLCTNTSALDVDEIAS 420
            R   S     L   D+VIEAVFE+M++K+ VFAEL  VCKP A L TNTS LD+D IA+
Sbjct: 366 ARFAGSTSYDALAEADVVIEAVFEDMAVKQAVFAELDRVCKPGAVLATNTSYLDIDAIAA 425

Query: 421 STDRPHLVIGTHFFSPAHVMKLLEVIPSQYSSPTTIATVMNLSKKIKKIGVVVGNCFGFV 480
              RP  VIG HFFSPAHVMKLLEV+     S   +AT  +L+KK++K+ V  G C GF+
Sbjct: 426 GIARPQDVIGLHFFSPAHVMKLLEVVVPARVSADVVATAFDLAKKLRKVPVRAGVCDGFI 485

Query: 481 GNRMLNPYYNQAYFLLEEGSKPEEVDQVLEEFGFKMGPFRVSDLAGLDVGWKSRKGQGLT 540
           GNRML  Y   A  L+EEG+ P ++D+ + E GF MGP++V DLAG D+GW +RK +  T
Sbjct: 486 GNRMLAVYRAAADHLMEEGASPYQIDKAVRELGFPMGPYQVIDLAGGDIGWATRKRRAST 545

Query: 541 GPTLLPGTPARKRGNRRYCPIPDVLCELGRFGQKTGKGWYQYDKPLGRIHKPDPWLSKFL 600
                      +  N RY  IPD LCE G FGQKT +G+Y+Y+    R   PDP +   +
Sbjct: 546 -----------RDPNARYVQIPDRLCERGWFGQKTSRGFYRYEAG-QRAGTPDPEVEAII 593

Query: 601 SRYRKTHHIEPRTISQDEILERCLYSLINEAFRILGEGIAASPEHIDVVYLHGYGWPRHK 660
              R+   I PR  S ++I+ R + ++INE   ++ E IA  P  +DV  ++G+G+P  +
Sbjct: 594 DAERERAGITPRAFSDEQIVRRYMAAMINEGANVIHERIALRPLDVDVTLMNGFGFPAWR 653

Query: 661 GGPMFYASTVGLPTVLEKLQKYYRQNPDIPQLEPSDYLKKLASQG 705
           GGPM YA T+GLP +L  ++++ +++P     +PS  L +L  +G
Sbjct: 654 GGPMHYADTIGLPALLADIREFEKRDPLF--WKPSPLLVELVERG 696


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: 1105
Number of extensions: 56
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: 706
Length adjustment: 39
Effective length of query: 684
Effective length of database: 667
Effective search space:   456228
Effective search space used:   456228
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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Steps (tab-delimited)
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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