GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Marivita geojedonensis DPG-138

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_085640004.1 MGEO_RS15835 FAD-dependent oxidoreductase

Query= SwissProt::Q08426
         (723 letters)



>NCBI__GCF_002115805.1:WP_085640004.1
          Length = 695

 Score =  493 bits (1268), Expect = e-143
 Identities = 291/699 (41%), Positives = 417/699 (59%), Gaps = 32/699 (4%)

Query: 11  LALIRLRNPPVNAISTTLLRDIKEGLQKAVIDHTIKAIVICGAEGKFSAGADIRGFSAPR 70
           +A+I + NPPVNA+   + + + E ++KA  D   +A +I G    F AGADIR F  P 
Sbjct: 13  IAMIAIDNPPVNALGQAVRQGLVEAVEKAEADGA-RAALIYGEGRSFPAGADIREFGKP- 70

Query: 71  TFGLTLGHVVDEIQRNEKPVVAAIQGMAFGGGLELALGCHYRIAHAEAQVGLPEVTLGLL 130
                L  V + ++ +   VV+A+ G A GGGLE+AL   YRIA   A+VGLPEV +G++
Sbjct: 71  PLEPWLPDVCNRLETSPVLVVSALHGTALGGGLEIALASDYRIATPAAKVGLPEVLIGVM 130

Query: 131 PGARGTQLLPRLTGVPAALDLITSGRRILADEALKLGILDKVVNSDPVEEAIRFAQRVSD 190
           PGA GTQ LPRL GV  ++D+ITSGR+I A EA  LGI+D+V +  P +  + + + +  
Sbjct: 131 PGAGGTQRLPRLVGVETSIDVITSGRQISAGEAFDLGIIDRVEDGAPRDIGLSYTRALLA 190

Query: 191 QPLESRRLCNKPIQSLPNMDSIFSEALLKMRRQHPGCLAQEACVRAVQAAVQYPYEVGIK 250
           +    R +   P     + D+ +  AL K R Q    ++    VR +QAA + P+E G+ 
Sbjct: 191 ENAPRRPIREMPAPQPIDFDAAYDSALRKARGQ----ISPAYAVRGIQAACELPFEEGLT 246

Query: 251 KEEELFLYLLQSGQARALQYAFFAERKANKWSTPSGASWKTASARPVSSVGVVGLGTMGR 310
           +E ELF  LL++ Q + L +AFFAER          A  K  +AR V+SV V+G GTMG 
Sbjct: 247 RERELFRALLETDQRQGLIHAFFAERAVGVL-----AELKDTNARDVNSVAVIGGGTMGA 301

Query: 311 GIVISFARARIPVIAVDSDKNQLATANKMITSVLE---KEASKMQQSGHPWSGPKPRLTS 367
           GI  SF  A  PV  ++  ++    A   IT  L    K     Q++    +GP   LT+
Sbjct: 302 GIATSFLLAGFPVTLLEMSEDAAHAARGRITGNLSGALKRGKIDQKTYDRLTGPALALTT 361

Query: 368 SVKELGGVDLVIEAVFEEMSLKKQVFAELSAVCKPEAFLCTNTSALDVDEIASSTDRPHL 427
           S  +L   DLVIEAVFE+M++K+ VF+ L A+CKP A L TNTS LD+++IA +T RP  
Sbjct: 362 SYDDLREADLVIEAVFEDMNVKRDVFSRLDAICKPGAVLATNTSYLDINKIADATQRPED 421

Query: 428 VIGTHFFSPAHVMKLLEVIPSQYSSPTTIATVMNLSKKIKKIGVVVGNCFGFVGNRMLNP 487
           VIG HFFSPAHVMKLLEV+ +  ++P T+AT   L+K++KK  V  G C GF+GNR+L  
Sbjct: 422 VIGLHFFSPAHVMKLLEVVVADRTAPDTVATGFALAKRLKKTAVRAGVCDGFIGNRILAA 481

Query: 488 YYNQAYFLLEEGSKPEEVDQVLEEFGFKMGPFRVSDLAGLDVGWKSRKGQGLTGPTLLPG 547
           Y   A  ++ +G+ P ++D  + EFGF MGPF+VSDLAGLD+ W +RK +  T       
Sbjct: 482 YRAAADHMVLDGATPYDIDAAIREFGFAMGPFQVSDLAGLDIAWAARKRRAAT------- 534

Query: 548 TPARKRGNRRYCP-IPDVLCELGRFGQKTGKGWYQYDKPLGRIHKPDPWLSKFLSRYRKT 606
                R  R   P + D LCE G FGQKTG+G+Y Y++      KP+P ++  +   R+T
Sbjct: 535 -----RDPRERVPLVADRLCEAGLFGQKTGQGYYLYNE---TPPKPNPEVAGIIESARET 586

Query: 607 HHIEPRTISQDEILERCLYSLINEAFRILGEGIAASPEHIDVVYLHGYGWPRHKGGPMFY 666
             I+PR  S+ EI  R L +++NEA +++G+GIA  P  +DVV L GYG+PR++GGP+ +
Sbjct: 587 LGIKPRAFSRPEIQRRYLCAMVNEAAKVVGDGIARRPLDVDVVLLMGYGFPRYRGGPLKW 646

Query: 667 ASTVGLPTVLEKLQKYYRQNPDIPQLEPSDYLKKLASQG 705
           A   GLP +L  +  Y +   D     P+  L++L ++G
Sbjct: 647 ADMDGLPKILSDITAYAQD--DRYFWSPAPLLEQLVAEG 683


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: 1152
Number of extensions: 52
Number of successful extensions: 8
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: 695
Length adjustment: 39
Effective length of query: 684
Effective length of database: 656
Effective search space:   448704
Effective search space used:   448704
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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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:

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:

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:

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:

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