GapMind for catabolism of small carbon sources

 

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

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate WP_085640004.1 MGEO_RS15835 FAD-dependent oxidoreductase

Query= metacyc::MONOMER-20678
         (699 letters)



>NCBI__GCF_002115805.1:WP_085640004.1
          Length = 695

 Score =  569 bits (1467), Expect = e-166
 Identities = 322/706 (45%), Positives = 441/706 (62%), Gaps = 28/706 (3%)

Query: 1   MSEVVTRATQDQVAIVTVDSPPVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFI 60
           M+ V+       +A++ +D+PPVNAL  AVR+G++E V  A AD A +A ++   GR+F 
Sbjct: 1   MTGVIRYNRDGDIAMIAIDNPPVNALGQAVRQGLVEAVEKAEADGA-RAALIYGEGRSFP 59

Query: 61  AGADITEFGKPPQPPALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAK 120
           AGADI EFGKPP  P L DV   LE SP   ++A+HGTALGGGLE+AL   +R+A   AK
Sbjct: 60  AGADIREFGKPPLEPWLPDVCNRLETSPVLVVSALHGTALGGGLEIALASDYRIATPAAK 119

Query: 121 LGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVENLVAG 180
           +GLPEV +G++PGAGGTQRLPR VG E ++ +I  G  I A EA   G+++ V +     
Sbjct: 120 VGLPEVLIGVMPGAGGTQRLPRLVGVETSIDVITSGRQISAGEAFDLGIIDRVEDGAPRD 179

Query: 181 -AVAFAKKVLAEKRPLRRLRDDDSKLAAAKADRSI-FTNAVAAMTKKARGLEAPFACADA 238
             +++ + +LAE  P R +R+         A + I F  A  +  +KARG  +P      
Sbjct: 180 IGLSYTRALLAENAPRRPIRE-------MPAPQPIDFDAAYDSALRKARGQISPAYAVRG 232

Query: 239 IGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPVSRV 298
           I AA +LPFEEGL +ERE F  L+ +DQ +   +AFFAER    +  + D T  R V+ V
Sbjct: 233 IQAACELPFEEGLTRERELFRALLETDQRQGLIHAFFAERAVGVLAELKD-TNARDVNSV 291

Query: 299 AIIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDA--- 355
           A+IG GTMG GIA SF  AG PVTL+E  E+      G +  N      RG +       
Sbjct: 292 AVIGGGTMGAGIATSFLLAGFPVTLLEMSEDAAHAARGRITGNLSGALKRGKIDQKTYDR 351

Query: 356 -PAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLS 414
                +AL T     +++++ADL+IEAVFE M VK++VF+ +DA  KPGAVLA+NTSYL 
Sbjct: 352 LTGPALALTTSY---DDLREADLVIEAVFEDMNVKRDVFSRLDAICKPGAVLATNTSYLD 408

Query: 415 IDEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVG 474
           I++IA  T+RP+DV+G+HFFSPA+VMKL E+V   +TAPD + T  ++AK++ K  V  G
Sbjct: 409 INKIADATQRPEDVIGLHFFSPAHVMKLLEVVVADRTAPDTVATGFALAKRLKKTAVRAG 468

Query: 475 VCDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSR 534
           VCDGF+GNR+LAA    ++ ++ +GA P  +DA + +FG  MGPF + DLAGLDI W +R
Sbjct: 469 VCDGFIGNRILAAYRAAADHMVLDGATPYDIDAAIREFGFAMGPFQVSDLAGLDIAWAAR 528

Query: 535 KDRGIKSE-------IADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAK 587
           K R    +       +AD LCEAG FGQKTG+GYY Y +    P P+PEV  +I      
Sbjct: 529 KRRAATRDPRERVPLVADRLCEAGLFGQKTGQGYYLYNE--TPPKPNPEVAGIIESARET 586

Query: 588 LGLKRRDITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHY 647
           LG+K R  +  EI  R +  M+NE A+++ + IA RP D+DVV L GYG+P YRGGP+ +
Sbjct: 587 LGIKPRAFSRPEIQRRYLCAMVNEAAKVVGDGIARRPLDVDVVLLMGYGFPRYRGGPLKW 646

Query: 648 ADSVGLKHIAERLSAYAKATNDPSLEPAPLLARLAAEGKTFASLTQ 693
           AD  GL  I   ++AYA+  +     PAPLL +L AEG+TF  L +
Sbjct: 647 ADMDGLPKILSDITAYAQ-DDRYFWSPAPLLEQLVAEGRTFDDLNK 691


Lambda     K      H
   0.317    0.134    0.383 

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: 1142
Number of extensions: 46
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: 699
Length of database: 695
Length adjustment: 39
Effective length of query: 660
Effective length of database: 656
Effective search space:   432960
Effective search space used:   432960
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 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