GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fumD in Magnetovibrio blakemorei MV-1

Align fumarate hydratase (EC 4.2.1.2); (S)-2-methylmalate dehydratase (EC 4.2.1.34) (characterized)
to candidate WP_069957537.1 BEN30_RS06515 fumarate hydratase

Query= BRENDA::P0AC33
         (548 letters)



>NCBI__GCF_001746755.1:WP_069957537.1
          Length = 549

 Score =  749 bits (1935), Expect = 0.0
 Identities = 363/537 (67%), Positives = 435/537 (81%), Gaps = 1/537 (0%)

Query: 3   NKPFHYQAPFPLKKDDTEYYLLTSEHVSVSEFEGQEILKVAPEALTLLARQAFHDASFML 62
           N+P  ++  F    D+TEY LLT E VS     G+ IL++ PE L+LLA  A  D S +L
Sbjct: 2   NEPAFHEL-FSFGPDETEYRLLTKEFVSTHTVSGRTILEIEPEGLSLLASTAMRDTSHLL 60

Query: 63  RPAHQQQVADILRDPEASENDKYVALQFLRNSDIAAKGVLPTCQDTGTAIIVGKKGQRVW 122
           RPAH +Q+A IL+DPEAS ND++VA++ L+N++I+A GVLP CQDTGTAII+GKKG+ VW
Sbjct: 61  RPAHLKQLASILKDPEASANDRFVAMELLKNANISAGGVLPMCQDTGTAIIMGKKGENVW 120

Query: 123 TGGGDEAALARGVYNTYIEDNLRYSQNAPLDMYKEVNTGTNLPAQIDLYAVDGDEYKFLC 182
           TGG DEAAL+ GV   Y E+NLRYSQ APL M+KEV TGTNLPAQID+ AV G  YKF+ 
Sbjct: 121 TGGQDEAALSEGVMKAYAENNLRYSQMAPLSMFKEVGTGTNLPAQIDIGAVPGGSYKFMF 180

Query: 183 IAKGGGSANKTYLYQETKALLTPGKLKNYLVEKMRTLGTAACPPYHIAFVIGGTSAETNL 242
           +AKGGGSANKT+L+Q+T ALL P  +  +L  ++ TLGTAACPPYH+A VIGG SAE NL
Sbjct: 181 MAKGGGSANKTFLHQKTAALLNPKSMAEFLKAEIATLGTAACPPYHLAVVIGGLSAELNL 240

Query: 243 KTVKLASAKYYDELPTEGNEHGQAFRDVELEKELLIEAQNLGLGAQFGGKYFAHDIRVIR 302
           KTVK+ASA Y D LPT+GN +GQAFRD+E+E E+L   QNLG+GAQFGGKYF HD+RVIR
Sbjct: 241 KTVKMASAHYLDGLPTQGNAYGQAFRDLEMEAEILKMTQNLGIGAQFGGKYFCHDVRVIR 300

Query: 303 LPRHGASCPVGMGVSCSADRNIKAKINRQGIWIEKLEHNPGKYIPEELRKAGEGEAVRVD 362
           LPRHGASCPVG+GVSCSADR I  KI  +GI++EKLE +P KY+PE   K    + V +D
Sbjct: 301 LPRHGASCPVGIGVSCSADRQILGKITAEGIFLEKLETDPAKYLPEITEKNLSDDVVSID 360

Query: 363 LNRPMKEILAQLSQYPVSTRLSLNGTIIVGRDIAHAKLKERMDNGEGLPQYIKDHPIYYA 422
           LN+PM +I AQLSQYP+ TR+ L G++IVGRD+AHAKLKER+D G+GLP YIK+HP+YYA
Sbjct: 361 LNQPMDQIRAQLSQYPIKTRIKLTGSLIVGRDLAHAKLKERLDAGQGLPDYIKNHPVYYA 420

Query: 423 GPAKTPEGYASGSLGPTTAGRMDSYVDQLQAQGGSMIMLAKGNRSQQVTDACKKHGGFYL 482
           GPAKTPEGYASGS GPTTAGRMDSYVDQ Q  GGS++MLAKGNRSQ VTDACKKHGGFYL
Sbjct: 421 GPAKTPEGYASGSFGPTTAGRMDSYVDQFQEAGGSLVMLAKGNRSQAVTDACKKHGGFYL 480

Query: 483 GSIGGPAAVLAQGSIKSLECVEYPELGMEAIWKIEVEDFPAFILVDDKGNDFFQQIQ 539
           GSIGG AA LA  SIK +EC+EYPELGMEAIWKI++ DFPAFI+VDDKGNDFF+ I+
Sbjct: 481 GSIGGAAAELAFESIKHIECIEYPELGMEAIWKIDIVDFPAFIIVDDKGNDFFEDIK 537


Lambda     K      H
   0.317    0.135    0.397 

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: 986
Number of extensions: 45
Number of successful extensions: 2
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: 548
Length of database: 549
Length adjustment: 36
Effective length of query: 512
Effective length of database: 513
Effective search space:   262656
Effective search space used:   262656
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 (21.6 bits)
S2: 53 (25.0 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