GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fumD in Azospirillum brasilense Sp245

Align fumarate hydratase (EC 4.2.1.2); (S)-2-methylmalate dehydratase (EC 4.2.1.34) (characterized)
to candidate AZOBR_RS10315 AZOBR_RS10315 fumarate hydratase

Query= BRENDA::P0AC33
         (548 letters)



>FitnessBrowser__azobra:AZOBR_RS10315
          Length = 544

 Score =  725 bits (1871), Expect = 0.0
 Identities = 353/529 (66%), Positives = 423/529 (79%)

Query: 12  FPLKKDDTEYYLLTSEHVSVSEFEGQEILKVAPEALTLLARQAFHDASFMLRPAHQQQVA 71
           FPL KDDT Y  LTS+HVSV EF+G++ILKV PE L LLA +AF D + +LRP H  Q+ 
Sbjct: 15  FPLAKDDTTYRKLTSDHVSVVEFDGEQILKVEPEGLRLLAEEAFKDINHLLRPGHLGQIR 74

Query: 72  DILRDPEASENDKYVALQFLRNSDIAAKGVLPTCQDTGTAIIVGKKGQRVWTGGGDEAAL 131
            IL DPEAS NDK+VAL  L+N++IAA G LP CQDTGTAII+GKKG+RV+T GGDEAAL
Sbjct: 75  AILDDPEASPNDKFVALDLLKNANIAAAGTLPMCQDTGTAIIMGKKGRRVFTKGGDEAAL 134

Query: 132 ARGVYNTYIEDNLRYSQNAPLDMYKEVNTGTNLPAQIDLYAVDGDEYKFLCIAKGGGSAN 191
           + G  + Y++ NLRYSQ AP+ MY+E NT  NLP Q+++YA   D YKFL +AKGGGSAN
Sbjct: 135 SEGARDAYLKRNLRYSQLAPISMYEEKNTRNNLPGQVEIYAEGEDAYKFLFMAKGGGSAN 194

Query: 192 KTYLYQETKALLTPGKLKNYLVEKMRTLGTAACPPYHIAFVIGGTSAETNLKTVKLASAK 251
           KT+L+Q T ++L P +L  +L +K+R LGT+ACPPYH+A VIGG SAE NLKTVKLASA+
Sbjct: 195 KTFLHQATPSVLAPDRLLKFLEDKIRYLGTSACPPYHLAIVIGGLSAEQNLKTVKLASAR 254

Query: 252 YYDELPTEGNEHGQAFRDVELEKELLIEAQNLGLGAQFGGKYFAHDIRVIRLPRHGASCP 311
           Y D LPTEG E   AFRD+ +E E+    Q +G+GAQFGGKYF HD+RVIRLPRHGAS P
Sbjct: 255 YLDNLPTEGGEDAHAFRDLAMEAEVHKLTQTMGIGAQFGGKYFCHDVRVIRLPRHGASMP 314

Query: 312 VGMGVSCSADRNIKAKINRQGIWIEKLEHNPGKYIPEELRKAGEGEAVRVDLNRPMKEIL 371
           +G+GVSCSADR    KI + GI++E+LE +P KY+PE       GE V++DLN+PM EIL
Sbjct: 315 IGVGVSCSADRQAVGKITKDGIFLEQLETDPAKYLPEITDGDLAGEVVKIDLNQPMSEIL 374

Query: 372 AQLSQYPVSTRLSLNGTIIVGRDIAHAKLKERMDNGEGLPQYIKDHPIYYAGPAKTPEGY 431
           A L QYP+ TRLSL G +IV RD+AHAKL+ R+D GE LP Y K+HPIYYAGPAKTPEGY
Sbjct: 375 ATLKQYPIRTRLSLTGPLIVARDLAHAKLRARLDAGEPLPDYFKNHPIYYAGPAKTPEGY 434

Query: 432 ASGSLGPTTAGRMDSYVDQLQAQGGSMIMLAKGNRSQQVTDACKKHGGFYLGSIGGPAAV 491
           ASGS GPTTAGRMDS+V+Q QA GGSM+MLAKGNRS +VT ACK HGGFYLGSIGG AA 
Sbjct: 435 ASGSFGPTTAGRMDSFVEQFQAAGGSMVMLAKGNRSPEVTAACKTHGGFYLGSIGGAAAR 494

Query: 492 LAQGSIKSLECVEYPELGMEAIWKIEVEDFPAFILVDDKGNDFFQQIQL 540
           LAQ  IK +ECVEYPELGMEAIW+IEVEDFPAFI+VDDKGNDFF++++L
Sbjct: 495 LAQDCIKKVECVEYPELGMEAIWRIEVEDFPAFIIVDDKGNDFFKELKL 543


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: 944
Number of extensions: 40
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: 544
Length adjustment: 35
Effective length of query: 513
Effective length of database: 509
Effective search space:   261117
Effective search space used:   261117
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: 52 (24.6 bits)

This GapMind analysis is from Sep 17 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