GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__azobra:AZOBR_RS10315 AZOBR_RS10315 fumarate
           hydratase
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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