GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aspA in Klebsiella michiganensis M5al

Align Aspartate ammonia-lyase; Aspartase; EC 4.3.1.1 (uncharacterized)
to candidate BWI76_RS16270 BWI76_RS16270 fumarate hydratase, class II

Query= curated2:P26899
         (475 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS16270 BWI76_RS16270 fumarate
           hydratase, class II
          Length = 466

 Score =  377 bits (969), Expect = e-109
 Identities = 199/456 (43%), Positives = 283/456 (62%), Gaps = 1/456 (0%)

Query: 8   YRVEKDFLGEKQIEADVYYGIQTLRASENFPITGYKIHEEMINALAIVKKAAALANMDVK 67
           YR EKD +G   + AD  +G QT R+ E+F I+  K+  E+I+ALA+ K+AAA  N D+ 
Sbjct: 4   YRSEKDSMGAIDVPADKLWGAQTQRSLEHFRISTEKMPVELIHALALTKRAAAKVNNDLG 63

Query: 68  RLYEGIGQAIVQAADEILEGKWHDQFIVDPIQGGAGTSMNMNANEVIGNRALEIMGHKKG 127
            L     QAI+QAADE+L G+  D F +   Q G+GT  NMN NEV+ NRA E++G  +G
Sbjct: 64  LLAAEKAQAIIQAADEVLAGQHPDAFPLAIWQTGSGTQSNMNMNEVLANRASELLGGARG 123

Query: 128 DYIHLSPNTHVNMSQSTNDVFPTAIHISTL-KLLEKLLKTMEDMHSVFKQKAQEFDSVIK 186
               + PN  VN SQS+NDVFPTA+H++ +  L EKL+  +  +      KA  F  ++K
Sbjct: 124 MERKVHPNDDVNKSQSSNDVFPTAMHVAAIIALREKLIPQLNVLKQTLNDKAVAFSDIVK 183

Query: 187 MGRTHLQDAVPIRLGQEFEAYSRVLERDIKRIKQSRQHLYEVNMGATAVGTGLNADPEYI 246
           +GRTHLQDA P+ LGQE   +  +LE ++K I  S  HL E+ +G TAVGTGLN  P+Y 
Sbjct: 184 IGRTHLQDATPLTLGQEISGWVAMLEHNLKHIDHSLPHLAELALGGTAVGTGLNTHPQYA 243

Query: 247 KQVVKHLADISGLPLVGADHLVDATQNTDAYTEVSASLKVCMMNMSKIANDLRLMASGPR 306
            +V   LA +SG P V A +  +A    DA      +LK    ++ KIAND+R +ASGPR
Sbjct: 244 VRVAAELAALSGQPFVTAPNKFEALATVDALVHAHGALKGLAASLMKIANDVRWLASGPR 303

Query: 307 AGLAEISLPARQPGSSIMPGKVNPVMAELINQIAFQVIGNDNTICLASEAGQLELNVMEP 366
            G+ EI++P  +PGSSIMPGKVNP   E +  +  QV+GND  + +   +G  ELNV  P
Sbjct: 304 CGIGEIAIPENEPGSSIMPGKVNPTQCEALTMLCCQVMGNDVAVNIGGASGNFELNVYRP 363

Query: 367 VLVFNLLQSISIMNNGFRSFTDNCLKGIEANEKRMKQYVEKSAGVITAVNPHLGYEAAAR 426
           +++ N LQS+ ++  G  SF ++C  GIE N +R+ Q + +S  ++TA+N H+GY+ AA 
Sbjct: 364 LVIHNFLQSVRLLAEGMASFNEHCAVGIEPNRERISQLLNESLMLVTALNTHIGYDKAAE 423

Query: 427 IAREAIMTGQSVRDLCLQHDVLTEEELDIILNPYEM 462
           IA++A   G +++   L    LTE+E D  + P EM
Sbjct: 424 IAKKAHKEGLTLKASALALGYLTEDEFDRWVRPQEM 459


Lambda     K      H
   0.317    0.133    0.370 

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: 471
Number of extensions: 11
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: 475
Length of database: 466
Length adjustment: 33
Effective length of query: 442
Effective length of database: 433
Effective search space:   191386
Effective search space used:   191386
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: 51 (24.3 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 preprint 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