GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Amantichitinum ursilacus IGB-41

Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate WP_053937056.1 WG78_RS06780 aspartate aminotransferase family protein

Query= BRENDA::P42588
         (459 letters)



>NCBI__GCF_001294205.1:WP_053937056.1
          Length = 400

 Score =  191 bits (486), Expect = 3e-53
 Identities = 134/390 (34%), Positives = 201/390 (51%), Gaps = 25/390 (6%)

Query: 71  GSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLA 130
           G+ + + D  G+E+ID  GG  + ++GH +P +V+A+  Q  K    S    +     LA
Sbjct: 26  GAGSRVWDQAGKEYIDFGGGIAVNSLGHCHPELVAALTEQGNKLWHISNVFTNEPALALA 85

Query: 131 KTLAALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPR---GKFTFIATSGAFHGKSLGA 187
           KTL   T  +    FFCNSG E+ EAALKLA+     +    K   ++   +FHG++   
Sbjct: 86  KTLVEHTFAERV--FFCNSGAEANEAALKLARRASIEKYGERKNKVLSALNSFHGRTFFT 143

Query: 188 LSATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVI 247
           +S   +  +   F P   G  H  + ++ ++   ++      DD A VI+EPIQGEGGV 
Sbjct: 144 VSVGGQPKYSDGFGPKPAGIEHFKYNDLASLEALID------DDTACVIIEPIQGEGGVT 197

Query: 248 LPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVM 307
                +L  VR LCD+F AL+I DEVQ+G GRTG ++A     V PDIL  AK LGGG  
Sbjct: 198 PATQEFLQGVRALCDKFNALLIFDEVQSGNGRTGSLYAYMDFGVVPDILSTAKGLGGG-F 256

Query: 308 PIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLL 367
           PIGA + TE+V   L      H TT+GGNPLA A A   I+++      +  + K + + 
Sbjct: 257 PIGAMLTTEKVAKHLVAG--THGTTYGGNPLATAVAGTAISIITRPETLSGVKAKSERIR 314

Query: 368 DGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIG-----YNFASEMFRQRVLVAGTLNNA 422
            G + +A +YP +V E RG G+L+ ++      G      N A+E   + VLV       
Sbjct: 315 AGLQAIADKYP-VVAEIRGMGLLIGVQLKAEYAGRSRDVLNAAAE---EGVLVLAA--GP 368

Query: 423 KTIRIEPPLTLTIEQCELVIKAARKALAAM 452
             +R  P L ++ ++ +  +    KA A +
Sbjct: 369 DVVRFAPSLVISDDEIDAGLARVEKAFARL 398


Lambda     K      H
   0.320    0.135    0.393 

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: 417
Number of extensions: 21
Number of successful extensions: 5
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: 459
Length of database: 400
Length adjustment: 32
Effective length of query: 427
Effective length of database: 368
Effective search space:   157136
Effective search space used:   157136
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 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