GapMind for catabolism of small carbon sources

 

Aligments for a candidate for patA in Klebsiella michiganensis M5al

Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate BWI76_RS07600 BWI76_RS07600 aspartate aminotransferase family protein

Query= BRENDA::Q9I6J2
         (456 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS07600 BWI76_RS07600 aspartate
           aminotransferase family protein
          Length = 445

 Score =  206 bits (525), Expect = 9e-58
 Identities = 135/405 (33%), Positives = 205/405 (50%), Gaps = 22/405 (5%)

Query: 38  IITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQAATRQMRELPFYNLFFQTAHP 97
           +I  A+G  +WD EGN  LD  + L  VN+GY    ++ A   Q+  L    +   TA+ 
Sbjct: 38  VIAGAKGCELWDYEGNTYLDFSSQLVNVNIGYQHPRVLAAMKAQLEAL--VTIAPATANL 95

Query: 98  PVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYWATKGQPQKKVVIGRWNGYH 157
              E AK I ++APEG + VFFT +G++AN+  +RM R Y        +  V+  +  YH
Sbjct: 96  ARGEAAKRIVELAPEGFSKVFFTNAGADANENAIRMARLYTG------RDKVLSAYRSYH 149

Query: 158 GSTVAGVSLGG--MKALHEQGDFPIPGIVHIAQPYWY-GEGGDMSPDEFGVWAAEQLEKK 214
           G+T + ++  G   +  +E       G VH   PY Y  E    + +E    A   L + 
Sbjct: 150 GNTGSAIAATGDWRRVPNEYSR----GHVHFFNPYLYRSEFNATTEEEECQRALAHLRRM 205

Query: 215 ILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILAKYDILFIADEVICGFGRTGEW 274
           I   G   +AA + E I G  G++VPP+ Y   +R +  ++ I+ I DEV+ GFGRTG W
Sbjct: 206 IECEGPNAIAAILLESIPGTAGILVPPEGYMQGVRALADEFGIILILDEVMAGFGRTGSW 265

Query: 275 FGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVLNQGGEFYHGFTYSGHPVAAAV 334
           F  +  G  PDL+  AKG+ +GY+P GGV++ + I    +    F  G TYSGHP+A A 
Sbjct: 266 FAFEQDGVVPDLVTFAKGVNAGYVPAGGVLISEPIARYFDD-HFFAGGLTYSGHPLAMAA 324

Query: 335 ALENIRILREEKIIEKVKAETAPYLQKRWQELAD-HPLVGEARGVGMVAALELVKNKKTR 393
            +  I  ++EEK++E         L+   + LA+ H ++G  RG G+  ALELV    +R
Sbjct: 325 IVATIDAMKEEKVVENAATIGNEVLRPGLEALAEKHAIIGNVRGRGLFQALELV---SSR 381

Query: 394 ERFTDKGVGMLC--REHCFRNGLIMRAVGDTMIISPPLVIDPSQI 436
           E  T  G   +   +      GL+   V + + + PP  I   Q+
Sbjct: 382 EHKTPLGAADMAAIKGALTEAGLLAFVVENRIHVVPPCTISAEQV 426


Lambda     K      H
   0.320    0.138    0.425 

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: 532
Number of extensions: 31
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: 456
Length of database: 445
Length adjustment: 33
Effective length of query: 423
Effective length of database: 412
Effective search space:   174276
Effective search space used:   174276
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 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