GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Koxy:BWI76_RS07600
          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:

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