GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gabT in Klebsiella michiganensis M5al

Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate BWI76_RS07600 BWI76_RS07600 aspartate aminotransferase family protein

Query= reanno::SB2B:6938540
         (460 letters)



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

 Score =  224 bits (571), Expect = 4e-63
 Identities = 145/453 (32%), Positives = 241/453 (53%), Gaps = 33/453 (7%)

Query: 12  LQAMDAAHHLHPFTDSADLAKRGTRVIERAEGVYIWDAKGNKLLDAMAGLWCVNVGYGRK 71
           ++ +D A+  H ++   +L      VI  A+G  +WD +GN  LD  + L  VN+GY   
Sbjct: 16  VRQLDRAYVFHSWSMQGNLHPL---VIAGAKGCELWDYEGNTYLDFSSQLVNVNIGYQHP 72

Query: 72  SIADAAYAQLQTLPFYNNFFQCTHEPAI------RLASKIASLAPGHMNRVFFTGSGSEA 125
            +  A  AQL+ L         T  PA         A +I  LAP   ++VFFT +G++A
Sbjct: 73  RVLAAMKAQLEAL--------VTIAPATANLARGEAAKRIVELAPEGFSKVFFTNAGADA 124

Query: 126 NDTNLRMVRRYWDLKGMPSKKTIISRKNAYHGSTVAGASLGGMGFMHQQGDLPIPGIVHI 185
           N+  +RM R Y        +  ++S   +YHG+T  G+++   G   +  +    G VH 
Sbjct: 125 NENAIRMARLY------TGRDKVLSAYRSYHGNT--GSAIAATGDWRRVPNEYSRGHVHF 176

Query: 186 DQPYWFGEGRDMSPEAFGIKTAQALEAKILEL-GEDKVAAFIAEPFQGAGGVIIPPDSYW 244
             PY +    + + E    + A A   +++E  G + +AA + E   G  G+++PP+ Y 
Sbjct: 177 FNPYLYRSEFNATTEEEECQRALAHLRRMIECEGPNAIAAILLESIPGTAGILVPPEGYM 236

Query: 245 NEIKRILEKYNILFILDEVISGFGRTGNWFAAQTLGLKPDLITIAKGMTSGYIPMGGVIV 304
             ++ + +++ I+ ILDEV++GFGRTG+WFA +  G+ PDL+T AKG+ +GY+P GGV++
Sbjct: 237 QGVRALADEFGIILILDEVMAGFGRTGSWFAFEQDGVVPDLVTFAKGVNAGYVPAGGVLI 296

Query: 305 SDRVADVLISDGGEFAHGFTYSGHPVAAAVALENIRILEEERLVDKVRTDTGPYLQDRLQ 364
           S+ +A     D   FA G TYSGHP+A A  +  I  ++EE++V+   T     L+  L+
Sbjct: 297 SEPIARYF--DDHFFAGGLTYSGHPLAMAAIVATIDAMKEEKVVENAATIGNEVLRPGLE 354

Query: 365 TLS-AHPLVGEVRGMGMVGAIELVADKHSMVRFGSEISAGMLCREACIESGLVMRAVGDT 423
            L+  H ++G VRG G+  A+ELV+ +      G+   A +  + A  E+GL+   V + 
Sbjct: 355 ALAEKHAIIGNVRGRGLFQALELVSSREHKTPLGAADMAAI--KGALTEAGLLAFVVENR 412

Query: 424 MIISPPLCITRDEIDE--LIFKASQALSLTLEK 454
           + + PP  I+ +++ +   IF A  A   +L K
Sbjct: 413 IHVVPPCTISAEQVAKGLAIFDAVFARFASLAK 445


Lambda     K      H
   0.321    0.137    0.408 

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: 524
Number of extensions: 35
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: 460
Length of database: 445
Length adjustment: 33
Effective length of query: 427
Effective length of database: 412
Effective search space:   175924
Effective search space used:   175924
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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