GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Koxy:BWI76_RS07600
          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 (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