GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Klebsiella michiganensis M5al

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate BWI76_RS26000 BWI76_RS26000 aspartate aminotransferase family protein

Query= BRENDA::Q9I6M4
         (426 letters)



>FitnessBrowser__Koxy:BWI76_RS26000
          Length = 406

 Score =  231 bits (589), Expect = 3e-65
 Identities = 143/402 (35%), Positives = 213/402 (52%), Gaps = 34/402 (8%)

Query: 30  RAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAYEPYIE 89
           + + S VWD +G+EY+DFAGGIAV   GH HP ++AA+ EQ  KL HT   V   EP + 
Sbjct: 30  KGKGSRVWDQQGKEYVDFAGGIAVTALGHCHPALVAALHEQGEKLWHTS-NVFTNEPALR 88

Query: 90  LAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIARAATG------RAGVIAFTGAYHGRT 143
           L  ++   V   F  + + + SG+EA E A K+AR  T       +  +IAF  A+HGR+
Sbjct: 89  LGRKL---VDATFADRVVFMNSGTEANETAFKLARHYTVTRHSPYKTKIIAFHNAFHGRS 145

Query: 144 MMTLGLTGKVVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKNDAQPQDIAA 203
           + T+ + G+   YS G G  P  I       +LH V                       A
Sbjct: 146 LFTVSVGGQP-KYSDGFGPKPADIVHVPFN-DLHAVKA--------------VMDDHTCA 189

Query: 204 IIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQLGIVPD 263
           +++EP+QGEGG    +  F+Q LR LCDQH  LL+ DEVQ G GRTG+ FA    G+ PD
Sbjct: 190 VVVEPIQGEGGVTAATPEFLQGLRDLCDQHQALLVFDEVQCGMGRTGSLFAYMHYGVTPD 249

Query: 264 LTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLKVFEEEKLLE 323
           + T AK++GGGFPIS +    +I  A   G  G TY G+P+ACA   A   +    ++L+
Sbjct: 250 ILTSAKALGGGFPISAMLTTHDIASAFHAGSHGSTYGGNPLACAVGGAAFDLINTPEVLD 309

Query: 324 RSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELVSKIVVRARE 383
              A  E     L++I A+  +  D+RG+G ++  EL      H  A +     +  A E
Sbjct: 310 GVTAKRELFVQHLQQIDARFDLFSDIRGMGLLIGAEL--KPQYHGKARD----FLYAAAE 363

Query: 384 KGLILLSCGTYYNVIRFLMPVTIPDAQLEKGLAILAECFDEL 425
            G+++L+ G   +V+RF+  + I D+ + +G+A  A+  + +
Sbjct: 364 AGVMVLNAGP--DVMRFVPSLVIDDSDIAEGMARFAQAVERV 403


Lambda     K      H
   0.319    0.137    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: 437
Number of extensions: 23
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: 426
Length of database: 406
Length adjustment: 31
Effective length of query: 395
Effective length of database: 375
Effective search space:   148125
Effective search space used:   148125
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: 50 (23.9 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