GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysN in Escherichia coli BW25113

Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate 15560 b1439 fused predicted DNA-binding transcriptional regulator/predicted amino transferase (NCBI)

Query= BRENDA::Q72LL6
         (397 letters)



>FitnessBrowser__Keio:15560
          Length = 468

 Score =  156 bits (395), Expect = 1e-42
 Identities = 113/379 (29%), Positives = 189/379 (49%), Gaps = 15/379 (3%)

Query: 22  IRELLKLTQRPGILSFAGGLPAPELFPKEEAAEAAARILREKGEVALQYSPTEGYAPLRA 81
           I ++L+ ++ P ++ FA   P P LFP ++   + A++ +    +++  +   G A LR 
Sbjct: 93  IFDMLQASRDPSVVPFASAFPDPRLFPLQQLNRSLAQVSKTATAMSVIENLPPGNAELRQ 152

Query: 82  FVA-----EWIGVRPEEVLITTGSQQALDLVGKVFLDEGSPVLLEAPSYMGAIQAFRLQG 136
            +A     + I + P+E++IT G+ +AL+L  +   + G  V++E P + GA+QA     
Sbjct: 153 AIARRYALQGITISPDEIVITAGALEALNLSLQAVTEPGDWVIVENPCFYGALQALERLR 212

Query: 137 PRFLTVPAG-EEGPDLDALEEVLKRERPRFLYLIPSFQNPTGGLTPLPARKRLLQMVMER 195
            + L+V    +EG DL ALE  L+    +  +L+ + QNP G       + +L+ ++ + 
Sbjct: 213 LKALSVATDVKEGIDLQALELALQEYPVKACWLMTNSQNPLGFTLTPQKKAQLVALLNQY 272

Query: 196 GLVVVEDDAYRELYFG-EARLPSLFELAREAGYPGVIYLGSFSKVLSPGLRVAFAVA--H 252
            + ++EDD Y ELYFG E  LP+         + GV++  SFSK L PG R+ +  A  H
Sbjct: 273 NVTLIEDDVYSELYFGREKPLPA----KAWDRHDGVLHCSSFSKCLVPGFRIGWVAAGKH 328

Query: 253 PEALQKLVQAKQGADLHTPMLNQMLVHELLKEGFSERLERVRRVYREKAQAMLHALDREV 312
              +Q+L Q        +PM    LV  L    +   L R+RR   E+ Q    AL R +
Sbjct: 329 ARKIQRL-QLMSTLSTSSPM-QLALVDYLSTRRYDAHLRRLRRQLAERKQRAWQALLRYL 386

Query: 313 PKEVRYTRPKGGMFVWMELPKGLSAEGLFRRALEENVAFVPGGPFFANGGGENTLRLSYA 372
           P EV+      G F+W+ELP+ L A  L   AL  +++  PG  F          R + A
Sbjct: 387 PAEVKIHHNDSGYFLWLELPEPLDAGELSLAALTHHISIAPGKMFSTGENWSRFFRFNTA 446

Query: 373 TLDREGIAEGVRRLGRALK 391
               E   + V++LG+ ++
Sbjct: 447 WQWGEREEQAVKQLGKLIQ 465


Lambda     K      H
   0.320    0.139    0.403 

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: 421
Number of extensions: 25
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: 397
Length of database: 468
Length adjustment: 32
Effective length of query: 365
Effective length of database: 436
Effective search space:   159140
Effective search space used:   159140
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