GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kamA in Marinobacter adhaerens HP15

Align L-lysine 2,3-aminomutase; LAM; KAM; EC 5.4.3.2 (characterized)
to candidate GFF2570 HP15_2514 lysine 2,3-aminomutase YodO family protein

Query= SwissProt::Q9XBQ8
         (416 letters)



>FitnessBrowser__Marino:GFF2570
          Length = 346

 Score =  186 bits (471), Expect = 1e-51
 Identities = 109/331 (32%), Positives = 169/331 (51%), Gaps = 3/331 (0%)

Query: 12  VSDADWNDWRWQVRNRIETVEELKKYIPLTKEEE-EGVAQCVKSLRMAITPYYLSLIDPN 70
           +SD +   W+  +   + + +EL + + L +E    G  Q  +  ++ +   +L+ ++  
Sbjct: 13  LSDHEQRSWQQLLSGAVTSPKELLRRLELPEEPWLAGAEQGHRLFQIRVPEPFLNRMEKG 72

Query: 71  DPNDPVRKQAIPTALELNKAAADLEDPLHEDTDSPVPGLTHRYPDRVLLLITDMCSMYCR 130
           +P DP+ +Q +P A E   A   + DPL E       GL  +Y  R LL++T  C++ CR
Sbjct: 73  NPADPLLRQVLPLADEAGHAPGFVSDPLEESGAIATTGLIRKYRSRALLMVTGQCAINCR 132

Query: 131 HCTRRRFAGQSDDSMPMERIDKAIDYIRNTPQVRDVLLSGGDALLVSDETLEYIIAKLRE 190
           +C RR F        P +R  + ID +  +P++ +V+ SGGD L V+D  L    + +  
Sbjct: 133 YCFRRHFPYDEQRLSPHDR-QRVIDVLGASPEINEVIFSGGDPLAVNDRLLSQWASAISG 191

Query: 191 IPHVEIVRIGSRTPVVLPQRITPELVNMLKKYH-PVWLNTHFNHPNEITEESTRACQLLA 249
           IPH+  +R+ +R PVV+PQR+  EL+  L      V +  H NHP EI   + RA   L 
Sbjct: 192 IPHIRRLRLHTRLPVVIPQRVCDELLKWLSTTPLQVVIVLHINHPAEIDGPTRRALGYLR 251

Query: 250 DAGVPLGNQSVLLRGVNDCVHVMKELVNKLVKIRVRPYYIYQCDLSLGLEHFRTPVSKGI 309
            AG  L NQSV+LRGVND   V++EL   L    V PYY++  D   G  HF     +  
Sbjct: 252 AAGATLLNQSVILRGVNDRTAVLEELSETLFDAGVLPYYLHAFDPVTGAHHFDVSDDEAR 311

Query: 310 EIIEGLRGHTSGYCVPTFVVDAPGGGGKTPV 340
            ++  L     G+ VP  V + PG   KTP+
Sbjct: 312 NLVRELLARLPGFLVPKLVREEPGKESKTPI 342


Lambda     K      H
   0.320    0.138    0.422 

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: 422
Number of extensions: 22
Number of successful extensions: 3
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: 416
Length of database: 346
Length adjustment: 30
Effective length of query: 386
Effective length of database: 316
Effective search space:   121976
Effective search space used:   121976
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