GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kamA in Pseudomonas fluorescens GW456-L13

Align L-lysine 2,3-aminomutase; LAM; EC 5.4.3.2 (characterized)
to candidate PfGW456L13_4924 Lysine 2,3-aminomutase (EC 5.4.3.2)

Query= SwissProt::Q8PYC9
         (419 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4924
          Length = 446

 Score =  105 bits (262), Expect = 3e-27
 Identities = 68/228 (29%), Positives = 115/228 (50%), Gaps = 13/228 (5%)

Query: 110 ITHRYPDRVLFL--ISNRCGMYCRHCTRKRR-VGNREHDYSEKAIREGIEYIRMHHEVRD 166
           I H+Y + VLF       C  YC  C R  + +G  E  ++ +  +E + Y+R+H EV D
Sbjct: 130 IQHKYRETVLFFPGAGQTCHAYCTFCFRWAQFIGEEELKFNARESQELVSYLRVHTEVTD 189

Query: 167 VLLSGGDALLVSDERLDWLLGELFSIPHVEIVRLGTRAPVTLPQRI-----TPELCEILG 221
           VL++GGD ++++   L   +  L  +PH++ +R+GT++    PQR       PEL E+  
Sbjct: 190 VLITGGDPMIMNTRSLAGYIEPLLDLPHLKNIRIGTKSVAYWPQRFVSDKDAPELLELFQ 249

Query: 222 KYPSVWLNT----HFNHPKEITPE-AKKAMNMLACAGIPLGNQSVLLRRVNDCPVIIKNL 276
           +  +   N     H+NHP EI    A++A+  +   G  +  Q+ ++R VN+ P     L
Sbjct: 250 RIVAAGKNLSIMGHYNHPVEIRQVIARQAIERIRSTGATVRMQAPVIRHVNENPADWAAL 309

Query: 277 CHELLKIKTRPYYLYQCDLSFGLEHFRTSVARGIEIIEMLRGHTSGLA 324
             E +++   PYY++    +    +F   +AR  EI +      SGLA
Sbjct: 310 WTEGVRLGAVPYYMFVERDTGPSHYFEMPLARAFEIFQAAYRTVSGLA 357


Lambda     K      H
   0.320    0.138    0.426 

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: 451
Number of extensions: 22
Number of successful extensions: 2
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: 419
Length of database: 446
Length adjustment: 32
Effective length of query: 387
Effective length of database: 414
Effective search space:   160218
Effective search space used:   160218
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