GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kamA in Caulobacter crescentus NA1000

Align lysine 2,3-aminomutase (EC 5.4.3.2) (characterized)
to candidate CCNA_00753 CCNA_00753 lysine 2,3-aminomutase

Query= BRENDA::G3F9W8
         (439 letters)



>FitnessBrowser__Caulo:CCNA_00753
          Length = 345

 Score =  247 bits (630), Expect = 5e-70
 Identities = 131/308 (42%), Positives = 188/308 (61%), Gaps = 3/308 (0%)

Query: 50  PPEEREKLQETIDKFPLAATPYYLSLIKTEDYANDPIFRQAVPVPDELRVEECELEDPLA 109
           P E    L+    ++ +A TP    LI   D  +DPI RQ VP P+EL     E  DP+ 
Sbjct: 20  PSERLPALEAVAARYAVAITPAMAELIDP-DRDDDPIARQFVPSPEELVSSPGEDGDPIG 78

Query: 110 EDSDSPVPGITHRYPDRVLFLVSNVCAMYCRHCTRKRKVGDRDRIP-TWEEMEVGITYIR 168
           + + SPV GI HRYPDRVL   ++ CA+YCR C R+  VG       T  +++    YI 
Sbjct: 79  DAAHSPVEGIVHRYPDRVLLKPTHTCAVYCRFCFRREMVGPEGLSNLTPAQLDAAFAYIA 138

Query: 169 EHPEVRDVLLSGGDPLMLPDDLLDRILTQLRAIPHVEVIRIGSRTPVVLPFRITDGLVNV 228
           + P++ +V+++GGDPL+L    L  ++ +L AI HV+++R  +R P V P  +T  LV  
Sbjct: 139 QRPQIWEVIVTGGDPLVLSPRRLADLMDRLEAIDHVKIVRFHTRVPAVDPGAVTPELVAA 198

Query: 229 LKKH-QPIWLNTHFNHPQEITPSAEKALAKLADAGIPLGNQSVLLAGVNDCPRIMKSLVQ 287
           LK+  + +++  H NH +E+TP+A  A A++ DAG+P+ +Q+VLL GVND P  +  L++
Sbjct: 199 LKRSSKTVYVALHANHARELTPAARAACAQIVDAGVPMVSQTVLLRGVNDNPETLVELMR 258

Query: 288 KLVKNRVRPYYLYQCDLSEGLSHFRTPVGKGIEIMENLIGHTSGFAVPTYVIDAPGGGGK 347
             V+ R+RPYYL+  DL+ G +H RT V +G  IM  L G  SG A PTYV+D PGG GK
Sbjct: 259 AFVETRIRPYYLHHGDLAPGTAHLRTTVAEGQAIMRALRGTLSGLAQPTYVLDIPGGHGK 318

Query: 348 IPVMPTYL 355
           +PV P YL
Sbjct: 319 VPVGPNYL 326


Lambda     K      H
   0.319    0.138    0.420 

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: 416
Number of extensions: 24
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: 439
Length of database: 345
Length adjustment: 30
Effective length of query: 409
Effective length of database: 315
Effective search space:   128835
Effective search space used:   128835
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 (21.7 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