GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kamA in Desulfoscipio geothermicus DSM 3669

Align L-lysine 2,3-aminomutase; LAM; KAM; EC 5.4.3.2 (characterized)
to candidate WP_092481457.1 BM299_RS00240 KamA family radical SAM protein

Query= SwissProt::Q9XBQ8
         (416 letters)



>NCBI__GCF_900115975.1:WP_092481457.1
          Length = 357

 Score =  286 bits (731), Expect = 9e-82
 Identities = 144/353 (40%), Positives = 233/353 (66%), Gaps = 15/353 (4%)

Query: 20  WRWQVRNRIETVEELKKYIPLTKEEEEGVAQCVKSLRMAITPYYLSLIDPNDPNDPVRKQ 79
           W++Q++N + T+++L+K+I +T+EE E +A    + +   TPY+  L+D +DPN P+RKQ
Sbjct: 4   WQYQMQNFVNTIDKLEKFINITQEEREAIAST--NTKWGTTPYFAGLMDRDDPNCPIRKQ 61

Query: 80  AIPTALE-LNKAAAD---LEDPLHEDTDSPVPGLTHRYPDRVLLLITDMCSMYCRHCTRR 135
            IP+  E +N+   +   +      + +     +  +Y DR+   + ++C+ YCRHC R+
Sbjct: 62  VIPSPREKVNRYGIENYLIYKENRSNEEKRPDTIARQYHDRIAFTVMNICANYCRHCFRK 121

Query: 136 RFAGQSDDSMPME-RIDKAIDYIRNTPQVRDVLLSGGDALLVSDETLEYIIAKLREIPHV 194
                 D+S+     +D+ + +IR   ++RDVL++GGD LL++++ LEYII+KLR+IPH+
Sbjct: 122 ELV--VDESLHFNFNVDEGLAWIREHNEIRDVLITGGDPLLLANDKLEYIISKLRDIPHI 179

Query: 195 EIVRIGSRTPVVLPQRITPELVNMLKKYH--PVWLNTHFNHPNEITEESTRACQLLADAG 252
           E++R GSR P+VLP RIT  L+ +L  +H  P+WLNT  NH  EITE++  A   L  AG
Sbjct: 180 EMIRFGSRVPIVLPHRITDGLLKVLGGFHKVPIWLNTQCNHAKEITEQTAEAVYKLMTAG 239

Query: 253 VPLGNQSVLLRGVNDCVHVMKELVNKLVKIRVRPYYIYQCDLSLGLEHFRTPVSKGIEII 312
           V +GNQ+VLL+G+ND     KEL  KL+ +R+RPYY++ C+ + G++HFRTPV KG E+I
Sbjct: 240 VNVGNQAVLLKGINDDKKSFKELHQKLLTVRIRPYYVFYCEPAPGIDHFRTPVEKGAELI 299

Query: 313 -EGLRGHTSGYCVPTFVVDAPGGGGKTPVMPN-YVISQSHDKVILRNFEGVIT 363
            + LRGHT+G   P +V+      GK P+MP+ Y++ ++ ++  L+N++G IT
Sbjct: 300 RDCLRGHTTGLAQPMYVMAT--NIGKIPLMPDYYIMDKNEEEYTLKNYKGQIT 350


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: 441
Number of extensions: 26
Number of successful extensions: 8
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: 357
Length adjustment: 30
Effective length of query: 386
Effective length of database: 327
Effective search space:   126222
Effective search space used:   126222
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 Apr 09 2024. 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