GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kamA in Methanospirillum lacunae Ki8-1

Align lysine 2,3-aminomutase (EC 5.4.3.2) (characterized)
to candidate WP_109968124.1 DK846_RS06500 KamA family radical SAM protein

Query= BRENDA::G3F9W8
         (439 letters)



>NCBI__GCF_003173355.1:WP_109968124.1
          Length = 374

 Score =  194 bits (492), Expect = 5e-54
 Identities = 116/304 (38%), Positives = 168/304 (55%), Gaps = 20/304 (6%)

Query: 39  SMLEKVLGITFPPEEREKLQETIDKFPLAATPYYLSLIKTEDYANDPIFRQAVPVPDELR 98
           S+ E  L     P++  K+++    +P  +  YYLSLI   +  NDPI R  +P P    
Sbjct: 8   SVHETSLSDVLDPDQVLKMEDVERVYPFRSNEYYLSLINHNN-PNDPIKRIILPDP---- 62

Query: 99  VEECELE-----DPLAEDSDSPVPGITHRYPDRVLFLVSNVCAMYCRHCTRKRKVGDRDR 153
              CEL      DP  E+  SP+PG+ H+YP   + LVSN C   CR C RKR     + 
Sbjct: 63  ---CELANPGSLDPSGEEEYSPLPGVQHKYPQTAMLLVSNTCGGICRFCFRKRLFTGENP 119

Query: 154 IPTWEEMEVGITYIREHPEVRDVLLSGGDPLMLPDDLLDRILTQLRAIPHVEVIRIGSRT 213
            P  +  +  + Y++   ++ DVLLSGGDPLML    LD+IL+ +R +P   +IRIG++ 
Sbjct: 120 PPICDTKKA-VDYLQTQKDLTDVLLSGGDPLMLGASKLDQILSMIRELPTKPIIRIGTKI 178

Query: 214 PVVLPFRITDG--LVNVLKKH----QPIWLNTHFNHPQEITPSAEKALAKLADAGIPLGN 267
           P   P R+TD   L +VL KH    + I+L +HFNHPQEIT S++ A++ L + G  L N
Sbjct: 179 PAYDPHRLTDDSDLRDVLAKHTSPEEKIYLISHFNHPQEITSSSKAAISALKNTGAELTN 238

Query: 268 QSVLLAGVNDCPRIMKSLVQKLVKNRVRPYYLYQCDLSEGLSHFRTPVGKGIEIMENLIG 327
           Q+ +L G+N+ P IM SL   L K  V PYY++QC  + G  H   P+ + + ++     
Sbjct: 239 QTPILQGINNEPDIMASLFNILSKLGVPPYYVFQCRPTSGNRHLTVPIEQAMHVIHEAQS 298

Query: 328 HTSG 331
             SG
Sbjct: 299 CCSG 302


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: 429
Number of extensions: 25
Number of successful extensions: 4
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: 374
Length adjustment: 31
Effective length of query: 408
Effective length of database: 343
Effective search space:   139944
Effective search space used:   139944
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 24 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