GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metH in Phyllobacterium brassicacearum STM 196

Align vitamin B12-dependent methionine synthase without a reactivation domain (EC 2.1.1.13) (characterized)
to candidate WP_106710138.1 CU102_RS06125 methyltetrahydrofolate cobalamin methyltransferase

Query= reanno::Miya:8499710
         (818 letters)



>NCBI__GCF_003010955.1:WP_106710138.1
          Length = 319

 Score =  180 bits (457), Expect = 9e-50
 Identities = 116/315 (36%), Positives = 171/315 (54%), Gaps = 16/315 (5%)

Query: 307 VLTTRAQAVHIGAGSPIRIIGERINPTGKKLLTAELQAGEFAQALRFADEQVEAGAPLLD 366
           ++ +  + + IG   P  +IGERINPTG+K L AE+  G F   ++ A EQV AGA +LD
Sbjct: 5   IVASATKEIIIGFDQPFCVIGERINPTGRKKLAAEMIEGNFDTVIKDALEQVAAGATMLD 64

Query: 367 VNVGAPMVDEAVLLPAL-------VERLVARHSLPLSLDSSNADAIAAALPFHPGSPLVN 419
           VN G   VD     P L       V+ LV    +PLS+DSS   AI AAL    G PLVN
Sbjct: 65  VNAGVTAVDPNATEPGLLVQTLEIVQNLV---DVPLSIDSSVTAAIEAALKVAKGRPLVN 121

Query: 420 SISGEPGRMEHLGPLCRDHGAPFILLPLKGRKLPVTAAERIAIIEELLQQADSLRIPRRL 479
           S++GE  ++E + PL + +  P + +      + +    R A+ ++++++A    IP   
Sbjct: 122 SVTGEEEKLEAILPLIKKYNVPVVAISNDETGISMDPDVRFAVAKKIVERAADFGIPSHD 181

Query: 480 VMVDVLALAVSSKAEAARHCLDTIRWCAAQ-GLPTTIGLSNISFGLPARELLNSTFLAMA 538
           ++VD L + + +  +A R     +R    +  + TT GLSNISFGLP R  +N+ F+ M 
Sbjct: 182 IVVDPLVMPIGALGDAGRQVFALLRRLREELKVNTTCGLSNISFGLPHRHGINAGFIPMV 241

Query: 539 AGAGLSSCIAHPGNARIREAVAASSVLLGLDANAESFIEGYSGWTPGGDATGATPAGVAG 598
            GAG++S I +P   +  EAV A++VL G DAN   +I+ Y    P   A GA P  V  
Sbjct: 242 IGAGMTSAIMNPCRPQEMEAVHAANVLNGTDANCTYWIKKYRDHQPA--AAGAAPVSVPA 299

Query: 599 GTGGG---TGGVKAK 610
            + GG    GG +A+
Sbjct: 300 DSAGGGRRRGGREAR 314


Lambda     K      H
   0.320    0.137    0.395 

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: 652
Number of extensions: 40
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: 818
Length of database: 319
Length adjustment: 34
Effective length of query: 784
Effective length of database: 285
Effective search space:   223440
Effective search space used:   223440
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: 52 (24.6 bits)

Align vitamin B12-dependent methionine synthase without a reactivation domain (EC 2.1.1.13) (characterized)
to candidate WP_106710129.1 CU102_RS06070 betaine--homocysteine S-methyltransferase

Query= reanno::Miya:8499710
         (818 letters)



>NCBI__GCF_003010955.1:WP_106710129.1
          Length = 337

 Score =  161 bits (407), Expect = 6e-44
 Identities = 105/290 (36%), Positives = 153/290 (52%), Gaps = 7/290 (2%)

Query: 14  LVFDGGMGTMLQSRGLPPGVSPELFCLARPDVLVGIHADYLRAGADVLTTNTFGGCIHKL 73
           L+ DG  GT L + GL  G +PEL+  A+P+ +  +H  ++ AGAD++ TN+FGG  H+L
Sbjct: 17  LLADGATGTNLFATGLEAGEAPELWNEAQPEKITALHQGFVDAGADIILTNSFGGTRHRL 76

Query: 74  GTGPGAPDVVEFNRAMARAAREAVLASGREAFVAGSVGPSGHFMRPLGDLDPAELVAAFR 133
                   V E N+  A  AR     +GR+  VAGSVGP+G  + PLG L   + VAAF 
Sbjct: 77  KLHHAQDRVFELNKKAAELARGVADQAGRKVIVAGSVGPTGELLVPLGTLTEQDAVAAFT 136

Query: 134 AQIRGLVQGGVDLILAETQFDLAEARAIVLAARAECDLPVGVSMTFEN-GVSLTGTRPEV 192
            Q+ GL  GGVD+   ET     E RA   AA  +  LP   + +F+  G ++ G  P+ 
Sbjct: 137 EQLEGLKAGGVDVAWIETMSAPGEIRAAAEAA-VKVGLPYVYTGSFDTAGKTMMGLPPKD 195

Query: 193 F--VQSMLNMGVDLVGTNCSAGPEQ-MAEVADELLAISEVPVLVEPNAGLPELVDGKTVF 249
              V   L      VG NC  G    +A + D   A     ++++ N G+PE   G  +F
Sbjct: 196 IHGVVDGLAQRPVAVGANCGVGASDILASLLDMSEADPSATIVIKGNCGIPEF-RGAEIF 254

Query: 250 RLGPDDFARHTARFAAS-GVRMLGGCCGTTPDHIAALRGALDNLSGGLVP 298
             G  +     A  A + G +++GGCCGT+ +H+AA+R ALD+ + G  P
Sbjct: 255 YSGTPELMADYAHLAINGGAKIIGGCCGTSFEHLAAMRKALDSHTHGARP 304


Lambda     K      H
   0.320    0.137    0.395 

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: 711
Number of extensions: 35
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: 818
Length of database: 337
Length adjustment: 35
Effective length of query: 783
Effective length of database: 302
Effective search space:   236466
Effective search space used:   236466
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: 52 (24.6 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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