Alignments for a candidate for metH in Phyllobacterium endophyticum PEPV15

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Phyllobacterium endophyticum PEPV15

Align vitamin B12-dependent methionine synthase without a reactivation domain (EC 2.1.1.13) (characterized)
to candidate WP_106718068.1 CU100_RS18335 methyltetrahydrofolate cobalamin methyltransferase

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



>NCBI__GCF_003010935.1:WP_106718068.1
          Length = 320

 Score =  181 bits (458), Expect = 7e-50
 Identities = 115/314 (36%), Positives = 171/314 (54%), Gaps = 13/314 (4%)

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

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

Query: 420 SISGEPGRMEHLGPLCRDHGAPFILLPLKGRKLPVTAAERIAIIEELLQQADSLRIPRRL 479
           S++GE  ++E + PL + +  P + +      + +    R A+ ++++++A    IP   
Sbjct: 122 SVTGEEEKLEAILPLIKKYNVPVVAISNDETGISMDPDVRFAVAKKIVERAADFGIPAHD 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+ +  A 
Sbjct: 242 IGAGMTSAIMNPCRPQEMEAVHAANVLNGTDANCTYWIKKYRDHQPAAPGVAASVSVPAD 301

Query: 599 GTGGG--TGGVKAK 610
             GGG   GG +A+
Sbjct: 302 SAGGGRRRGGREAR 315


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: 668
Number of extensions: 44
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: 320
Length adjustment: 34
Effective length of query: 784
Effective length of database: 286
Effective search space:   224224
Effective search space used:   224224
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_106718059.1 CU100_RS18285 betaine--homocysteine S-methyltransferase

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



>NCBI__GCF_003010935.1:WP_106718059.1
          Length = 337

 Score =  162 bits (411), Expect = 2e-44
 Identities = 106/290 (36%), Positives = 154/290 (53%), Gaps = 7/290 (2%)

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

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

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

Query: 193 F--VQSMLNMGVDLVGTNCSAGPEQ-MAEVADELLAISEVPVLVEPNAGLPELVDGKTVF 249
              V   L+     VG NC  G    +A + D   A     ++++ N G+PE   G  +F
Sbjct: 196 IHGVVDGLSQPPVAVGANCGVGASDILATLLDMSDADPSATIVIKGNCGIPEF-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: 705
Number of extensions: 36
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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the original publication.

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

GapMind for Amino acid biosynthesis