Alignments for a candidate for metH in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Phaeobacter inhibens BS107

Align Methionine synthase (cobalamin-dependent) (EC 2.1.1.13) (characterized)
to candidate GFF1321 PGA1_c13370 putative homocysteine S-methyltransferase

Query= reanno::DvH:207036
         (804 letters)



>FitnessBrowser__Phaeo:GFF1321
          Length = 338

 Score =  158 bits (399), Expect = 5e-43
 Identities = 106/298 (35%), Positives = 150/298 (50%), Gaps = 16/298 (5%)

Query: 4   FRQALRAGRRLLFDGGLGTMLQARGLPAGVSPEQFCLDRPDVLRGIHADYVRAGADILTT 63
           F   L     LL DG  GT L   GL +G +PE + +D P  +  ++   V AG+D+  T
Sbjct: 5   FTTLLETKDALLADGATGTNLFNMGLQSGDAPELWNVDEPKKITALYQGAVDAGSDLFLT 64

Query: 64  NTFGGS--RFKLGDGFDVV-DFNRRMAAIAREAADASGRQAFVAGSIGPTGHFVKPLGEV 120
           NTFGG+  R KL D    V + N   A + R  AD S R+  VAGS+GPTG  ++P+GE+
Sbjct: 65  NTFGGTAARLKLHDAHRRVRELNVAGAELGRNVADRSERKIAVAGSVGPTGEIMQPVGEL 124

Query: 121 EPAALVAAFREQVRGLVAGGADLLMIETQFDLAEARAAVVAARAECSLPIAVSMTFEN-G 179
             A  V  F EQ   L  GG D+L +ET     E RAA  A +    +P   +M+F+  G
Sbjct: 125 SHALAVEMFHEQAEALKEGGVDVLWLETISAPEEYRAAAEAFKL-ADMPWCGTMSFDTAG 183

Query: 180 VSLTGSTPEVFVATMLNLGVDL------LGTNCSAGPDQMHDVVASLLASASV-PVLVEP 232
            ++ G T     A M  L  +        G NC  G   +   V    A  +  P++ + 
Sbjct: 184 RTMMGVTS----ADMAQLVEEFDPAPLAFGANCGTGASDILRTVLGFAAQGTTRPIISKG 239

Query: 233 NAGLPELIDGKTVFRLPPAPFAEKTAAFAAMGARVLGGCCGTTPDHIAALRQAVADIP 290
           NAG+P+ +DG   +   P    E  A     GA+++GGCCGT PDH+ A+R+A+   P
Sbjct: 240 NAGIPKYVDGHIHYDGTPTLMGEYAAMARDCGAKIIGGCCGTMPDHLRAMREALDTRP 297


Lambda     K      H
   0.320    0.137    0.392 

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: 653
Number of extensions: 50
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: 804
Length of database: 338
Length adjustment: 35
Effective length of query: 769
Effective length of database: 303
Effective search space:   233007
Effective search space used:   233007
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 Methionine synthase (cobalamin-dependent) (EC 2.1.1.13) (characterized)
to candidate GFF1582 PGA1_c16040 pterin binding domain-containing protein

Query= reanno::DvH:207036
         (804 letters)



>FitnessBrowser__Phaeo:GFF1582
          Length = 353

 Score =  155 bits (391), Expect = 5e-42
 Identities = 101/299 (33%), Positives = 153/299 (51%), Gaps = 16/299 (5%)

Query: 302 VLTTRSHLVRVGGDAPVRIIGERINPTGKKQLIAELQAGDFSLALRFSDEQVEAGAPILD 361
           V+ +++    +G D P  +IGERINPTG+K+L AEL+AGDFS   + +  QV AGA ILD
Sbjct: 5   VVESKTKTAILGFDEPFCVIGERINPTGRKKLAAELEAGDFSTVEKDALAQVMAGANILD 64

Query: 362 VNVGA-------PMVDEEVLLPDLVQRLITRHGVPLSIDSSNAAAIERALPYCPGSTLVN 414
           +N G        P   E  L+  +V+ +      PL IDSS   A+E  L    G  L+N
Sbjct: 65  INAGVVYNSNPNPNETEPPLMTKIVELVQGLTDTPLCIDSSVPGALEAGLQAAEGRPLLN 124

Query: 415 SISGEPGRMERLGPLCRDHGAPFILLPLKGRKLPVAATERIAIIEELLVQAEGLGIPRRL 474
           S++GE  R+E + PL + +  P + +      +      R A+ ++++ +A   GIP   
Sbjct: 125 SVTGEEERLEHVLPLVKKYNVPVVAISNDDTGISEDPDVRFAVAKKIVERAADFGIPAHD 184

Query: 475 VMVDVLALAVSSKAEAARQCLETIRWCTAN-GFATTIGLSNISFGLPARELLNGTFLAMA 533
           ++VD L + + + A A +Q    +R      G  TT G SN+SFGLP R  +N  FL MA
Sbjct: 185 IVVDPLVMPIGAMATAGQQVFALVRRLREELGVNTTCGASNVSFGLPNRHGINNAFLPMA 244

Query: 534 AGAGLSSCIAHP-----GNGRIRE---TVACADVLLARDANAERFIDAYAAWTPATQGG 584
            GAG++S I +P        +I E    V  A ++L      E F+  +   +   + G
Sbjct: 245 MGAGMTSAIMNPVALPITQKKIAEKKAEVEAAGIILPEGMEDEAFVQMFGLGSTKPRAG 303


Lambda     K      H
   0.320    0.137    0.392 

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: 687
Number of extensions: 43
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: 804
Length of database: 353
Length adjustment: 35
Effective length of query: 769
Effective length of database: 318
Effective search space:   244542
Effective search space used:   244542
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 Apr 09 2024. The underlying query database was built on Apr 09 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 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 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