Alignments for a candidate for metH in Desulfovibrio vulgaris Miyazaki F

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Desulfovibrio vulgaris Miyazaki F

Align vitamin B12-dependent methionine synthase without a reactivation domain (EC 2.1.1.13) (characterized)
to candidate 8499710 DvMF_0476 homocysteine S-methyltransferase (RefSeq)

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



>FitnessBrowser__Miya:8499710
          Length = 818

 Score = 1590 bits (4118), Expect = 0.0
 Identities = 818/818 (100%), Positives = 818/818 (100%)

Query: 1   MPDFRQALRSGRRLVFDGGMGTMLQSRGLPPGVSPELFCLARPDVLVGIHADYLRAGADV 60
           MPDFRQALRSGRRLVFDGGMGTMLQSRGLPPGVSPELFCLARPDVLVGIHADYLRAGADV
Sbjct: 1   MPDFRQALRSGRRLVFDGGMGTMLQSRGLPPGVSPELFCLARPDVLVGIHADYLRAGADV 60

Query: 61  LTTNTFGGCIHKLGTGPGAPDVVEFNRAMARAAREAVLASGREAFVAGSVGPSGHFMRPL 120
           LTTNTFGGCIHKLGTGPGAPDVVEFNRAMARAAREAVLASGREAFVAGSVGPSGHFMRPL
Sbjct: 61  LTTNTFGGCIHKLGTGPGAPDVVEFNRAMARAAREAVLASGREAFVAGSVGPSGHFMRPL 120

Query: 121 GDLDPAELVAAFRAQIRGLVQGGVDLILAETQFDLAEARAIVLAARAECDLPVGVSMTFE 180
           GDLDPAELVAAFRAQIRGLVQGGVDLILAETQFDLAEARAIVLAARAECDLPVGVSMTFE
Sbjct: 121 GDLDPAELVAAFRAQIRGLVQGGVDLILAETQFDLAEARAIVLAARAECDLPVGVSMTFE 180

Query: 181 NGVSLTGTRPEVFVQSMLNMGVDLVGTNCSAGPEQMAEVADELLAISEVPVLVEPNAGLP 240
           NGVSLTGTRPEVFVQSMLNMGVDLVGTNCSAGPEQMAEVADELLAISEVPVLVEPNAGLP
Sbjct: 181 NGVSLTGTRPEVFVQSMLNMGVDLVGTNCSAGPEQMAEVADELLAISEVPVLVEPNAGLP 240

Query: 241 ELVDGKTVFRLGPDDFARHTARFAASGVRMLGGCCGTTPDHIAALRGALDNLSGGLVPDP 300
           ELVDGKTVFRLGPDDFARHTARFAASGVRMLGGCCGTTPDHIAALRGALDNLSGGLVPDP
Sbjct: 241 ELVDGKTVFRLGPDDFARHTARFAASGVRMLGGCCGTTPDHIAALRGALDNLSGGLVPDP 300

Query: 301 ARRDGIVLTTRAQAVHIGAGSPIRIIGERINPTGKKLLTAELQAGEFAQALRFADEQVEA 360
           ARRDGIVLTTRAQAVHIGAGSPIRIIGERINPTGKKLLTAELQAGEFAQALRFADEQVEA
Sbjct: 301 ARRDGIVLTTRAQAVHIGAGSPIRIIGERINPTGKKLLTAELQAGEFAQALRFADEQVEA 360

Query: 361 GAPLLDVNVGAPMVDEAVLLPALVERLVARHSLPLSLDSSNADAIAAALPFHPGSPLVNS 420
           GAPLLDVNVGAPMVDEAVLLPALVERLVARHSLPLSLDSSNADAIAAALPFHPGSPLVNS
Sbjct: 361 GAPLLDVNVGAPMVDEAVLLPALVERLVARHSLPLSLDSSNADAIAAALPFHPGSPLVNS 420

Query: 421 ISGEPGRMEHLGPLCRDHGAPFILLPLKGRKLPVTAAERIAIIEELLQQADSLRIPRRLV 480
           ISGEPGRMEHLGPLCRDHGAPFILLPLKGRKLPVTAAERIAIIEELLQQADSLRIPRRLV
Sbjct: 421 ISGEPGRMEHLGPLCRDHGAPFILLPLKGRKLPVTAAERIAIIEELLQQADSLRIPRRLV 480

Query: 481 MVDVLALAVSSKAEAARHCLDTIRWCAAQGLPTTIGLSNISFGLPARELLNSTFLAMAAG 540
           MVDVLALAVSSKAEAARHCLDTIRWCAAQGLPTTIGLSNISFGLPARELLNSTFLAMAAG
Sbjct: 481 MVDVLALAVSSKAEAARHCLDTIRWCAAQGLPTTIGLSNISFGLPARELLNSTFLAMAAG 540

Query: 541 AGLSSCIAHPGNARIREAVAASSVLLGLDANAESFIEGYSGWTPGGDATGATPAGVAGGT 600
           AGLSSCIAHPGNARIREAVAASSVLLGLDANAESFIEGYSGWTPGGDATGATPAGVAGGT
Sbjct: 541 AGLSSCIAHPGNARIREAVAASSVLLGLDANAESFIEGYSGWTPGGDATGATPAGVAGGT 600

Query: 601 GGGTGGVKAKAATLEEAVIRGDREGALALVERALSEGADPFSLVQEKLIPGITEVGRRYE 660
           GGGTGGVKAKAATLEEAVIRGDREGALALVERALSEGADPFSLVQEKLIPGITEVGRRYE
Sbjct: 601 GGGTGGVKAKAATLEEAVIRGDREGALALVERALSEGADPFSLVQEKLIPGITEVGRRYE 660

Query: 661 RREYFLPQLIRSAETMQHAFRKLQPLLEAQRGHEARPVIIMATVEGDIHDIGKNIVTLML 720
           RREYFLPQLIRSAETMQHAFRKLQPLLEAQRGHEARPVIIMATVEGDIHDIGKNIVTLML
Sbjct: 661 RREYFLPQLIRSAETMQHAFRKLQPLLEAQRGHEARPVIIMATVEGDIHDIGKNIVTLML 720

Query: 721 GNHGFDVVDLGKDVKAADIVEAAERHGARVIGLSALMTTTMVRMEDTVRLVRERGLPVKV 780
           GNHGFDVVDLGKDVKAADIVEAAERHGARVIGLSALMTTTMVRMEDTVRLVRERGLPVKV
Sbjct: 721 GNHGFDVVDLGKDVKAADIVEAAERHGARVIGLSALMTTTMVRMEDTVRLVRERGLPVKV 780

Query: 781 MVGGAVVTPAYAEAIGADGYSADAVEAVRVAKELLTVQ 818
           MVGGAVVTPAYAEAIGADGYSADAVEAVRVAKELLTVQ
Sbjct: 781 MVGGAVVTPAYAEAIGADGYSADAVEAVRVAKELLTVQ 818


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: 2308
Number of extensions: 92
Number of successful extensions: 1
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: 818
Length adjustment: 41
Effective length of query: 777
Effective length of database: 777
Effective search space:   603729
Effective search space used:   603729
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: 56 (26.2 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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