Alignments for a candidate for metH in Desulfovibrio zosterae DSM 11974

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Desulfovibrio zosterae DSM 11974

Align vitamin B12-dependent methionine synthase without a reactivation domain (EC 2.1.1.13) (characterized)
to candidate WP_027720742.1 H589_RS0103440 methionine synthase

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



>NCBI__GCF_000425265.1:WP_027720742.1
          Length = 806

 Score =  920 bits (2379), Expect = 0.0
 Identities = 486/818 (59%), Positives = 600/818 (73%), Gaps = 16/818 (1%)

Query: 1   MPDFRQALRSGRRLVFDGGMGTMLQSRGLPPGVSPELFCLARPDVLVGIHADYLRAGADV 60
           MPDFR+AL  GR   FDGG GT LQSRGLP G+SPE+F L RPDV+  +H DY+ AGA+V
Sbjct: 1   MPDFRKALGDGRVYFFDGGYGTFLQSRGLPAGMSPEVFGLERPDVIKSVHQDYVDAGANV 60

Query: 61  LTTNTFGGCIHKLGTGPGAPDVVEFNRAMARAAREAVLASGREAFVAGSVGPSGHFMRPL 120
           LTTNTFGG   KLG      DV+  NR MA  AR     +G   FV GSVGP+GHF++PL
Sbjct: 61  LTTNTFGGSRPKLGADV---DVIALNREMALLARSI---AGDTVFVGGSVGPTGHFVQPL 114

Query: 121 GDLDPAELVAAFRAQIRGLVQGGVDLILAETQFDLAEARAIVLAARAECDLPVGVSMTFE 180
           G++   E+V  ++ QI+GLV+GGVDLIL ET FDLAEARA+V+AAR  CDLPV +SMTFE
Sbjct: 115 GEMTFKEMVEIYKEQIQGLVEGGVDLILGETHFDLAEARAVVIAAREVCDLPVAISMTFE 174

Query: 181 N-GVSLTGTRPEVFVQSMLNMGVDLVGTNCSAGPEQMAEVADELLAISEVPVLVEPNAGL 239
           +    LTGT P  FV +M NMGV+L+GTNCSAGPEQ+ EV   +      P+LVE NAGL
Sbjct: 175 SPSACLTGTSPLTFVDAMQNMGVELMGTNCSAGPEQIFEVLKNMQPRLSSPLLVEANAGL 234

Query: 240 PELVDGK-TVFRLGPDDFARHTARFAASGVRMLGGCCGTTPDHIAALRGALDNLSGGLVP 298
           PEL + + TVFRL P+ FA  + RF   G + +GGCCGT PDHI ALR A+ +      P
Sbjct: 235 PELDENRNTVFRLKPEPFAEQSVRFLEVGAKFIGGCCGTGPDHIRALRAAVGDARWKR-P 293

Query: 299 DPARRDGIVLTTRAQAVHIGAGSPIRIIGERINPTGKKLLTAELQAGEFAQALRFADEQV 358
            P     +VLT+R ++V IG      IIGERINPTGKK+L AELQ G+F +A++FA+EQV
Sbjct: 294 VPQDDCQMVLTSRGESVAIGFEQRGVIIGERINPTGKKVLIAELQKGQFTEAMKFAEEQV 353

Query: 359 EAGAPLLDVNVGAPMVDEAVLLPALVERLVARHSLPLSLDSSNADAIAAALPFHPGSPLV 418
            AGAP+LDVNVGAPMVDE   LPAL + + A++S PLS+DS+N DA+ AAL  +PG+PLV
Sbjct: 354 TAGAPVLDVNVGAPMVDEVQTLPALTKEIFAQYSAPLSIDSTNPDAVEAALWEYPGTPLV 413

Query: 419 NSISGEPGRMEHLGPLCRDHGAPFILLPLKGRKLPVTAAERIAIIEELLQQADSLRIPRR 478
           NSISGEPGRME LGPLC+  GAPFILLP+ G KLP T  ERI ++  LL+QAD + IPRR
Sbjct: 414 NSISGEPGRMERLGPLCKKFGAPFILLPIIGSKLPFTCEERIEVVSNLLKQADEIGIPRR 473

Query: 479 LVMVDVLALAVSSKAEAARHCLDTIRWCAAQ-GLPTTIGLSNISFGLPARELLNSTFLAM 537
           L+MVD LAL VSSK  AARHCLD IR C  +  LPT +GLSN+SFGLPARELLNS+FL +
Sbjct: 474 LIMVDALALTVSSKPTAARHCLDFIRHCKEEWNLPTVLGLSNVSFGLPARELLNSSFLTL 533

Query: 538 AAGAGLSSCIAHPGNARIREAVAASSVLLGLDANAESFIEGYSGWTPGGDATGATPAGVA 597
             G G+ + IA+P ++R+REA+ ++ VLL  D  AE FIE +S WTP GD +G +     
Sbjct: 534 CQGQGMCAFIANPNSSRLREALYSAEVLLARDPQAEQFIEKFSDWTPSGDNSGGS----- 588

Query: 598 GGTGGGTGGVKAKAATLEEAVIRGDREGALALVERALSEGADPFSLVQEKLIPGITEVGR 657
            G GG     K+ A  L +AV++GDR   +ALVER L  G  PF LV   LIP I EVG 
Sbjct: 589 -GVGGSKAPDKSGADNLFDAVVKGDRGNIVALVERDLEAGRKPFELVNGDLIPAIMEVGE 647

Query: 658 RYERREYFLPQLIRSAETMQHAFRKLQPLLEAQRGHEARPVIIMATVEGDIHDIGKNIVT 717
           +YE +EYFLPQL++SAET+Q AF KL+PLLE + G + +  IIMATVEGDIHDIGKNIV 
Sbjct: 648 KYESKEYFLPQLLQSAETLQKAFEKLKPLLEEEGGDQEKDTIIMATVEGDIHDIGKNIVC 707

Query: 718 LMLGNHGFDVVDLGKDVKAADIVEAAERHGARVIGLSALMTTTMVRMEDTVRLVRERGLP 777
           LML NHGF+V+DLGKDV A +IV+A + H A+++GLSALMTTTMVRMEDT+ L++ERGL 
Sbjct: 708 LMLRNHGFNVIDLGKDVPAENIVKAVQEHQAKIVGLSALMTTTMVRMEDTINLLKERGLN 767

Query: 778 VKVMVGGAVVTPAYAEAIGADGYSADAVEAVRVAKELL 815
            KVM+GGAV+T  + ++IGADG+S DAV AV+VAK+LL
Sbjct: 768 TKVMIGGAVITGGFCDSIGADGWSTDAVAAVKVAKQLL 805


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: 1713
Number of extensions: 74
Number of successful extensions: 7
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: 806
Length adjustment: 41
Effective length of query: 777
Effective length of database: 765
Effective search space:   594405
Effective search space used:   594405
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 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

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

Related tools

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