Alignments for a candidate for metH in Malonomonas rubra DSM 5091

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Malonomonas rubra DSM 5091

Align Methionine synthase; EC 2.1.1.13; 5-methyltetrahydrofolate--homocysteine methyltransferase; Methionine synthase, vitamin-B12 dependent; MS (uncharacterized)
to candidate WP_072909508.1 BUB13_RS14570 5-methyltetrahydrofolate--homocysteine methyltransferase

Query= curated2:O33259
         (1192 letters)



>NCBI__GCF_900142125.1:WP_072909508.1
          Length = 809

 Score =  629 bits (1623), Expect = 0.0
 Identities = 386/867 (44%), Positives = 518/867 (59%), Gaps = 62/867 (7%)

Query: 327  SVSSLYTAIPFAQDASVLVIGERTNANGSKGFREAMIAEDYQKCLDIAKDQTRDGAHLLD 386
            SVSSLY A+   Q+   L+IGER N NGSK FREA++AED+  CL +A DQ   GA +LD
Sbjct: 4    SVSSLYQAVELNQEIPPLLIGERCNPNGSKAFREALLAEDWDSCLKMALDQEARGAQVLD 63

Query: 387  LCVDYVGRDGVADMKALASRLATSSTLPIMLDSTETAVLQAGLEHLGGRCAINSVNYEDG 446
            LCV Y GRD ++DM  L    A S   P+MLDST    L A L    GR  INS+N EDG
Sbjct: 64   LCVAYAGRDELSDMNTLVKLFAGSCKAPLMLDSTSPETLSAVLPLYPGRAIINSINLEDG 123

Query: 447  DGPESRFAKTMALVAEHGAAVVALTIDEEGQARTAQKKVEIAERLINDITGNWGVDESSI 506
                +   K  AL  ++GAAVVALTI EEG A T +KKV  A+ +        G+    I
Sbjct: 124  G---ANLDKICALAKKYGAAVVALTITEEGMALTCEKKVAAAKEIYRLAVEKHGLRAQDI 180

Query: 507  LIDTLTFTIATGQEESRRDGIETIEAIRELKKRHPDVQTTLGLSNISFGLNPAARQVLNS 566
            L D LTFT+ +G E+ R   I+T++AI+++KK  P V  TLG+SNISFGL PAAR+VLNS
Sbjct: 181  LFDLLTFTVGSGDEKMRDAAIQTLDAIKQVKKELPGVGFTLGVSNISFGLRPAARKVLNS 240

Query: 567  VFLHECQEAGLDSAIVHASKILPMNRIPEEQRNVALDLVYDRRREDYDPLQELMRLFEGV 626
            VFLHE   AGL++AIV A+K+LP   I +E R + LDL+++R     D L   +  FE  
Sbjct: 241  VFLHEAVAAGLNTAIVDAAKVLPYVAISDEDRQLCLDLLFNR---SDDALMNFIEHFEQA 297

Query: 627  SAASSKEDRLAELAGLPLFERLAQRIVDGERNGLDADLDEAMTQKPPLQIINEHLLAGMK 686
               S +E+     +   L E+L Q+++ G++ GL+  L E   +  PL IIN  L+  M+
Sbjct: 298  VEESDEEE-----SDTLLEEQLRQKVLKGDKEGLEDLLTELRGRWQPLDIINGLLVPAMR 352

Query: 687  TVGELFGSGQMQLPFVLQSAEVMKAAVAYLEPHMERSDDDSGKGRIVLATVKGDVHDIGK 746
             VGELFG G++ LPFVLQSAEVMK +V  LEP+ME+  D+ G+  I+LATV GDVHDIGK
Sbjct: 353  EVGELFGRGELLLPFVLQSAEVMKQSVNLLEPYMEKLSDE-GRTSILLATVAGDVHDIGK 411

Query: 747  NLVDIILSNNGYEVVNIGIKQPIATILEVAEDKSADVVGMSGLLVKSTVVMKENLEEMNT 806
            NLVDIILSNNGY+V NIGIK P   I+  A++   DVVG+SGLLVKS ++MKEN+ +   
Sbjct: 412  NLVDIILSNNGYKVHNIGIKVPAEEIIAKAKELQVDVVGLSGLLVKSALLMKENMLQFQA 471

Query: 807  RGVAEKFPVLLGGAALTRSYVENDLAEIYQGEVHYARDAFEGLKLMDTIMSAKRGEAPDE 866
             G+ +  PVLLGGAALT  +V  D    Y+ +V Y  DAF GLK                
Sbjct: 472  AGLTQ--PVLLGGAALTPKFVAEDCVPGYENQVVYCADAFAGLK---------------- 513

Query: 867  NSPEAIKAREKEAERKARHQRSKRIAAQRKAAEEPVEVPERSDVAADIEVPAPPFWGSRI 926
                AI+  E  + +  R + S  +AA +   ++  E  +RS +      P+ PF G +I
Sbjct: 514  ----AIRDFESGSLQSTRWE-SAAVAANKPGPQQ--EGIDRSQIP-----PSVPFLGEKI 561

Query: 927  VKGLAVADYTGLLDERALFLGQWGL-RGQRGGEGPSYEDLVETEGRPRLRYWLDRLSTDG 985
            ++ L        L++ ALF G+WG  RG+   E   Y +L +    P      D+  ++ 
Sbjct: 562  IEDLPAEPLFNYLNQAALFRGRWGYRRGKMSKE--EYAELTDKTVLPLYARLKDQALSEN 619

Query: 986  ILAHAAVVYGYFPAVSEGNDIVVLTEPKPDAPVRYRFHFPRQQRGRFLCIADFIRSRELA 1045
             L    V YGYF   SEG+ ++V            RF FPRQ     LCIAD+ RS E  
Sbjct: 620  WL-QPKVAYGYFDCCSEGDSLLV-----HSTSGEKRFDFPRQPAPPHLCIADYFRSAE-- 671

Query: 1046 AERGEVDVLPFQLVTMGQPIADFANELFASNAYRDYLEVHGIGVQLTEALAEYWHRRIRE 1105
             E G  D + F +VT+G  +A+  +EL+AS++Y DYL +HG+GV+LT+ LAEYWH ++R 
Sbjct: 672  -EGG--DKVGFFVVTIGDRLAEMTSELYASDSYHDYLMLHGLGVELTDGLAEYWHEQMRI 728

Query: 1106 ELKFSGDRAMAAEDPEAKEDYFKLGYRGARFAFGYGACPDLEDRAKMMALLEPERIGVTL 1165
            E+   G +  A  D  A   Y   GY+G+R+ FGY ACPDLE    +  L++ ++IGV L
Sbjct: 729  EM---GLQQQAQADVAA---YVAQGYQGSRYGFGYPACPDLEAHLPLFELVKAQQIGVGL 782

Query: 1166 SEELQLHPEQSTDAFVLHHPEAKYFNV 1192
            +E  ++ PE ST A V+HHP+AKYF V
Sbjct: 783  TESFEMVPEMSTSAIVVHHPQAKYFAV 809


Lambda     K      H
   0.317    0.135    0.386 

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: 2040
Number of extensions: 97
Number of successful extensions: 10
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: 1192
Length of database: 809
Length adjustment: 44
Effective length of query: 1148
Effective length of database: 765
Effective search space:   878220
Effective search space used:   878220
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 57 (26.6 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
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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