Alignments for a candidate for metH in Leptospirillum ferrooxidans C2-3

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Leptospirillum ferrooxidans C2-3

Align Methionine synthase (cobalamin-dependent) (EC 2.1.1.13) (characterized)
to candidate WP_014449805.1 LFE_RS08455 5-methyltetrahydrofolate--homocysteine methyltransferase

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



>NCBI__GCF_000284315.1:WP_014449805.1
          Length = 828

 Score =  561 bits (1446), Expect = e-164
 Identities = 321/796 (40%), Positives = 482/796 (60%), Gaps = 12/796 (1%)

Query: 14  LLFDGGLGTMLQARGLPAGVSPEQFCLDRPDVLRGIHADYVRAGADILTTNTFGGSRFKL 73
           LL DG +G +LQ+RGLPAG +P+ + +++P  ++ +H +YV AG+DI+ TNTFG SR +L
Sbjct: 13  LLLDGSMGALLQSRGLPAGYAPDLWNIEKPQEIQAVHTEYVNAGSDIILTNTFGASRLRL 72

Query: 74  GDGFDVVDFNRRMAAIAREAADASGR-QAFVAGSIGPTGHFVKPLGEVEPAALVAAFREQ 132
            + ++  D  R +   A + A  + R +A+VAG IGP+G  + P G++     +A F EQ
Sbjct: 73  SE-YNAQDRIREINFQAVDLAQRASRGKAYVAGDIGPSGTTIAPFGDLPFDDAIAIFYEQ 131

Query: 133 VRGLVAGGADLLMIETQFDLAEARAAVVAARAECS--LPIAVSMTFE-NGVSLTGSTPEV 189
            + L+  GADL+ IET FD+ E RAA++  R   +  +P+   MTF  +G++ +GS PE 
Sbjct: 132 AKLLLEAGADLIAIETMFDIQEMRAALIGVREATNGRIPLMALMTFNMDGITDSGSDPET 191

Query: 190 FVATMLNLGVDLLGTNCSAGPDQMHDVVASLLASASVPVLVEPNAGLPELIDGKTVFRLP 249
             + +   GVD++G NCS GP+ M  VV+ L  +    + VEPNAGLP   +G+T++   
Sbjct: 192 AASVLEGFGVDIMGLNCSVGPEAMVPVVSRLGQTTDTFIAVEPNAGLPVHRNGETLYLTG 251

Query: 250 PAPFAEKTAAFAAMGARVLGGCCGTTPDHIAALRQAVADI-PATLPVDSGVGIVLTTRSH 308
               A+   +F   GA ++GGCCGTTP++I  L + V    P + P  S + I  ++R+ 
Sbjct: 252 AEEVAKFAPSFVEAGANIIGGCCGTTPEYIRILAKTVKGASPISRPTPSLLKI--SSRTS 309

Query: 309 LVRVGGDAPVRIIGERINPTGKKQLIAELQAGDFSLALRFSDEQVEAGAPILDVNVGAPM 368
           +  +G   P  I+GE+INPTGKK     +  G   L +  + ++ EAGA  LDVNVG P+
Sbjct: 310 MTLIGDGVPFLIVGEKINPTGKKIFSEAIANGQVDLIVAEARKEAEAGAGALDVNVGVPL 369

Query: 369 VDEEVLLPDLVQRLITRHGVPLSIDSSNAAAIERALPYCPGSTLVNSISGEPGRMERLGP 428
           V+E  ++   +  +     +PL IDSS A+A+E  L   PG  LVNS++ E  R+E + P
Sbjct: 370 VNEAEMMAKAITAIQNVVSLPLVIDSSYASALESGLKLYPGRALVNSVNAEDERLEEVLP 429

Query: 429 LCRDHGAPFILLPLKGRKLPVAATERIAIIEELLVQAEGLGIPRRLVMVDVLALAVSSKA 488
           L R +GA  I L + G  +P  A ER+   E++L +AE LG+  R ++ D LAL VS+  
Sbjct: 430 LIRKYGAAVIAL-VSGDNIPETAAERMKNAEKILRRAEELGLKPRDLIFDTLALTVSAVQ 488

Query: 489 EAARQCLETIRWCTAN-GFATTIGLSNISFGLPARELLNGTFLAMAAGAGLSSCIAHPGN 547
           EAA+Q L+TI          T +GLSN+SFGLPAR++++  FL+MA GAGL + I  P +
Sbjct: 489 EAAKQTLDTITLIKKELRLPTILGLSNVSFGLPARKIVHNNFLSMAIGAGLDAAICDPYD 548

Query: 548 GRIRETVACADVLLARDANAERFIDAYAAWTPATQGGPVASGPGLASQPPATTLEEAVVK 607
             + +T+A + +   RD +   +++  AAWTPA QG   AS    A +  +  + +A+++
Sbjct: 549 QVLHQTIAASSLFARRDPDCRIYLNKAAAWTPA-QGNHPASKEA-APKTTSEAIRQAILE 606

Query: 608 GDRDGVTAIVESELAAGADPFDLVQTKLIPAINEVGVKYERREYFLPQLIRSAETMQTAF 667
           G+RDG+ A+ +  L  G   F +    + PAI  +G  + +R  F+P LI  A+ M+   
Sbjct: 607 GERDGIAALCQKGLDEGLSAFTIFLDIMTPAIRHLGDLFGQRVKFIPHLIAGADAMKKGV 666

Query: 668 RRLQPLLEEMRGAEVRPVIIMATVEGDIHDIGKNIVSLMLGNHGFEVVDLGKDVKAETIV 727
             LQP LE     E +  ++ ATV+GDIHDIGKNI  LML N GF V+DLG++V  + I+
Sbjct: 667 EVLQPHLEADGPVEPKGCVVFATVKGDIHDIGKNICILMLRNFGFSVIDLGRNVPLDDIL 726

Query: 728 DAAETHGARIIGLSALMTTTMVRMEDTVKLVRARGLDVKVIVGGAVVTKAFADAIGADGY 787
            AAE H A+II LSALMTTTM++M+  ++ +R + L  KV+VGGAVVT  F+  I ADGY
Sbjct: 727 AAAEKHQAQIIALSALMTTTMMQMKTAIETIREKNLPYKVMVGGAVVTPKFSTEIKADGY 786

Query: 788 SADAVEAVRLAKSLLA 803
             D  + V LA+ L++
Sbjct: 787 GKDVGDVVPLAEKLIS 802


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: 1579
Number of extensions: 82
Number of successful extensions: 9
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: 828
Length adjustment: 41
Effective length of query: 763
Effective length of database: 787
Effective search space:   600481
Effective search space used:   600481
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.

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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