Alignments for a candidate for metH in Pelobacter propionicus DSM 2379

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Pelobacter propionicus DSM 2379

Align Methionine synthase (cobalamin-dependent) (EC 2.1.1.13) (characterized)
to candidate WP_011735322.1 PPRO_RS07025 5-methyltetrahydrofolate--homocysteine methyltransferase

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



>NCBI__GCF_000015045.1:WP_011735322.1
          Length = 806

 Score =  605 bits (1560), Expect = e-177
 Identities = 360/813 (44%), Positives = 487/813 (59%), Gaps = 22/813 (2%)

Query: 1   MPDFRQALRAGRRLLFDGGLGTMLQARGLPAGVSPEQFCLDRPDVLRGIHADYVRAGADI 60
           M  F +A++  R L+ DG +GTMLQ RGL  G SPE+  L  PDV+  +H +Y+ AGADI
Sbjct: 1   MTPFLEAIQE-RVLILDGAMGTMLQERGLRPGQSPEELNLTMPDVVASVHREYIEAGADI 59

Query: 61  LTTNTFGGSRFKLGD-GFD--VVDFNRRMAAIAREAADASGRQAFVAGSIGPTGHFVKPL 117
           + TN+FGGSRFKL   G +  + + N R   IAR   +A GR A+V GS+GPTG FV+PL
Sbjct: 60  IITNSFGGSRFKLAHFGLEGRLAEINARAVEIAR--GEARGR-AYVGGSMGPTGQFVEPL 116

Query: 118 GEVEPAALVAAFREQVRGLVAGGADLLMIETQFDLAEARAAVVAAR-AECSLPIAVSMTF 176
           GEV    +  +FREQ   LV+ G DL+ +ET  D+ E RAAV+A R    ++PI   MTF
Sbjct: 117 GEVSFDRMKESFREQAEALVSAGVDLISLETFLDIKECRAAVIAIREVSPTIPIIAMMTF 176

Query: 177 E-NGVSLTGSTPEVFVATMLNLGVDLLGTNCSAGPDQMHDVVASLLASASVPVLVEPNAG 235
           + NG S+ G+ PE    T+   GVD++G+NC  G + +HD++  +    S+P++ + NAG
Sbjct: 177 DDNGRSVLGTPPEAAAITLAAAGVDIVGSNCGLGVEGIHDILVRMRRVTSLPLISQANAG 236

Query: 236 LPELIDGKTVFRLPPAPFAEKTAAFAAMGARVLGGCCGTTPDHIAALRQAVADIPATL-- 293
           LP L DG TVF   P    +      ++G RV+GGCCGTTP HI A+++A+A        
Sbjct: 237 LPILKDGITVFPGTPREMTDYHDRLISLGVRVIGGCCGTTPAHIRAMKEALAGRQQVWQE 296

Query: 294 PVDSGVGIVLTTRSHLVRVGGDAPVRIIGERINPTGKKQLIAELQAGDFSLALRFSDEQV 353
           P       +L+ R     VG      IIGERINPTGKK    ELQ G  S   R + EQ 
Sbjct: 297 PTHLEGMTLLSCRGGWTAVGPGQKTAIIGERINPTGKKLYSKELQEGKVSYIRREAMEQA 356

Query: 354 EAGAPILDVNVGAPMVDEEVLLPDLVQRLITRHGVPLSIDSSNAAAIERALPYCPGSTLV 413
           + GA +LD+NVGAP +DE V +   V       GVPL +DSS+ AA+E  L    G  L+
Sbjct: 357 QLGATLLDLNVGAPGIDEPVAMERAVFCASGAVGVPLVLDSSSPAALEAGLKAADGKVLI 416

Query: 414 NSISGEPGRMERLGPLCRDHGAPFILLPLKGRKLPVAATERIAIIEELLVQAEGLGIPRR 473
           NS+SGE   + R+ PL + +GA  I L L  + +P +A  R+AI   +   A   GIP +
Sbjct: 417 NSVSGEAKSLSRVLPLAKKYGAALIGLTLDAKGIPDSAEGRLAIARRIRNAARRQGIPDQ 476

Query: 474 LVMVDVLALAVSSKAEAARQCLETIRWCTAN-GFATTIGLSNISFGLPARELLNGTFLAM 532
            +++D L L VS++ + A + L TIR      G +T +G+SNISFGLP R L++ +F +M
Sbjct: 477 DIIIDCLTLTVSAEQKRAAETLRTIRLVKEKLGLSTVLGVSNISFGLPQRPLISSSFFSM 536

Query: 533 AAGAGLSSCIAHPGNGRIRETVACADVLLARDANAERFIDAYA-AWTPATQGGPVASGPG 591
           A  AGL + I +P    + +    A VLL RD  AE FI  Y      AT   PV+  P 
Sbjct: 537 AMAAGLDAAIINPREKAMMDAWRSAMVLLNRDPRAEAFIQTYRDEQAVATPAAPVSDAP- 595

Query: 592 LASQPPATTLEEAVVKGDRDGVTAIVESELAAGADPFDLVQTKLIPAINEVGVKYERREY 651
              Q     L +AV+ GDRDG+  +VE  LA G  P  +     +P + EVG ++E+  +
Sbjct: 596 ---QEIRQRLGQAVINGDRDGIIGLVEEALAQGLAPLQISNEGFLPGLEEVGRRFEKNIF 652

Query: 652 FLPQLIRSAETMQTAFRRLQPLLEEMRG--AEVRPVIIMATVEGDIHDIGKNIVSLMLGN 709
           FLPQ+++SA+TM   F RL+   EEM+G   E R  I+MATVEGDIHDIGKNIV  +L N
Sbjct: 653 FLPQVMQSADTMHAGFARLK---EEMKGQPLESRGRILMATVEGDIHDIGKNIVCTLLEN 709

Query: 710 HGFEVVDLGKDVKAETIVDAAETHGARIIGLSALMTTTMVRMEDTVKLVRARGLDVKVIV 769
           HGFEV D+GK+V A TIV  A   G   +GLSALMTTTM  M+  +K ++A G+    ++
Sbjct: 710 HGFEVFDIGKNVSAATIVAKAREFGVDAVGLSALMTTTMAEMDTVLKKLKAVGIKAFTMI 769

Query: 770 GGAVVTKAFADAIGADGYSADAVEAVRLAKSLL 802
           GGAVVT+ +AD IGAD Y+ DA+EAV   K LL
Sbjct: 770 GGAVVTQEYADRIGADIYARDAMEAVAKVKKLL 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: 1575
Number of extensions: 78
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: 804
Length of database: 806
Length adjustment: 41
Effective length of query: 763
Effective length of database: 765
Effective search space:   583695
Effective search space used:   583695
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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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