Alignments for a candidate for metH in Geobacter metallireducens GS-15

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Geobacter metallireducens GS-15

Align Methionine synthase (cobalamin-dependent) (EC 2.1.1.13) (characterized)
to candidate WP_004512245.1 GMET_RS02740 5-methyltetrahydrofolate--homocysteine methyltransferase

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



>NCBI__GCF_000012925.1:WP_004512245.1
          Length = 804

 Score =  607 bits (1566), Expect = e-178
 Identities = 362/810 (44%), Positives = 492/810 (60%), Gaps = 23/810 (2%)

Query: 4   FRQALRAGRRLLFDGGLGTMLQARGLPAGVSPEQFCLDRPDVLRGIHADYVRAGADILTT 63
           F QA++  R L+ DG +GTMLQ RGL  G SPE+  L  PDV+ G+H +Y+ AGADI+ T
Sbjct: 5   FLQAIKE-RVLVLDGAMGTMLQERGLRPGQSPEELNLTMPDVVAGVHREYLEAGADIIVT 63

Query: 64  NTFGGSRFKL---GDGFDVVDFNRRMAAIAREAADASGRQAFVAGSIGPTGHFVKPLGEV 120
           NTFGG+R KL   G    V + N R   IARE     G +A+VA S+GPTG FV+P+GE 
Sbjct: 64  NTFGGTRPKLEHYGLEEKVREINARAVEIAREVC---GDRAYVAASMGPTGLFVEPVGEA 120

Query: 121 EPAALVAAFREQVRGLVAGGADLLMIETQFDLAEARAAVVAAR-AECSLPIAVSMTFEN- 178
              A+ A FREQ   L+  GADL+ +ET  D+ E RAAV+A R    ++P+   +TF+N 
Sbjct: 121 TFDAMAAFFREQAAALIEAGADLITLETFLDIKEIRAAVIAIREVSPTIPVIAQLTFDNE 180

Query: 179 GVSLTGSTPEVFVATMLNLGVDLLGTNCSAGPDQMHDVVASLLASASVPVLVEPNAGLPE 238
           G ++ G+ PE    T+   G D++G+NC  GPD +  V+ ++     +P++ + NAGLP+
Sbjct: 181 GRTVLGTPPEAAAVTLAAAGADIVGSNCGLGPDGICAVLGAMRGVTRLPLISQANAGLPK 240

Query: 239 LIDGKTVFRLPPAPFAEKTAAFAAMGARVLGGCCGTTPDHIAALRQAVADIPATLPVDSG 298
           L+DGKTVF   P            +  RV+GGCCGTTP HI A+++A+A    +   D G
Sbjct: 241 LVDGKTVFPGTPDDMTAFHDRMLGLNVRVIGGCCGTTPTHIRAIKEALAGRDQSWR-DCG 299

Query: 299 --VGIV-LTTRSHLVRVGGDAPVRIIGERINPTGKKQLIAELQAGDFSLALRFSDEQVEA 355
              G+  L +R+ +V +GG  P  IIGERINPTGKK    EL+ G  +   R + EQ  A
Sbjct: 300 PPAGVTFLASRTSVVALGGGLPAAIIGERINPTGKKAFAQELREGKITTIRREAMEQTAA 359

Query: 356 GAPILDVNVGAPMVDEEVLLPDLVQRLITRHGVPLSIDSSNAAAIERALPYCPGSTLVNS 415
           GA +LDVNVG P +DE   +   V  +     VPL +DSS+ AA+ER L    G  LVNS
Sbjct: 360 GAHLLDVNVGTPGIDEPAAMERAVFCVTGSVAVPLVLDSSDPAALERGLKAADGKVLVNS 419

Query: 416 ISGEPGRMERLGPLCRDHGAPFILLPLKGRKLPVAATERIAIIEELLVQAEGLGIPRRLV 475
           ++GE   +ER+ PL + +GA  I L L    +P  A  R+A+ E ++  AEG GI R  V
Sbjct: 420 VNGETKSIERVLPLVKKYGAAVIGLALDETGIPETAEGRLAVAERIVAAAEGRGISRNDV 479

Query: 476 MVDVLALAVSSKAEAARQCLETIRWC-TANGFATTIGLSNISFGLPARELLNGTFLAMAA 534
           ++D L L VS++ + A + L  +R      G  T +G+SNISFGLP R L++  F AMA 
Sbjct: 480 VIDCLTLTVSAEQKRAMETLRAVRLVKEIIGCPTVLGVSNISFGLPRRPLISSAFFAMAL 539

Query: 535 GAGLSSCIAHPGNGRIRETVACADVLLARDANAERFIDAYAAWTPATQGGPVASGPGLAS 594
            AGL + I +P    +      A VLL RD +A  +I AYA  T A    P ASG  L  
Sbjct: 540 AAGLDAAIVNPKEEEMMAAWRSAMVLLNRDPSAAAYIAAYAG-TAAAAPEPAASGEALDI 598

Query: 595 QPPATTLEEAVVKGDRDGVTAIVESELAAGADPFDLVQTKLIPAINEVGVKYERREYFLP 654
           +     L+ AV+ GDR+ + A+VE  L  G +P  +    L+P + EVG ++E+   FLP
Sbjct: 599 R---ERLKRAVITGDRENIVALVEEALGQGLEPLQVSNEGLLPGLEEVGRRFEKNLVFLP 655

Query: 655 QLIRSAETMQTAFRRLQPLLEEMRG--AEVRPVIIMATVEGDIHDIGKNIVSLMLGNHGF 712
           Q+++SA+TMQ AF RL+   E M+G  A  R  I+MATVEGDIHDIGKNIV  +L NHGF
Sbjct: 656 QVMQSADTMQAAFGRLR---EVMKGSPAASRGKILMATVEGDIHDIGKNIVCTLLENHGF 712

Query: 713 EVVDLGKDVKAETIVDAAETHGARIIGLSALMTTTMVRMEDTVKLVRARGLDVKVIVGGA 772
           EV+DLGK+V A+ IV  A   G   +GLSALMTTTM  ME+ +  ++  G+    +VGGA
Sbjct: 713 EVIDLGKNVPADRIVGKARELGVDAVGLSALMTTTMTEMENVIARLKEAGIRTFTMVGGA 772

Query: 773 VVTKAFADAIGADGYSADAVEAVRLAKSLL 802
           VVT+ +AD IGAD Y+ DA+EAV   K+LL
Sbjct: 773 VVTQEYADEIGADLYARDAMEAVARIKALL 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: 1658
Number of extensions: 91
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: 804
Length adjustment: 41
Effective length of query: 763
Effective length of database: 763
Effective search space:   582169
Effective search space used:   582169
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