Alignments for a candidate for metH in Nitriliruptor alkaliphilus DSM 45188

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Nitriliruptor alkaliphilus DSM 45188

Align cobalamin-dependent methionine synthase (EC 2.1.1.13) (characterized)
to candidate WP_083442071.1 NITAL_RS03045 methionine synthase

Query= metacyc::G18NG-11090-MONOMER
         (1221 letters)



>NCBI__GCF_000969705.1:WP_083442071.1
          Length = 1207

 Score = 1121 bits (2899), Expect = 0.0
 Identities = 623/1246 (50%), Positives = 810/1246 (65%), Gaps = 93/1246 (7%)

Query: 27   LIGDGAMGTQLQGFDLDVEKDF--LDLEGCNEILNDTRPDVLRQIHRAYFEAGADLVETN 84
            ++ DGAMGT LQ  DL  + DF   DLEGCNEIL DTRPDV+  +HR++ E G D VET+
Sbjct: 1    MVLDGAMGTSLQDADLTAD-DFGSSDLEGCNEILVDTRPDVVEAVHRSFLEVGCDAVETD 59

Query: 85   TFGCNLPNLADYDIADRCRELAYKGTAVAREVADEMG-PGRNGMRRFVVGSLGPGTKLP- 142
            TFG     L +Y + DR  EL  K   +AR  AD    P R    RFV+GS+GPGT+ P 
Sbjct: 60   TFGGAPWVLDEYGLGDRTEELNEKAALLARAAADAYSTPDRP---RFVIGSIGPGTRSPT 116

Query: 143  -SLGHAPYAD--------LRGHYKEAALGIIDGGGDAFLIETAQDLLQVKAAVHGVQDAM 193
             SLG  P           +   Y+     ++DGG D   IET+ DLLQ+KAAV    D  
Sbjct: 117  LSLGKDPATTKDFIDVPTMEDGYRRQIRALLDGGTDVIWIETSFDLLQIKAAVAAANDVF 176

Query: 194  AELDTFLPIICHVTVETT-GTMLMGSEIGAALTALQPLGIDMIGLNCATGPDEMSEHLRY 252
             E  + +P+    T+E    TML+G+E  AAL AL PL +D++G+NCATGP++M EH+R 
Sbjct: 177  EERGSRVPLAVQFTIEKDINTMLLGTEPLAALAALDPLSLDLLGMNCATGPEDMREHVRT 236

Query: 253  LSKHADIPVSVMPNAGLPVLGKNGAEYPLEAEDLAQALAGFVSEYGLSMVGGCCGTTPEH 312
            LS+ + +P+SV+PNAG+P L      YPL+   LAQA   FV++ G+S+VGGCCGTTP+H
Sbjct: 237  LSRASRLPLSVLPNAGMPELIDGATVYPLDPAGLAQAQREFVTDLGVSIVGGCCGTTPDH 296

Query: 313  IRAVRDAVVGV-----------------------PEQETSTLTKIPAGPVEQASREVEKE 349
            I AV +AV  +                       P+       + P G        VE  
Sbjct: 297  IAAVVEAVADLAPRPRVLDRPDQAKPGFAGSLVLPDASGGRPMEGPGGAPAPTPVTVEYR 356

Query: 350  DSVASLYTSVPLSQETGISMIGERTNSNGSKAFREAMLSGDWEKCVDIAKQQTRDGAHML 409
             S+ASLY++VPL Q+T    IGER N+NGSKAFRE +L+ DW+  V +AK QTR+GAH+L
Sbjct: 357  PSLASLYSAVPLEQDTAFLAIGERANANGSKAFREILLAEDWDGTVALAKSQTREGAHVL 416

Query: 410  DLCVDYVGRDGTADMATLAALLATSSTLPIMIDSTEPEVIRTGLEHLGGRSIVNSVNFED 469
            D+CVDYVGR+G  DM  +    AT STLP++IDST+ +V+   L  LGGR+++NSVN ED
Sbjct: 417  DVCVDYVGREGAPDMIEVVDRYATQSTLPLVIDSTQSDVVEAALLRLGGRAVINSVNLED 476

Query: 470  GDGPESRYQRIMKLVKQHGAAVVALTIDEEGQARTAEHKVRIAKRLIDDITGSYGLDIKD 529
            G    ++   ++ L K++GAAVV L IDEEGQARTA+ KV++++R+ +     +GL+ +D
Sbjct: 477  G---RNKADLLLPLAKRYGAAVVVLAIDEEGQARTADWKVQVSQRVAEIAIDEFGLEPQD 533

Query: 530  IVVDCLTFPISTGQEETRRDGIETIEAIRELKKLYPEIHTTLGLSNISFGLNPAARQVLN 589
            ++ DCLTFP+ +GQE+ RRD +ET+EAI  + +L P   TTLG+SN+SFGL+ AARQVLN
Sbjct: 534  LIFDCLTFPLGSGQEDLRRDALETLEAIERISQLIPGCGTTLGVSNVSFGLSAAARQVLN 593

Query: 590  SVFLNECIEAGLDSAIAHSSKILPMNRIDDRQREVALDMVYDRRTE------------DY 637
            SVFL E ++ GL SAI H  KILP++RI D Q   ALD+V+DRR E             Y
Sbjct: 594  SVFLKEAVDRGLTSAIVHPGKILPLHRIPDEQVATALDLVHDRRGEAGTSEGAATQGAKY 653

Query: 638  DPLQEFMQLFEGVSAADAKDARAEQLAAMPLFERLAQRIIDGDKNGLEDDLEAGMKEKSP 697
            DPL  FM LFEG    D +    E+LA++P+ +RL +RI+DG++ GLE DL+  + +  P
Sbjct: 654  DPLHHFMALFEGEVEQDDR----EELASLPIDQRLHRRIVDGEREGLEADLDEALADTPP 709

Query: 698  IAIINEDLLNGMKTVGELFGSGQMQLPFVLQSAETMKTAVAYLEPFMEEEAEATGSAQAE 757
            + IIN  LL GMK VG+LF SG MQLPFVLQSAE MKTAVAYLEP +E  A   GS+   
Sbjct: 710  LDIINTHLLGGMKEVGQLFASGAMQLPFVLQSAEAMKTAVAYLEPHIE--ASGGGSSN-- 765

Query: 758  GKGKIVVATVKGDVHDIGKNLVDIILSNNGYDVVNLGIKQPLSAMLEAAEEHKADVIGMS 817
             KG IV+ATVKGDVHDIGKNLVDIIL NNGY+V NLGIKQP+  +L AAEEH  D IGMS
Sbjct: 766  -KGSIVLATVKGDVHDIGKNLVDIILRNNGYEVHNLGIKQPIDTILHAAEEHGVDAIGMS 824

Query: 818  GLLVKSTVVMKENLEEMNNAGASNYPVILGGAALTRTYVENDLNEVYTGEVYYARDAFEG 877
            GLLVKSTV+MK+NLEEMN  G + YPV+LGGAALTR YVE+DL  +Y G+V+Y +DAFEG
Sbjct: 825  GLLVKSTVIMKDNLEEMNVRGLARYPVLLGGAALTRGYVEDDLRAIYEGQVFYCKDAFEG 884

Query: 878  LRLMDEVMAEKRGEGLDPNSPEAIEQAKKKAERKARNERSRKIAAERKANAAPVIVPE-- 935
            L ++D VMA     G DP    A E  +   ER+ R    RK   +R   A P +  +  
Sbjct: 885  LSVLDTVMA-----GDDP----AAEIPEGFGERRER----RKPTRQRAPEAPPAVDAQGR 931

Query: 936  -RSDVSTDTPTAAPPFWGTRIVKGLPLAEFLGNLDERALFMGQWGLKSTRGNEGPSYEDL 994
             RS V+TD    APPFWG R+V+G+P+ E    L+E ALF  QWG     G+    Y  L
Sbjct: 932  PRSTVATDVDVPAPPFWGQRVVRGVPVDEVAPLLNEVALFRNQWGFGPGDGSP-DEYAQL 990

Query: 995  VETEGRPRLRYWLDRLKSEGILDHVALVYGYFPAVAEGDDVVILESPDPHAAERMRFSFP 1054
            +E + RP LR WL R K+E ++    +VYGY+PA  +GDD+V+     P   E +RF+FP
Sbjct: 991  LEEKARPVLREWLARAKAEKVIT-PEVVYGYYPANGDGDDLVVWHPDAPLQRELVRFAFP 1049

Query: 1055 RQQRGRFLCIADFIRPREQAVKDGQVDVMPFQLVTMGNPIADFANELFAANEYREYLEVH 1114
            RQ RGRFL I DF RP    V  G+VDV+  Q+VTMG+ I++ A +LFA + Y++YL  H
Sbjct: 1050 RQDRGRFLNIGDFFRP----VDSGEVDVLGVQVVTMGHRISEVAQDLFAQDRYQDYLFAH 1105

Query: 1115 GIGVQLTEALAEYWHSRVRSELKLNDGGSVADFDPEDKTKFFDLDYRGARFSFGYGSCPD 1174
            G GV++ EALAE WH R+R EL       +A  D      +F   YRG+R+SFGY +CPD
Sbjct: 1106 GFGVEMAEALAELWHRRIREEL------GIAGHDGPTPQDWFRQGYRGSRYSFGYAACPD 1159

Query: 1175 LEDRAKLVELLEPGRIGVELSEELQLHPEQSTDAFVLYHPEAKYFN 1220
            LE + +L EL++P +IGVEL+EE  LHPEQST A V++HPEAKYFN
Sbjct: 1160 LEMQEQLFELVDPSQIGVELTEEFMLHPEQSTSAIVVHHPEAKYFN 1205


Lambda     K      H
   0.316    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: 3614
Number of extensions: 212
Number of successful extensions: 16
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: 1221
Length of database: 1207
Length adjustment: 47
Effective length of query: 1174
Effective length of database: 1160
Effective search space:  1361840
Effective search space used:  1361840
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 (21.6 bits)
S2: 59 (27.3 bits)

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

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Candidates (tab-delimited)
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