Alignments for a candidate for metH in Rhodomicrobium vannielii ATCC 17100

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Rhodomicrobium vannielii ATCC 17100

Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_013420197.1 RVAN_RS13110 methionine synthase

Query= CharProtDB::CH_090726
         (1227 letters)



>NCBI__GCF_000166055.1:WP_013420197.1
          Length = 893

 Score = 1043 bits (2698), Expect = 0.0
 Identities = 531/883 (60%), Positives = 659/883 (74%), Gaps = 11/883 (1%)

Query: 351  GEDSLFVNVGERTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAE 410
            G    F+ VGERTNVTGSAKF++LI+   Y  AL VAR+QVE+GA ++D+NMDEG+LD+E
Sbjct: 3    GTGQQFIIVGERTNVTGSAKFRKLIEAGDYDAALSVAREQVESGANVLDVNMDEGLLDSE 62

Query: 411  AAMVRFLNLIAGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHA 470
             AM  FL+LIA EPDI+RVP+MIDSSKW VIE GLKC+QGK IVNSIS+KEG + F+ HA
Sbjct: 63   KAMTTFLHLIASEPDISRVPVMIDSSKWTVIEAGLKCVQGKPIVNSISLKEGEEPFLDHA 122

Query: 471  KLLRRYGAAVVVMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVAT 530
            K + RYGAA VVMAFDE GQADT  RK+ ICRRA+K+LTE++GF PEDIIFDPN+FAV T
Sbjct: 123  KKVMRYGAAAVVMAFDEVGQADTEERKVSICRRAFKLLTEKIGFSPEDIIFDPNVFAVGT 182

Query: 531  GIEEHNNYAQDFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRN 590
            GI++HNNY  DFI A   I++E+PH  +SGGVSN+SFSFRGN+PVR+A+H VFLY+AI+ 
Sbjct: 183  GIDDHNNYGVDFIEATRRIRQEMPHCHVSGGVSNLSFSFRGNEPVRQAMHTVFLYHAIKA 242

Query: 591  GMDMGIVNAGQLAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQ 650
            GMDMGIVNAGQL +YDDL  ELR+  EDV+LNRR D T+RLLE A++++G  +     A 
Sbjct: 243  GMDMGIVNAGQLGVYDDLNPELRELAEDVVLNRRADATDRLLEAADRFKGGGSKKA--AP 300

Query: 651  QAEWRSWEVNKRLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGE 710
               WR   V  RL+++L+ GIT++I+ DTEEAR    RP+ VIEGPLM GMN VGDLFG 
Sbjct: 301  DLTWRERSVADRLKHALIHGITDYIDADTEEARASLGRPMHVIEGPLMGGMNAVGDLFGA 360

Query: 711  GKMFLPQVVKSARVMKQAVAYLEPFIEASKEQG----KTNGKMVIATVKGDVHDIGKNIV 766
            GKMFLPQVVKSARVMK+AVAYL PF+E  K  G    +  G++++ATVKGDVHDIGKNIV
Sbjct: 361  GKMFLPQVVKSARVMKKAVAYLMPFMEEEKAAGGGEAQAAGRIIMATVKGDVHDIGKNIV 420

Query: 767  GVVLQCNNYEIVDLGVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGF 826
            GVVLQCNNYE++DLGVMVP ++IL  A+E  AD+IGLSGLITPSLDEMV VA EMERQGF
Sbjct: 421  GVVLQCNNYEVIDLGVMVPPQQILDAAREHKADVIGLSGLITPSLDEMVFVASEMERQGF 480

Query: 827  TIPLLIGGATTSKAHTAVKIEQNYS-GPTVYVQNASRTVGVVAALLSDTQRDDFVARTRK 885
             +PLLIGGATTS+ HTAVKI  NY+ G  VYV +ASR VGVV++LL   +RD +V + R+
Sbjct: 481  EVPLLIGGATTSQVHTAVKIAPNYARGQAVYVTDASRAVGVVSSLLGG-ERDTYVGKLRE 539

Query: 886  EYETVRIQHGRKKPRTPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVE-ASIETLRNY 944
             Y  V + H R +     +TL  AR N F   W  Y PP    +G + +E   + TL  Y
Sbjct: 540  TYTKVALAHERGRAAKMRLTLAQARANRFDPGWHGYVPPKPSFIGARALENYDLATLVPY 599

Query: 945  IDWTPFFMTWSLAGKYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPA 1004
            IDWTPFF  W + G YP IL D   G  A  L++DA  ML ++  E+      V G +PA
Sbjct: 600  IDWTPFFSAWEMKGTYPGILTDNKYGDAASSLYRDAQAMLAQIVEERWFRANAVYGFWPA 659

Query: 1005 NRV-GDDIEIYRDETRTHVINVSHHLRQQTEK-TGFANYCLADFVAPKLSGKADYIGAFA 1062
            N +  DDI IY D++RT  I     LRQQ  + +G AN  L+DF+AP+ +  ADYIG FA
Sbjct: 660  NALEDDDIAIYADDSRTETIATFRTLRQQIARDSGRANIALSDFIAPEATNIADYIGGFA 719

Query: 1063 VTGGLEEDALADAFEAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSN 1122
            VT G+ ED +A+ F   +DDY++I+VKALADRLAEAFAE+LH RVR+ +WGYA +E L+ 
Sbjct: 720  VTAGIGEDVIAERFSRANDDYSRILVKALADRLAEAFAEHLHARVRREFWGYAADEALAP 779

Query: 1123 EELIRENYQGIRPAPGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYF 1182
             EL+ E Y+GIRPAPGYPA P+HTEK  +++LL+  + TG+ LTES+AM P ASVSG YF
Sbjct: 780  HELLAETYRGIRPAPGYPAQPDHTEKTPLFDLLDATRATGIALTESYAMTPPASVSGLYF 839

Query: 1183 SHPDSKYYAVAQIQRDQVEDYARRKGMSVTEVERWLAPNLGYD 1225
            SHP+S Y+ V +I+RDQVEDYARRKG +V E ERWLAP L Y+
Sbjct: 840  SHPESYYFGVGKIERDQVEDYARRKGWTVAEAERWLAPILNYE 882


Lambda     K      H
   0.318    0.134    0.391 

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: 2599
Number of extensions: 101
Number of successful extensions: 8
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: 1227
Length of database: 893
Length adjustment: 45
Effective length of query: 1182
Effective length of database: 848
Effective search space:  1002336
Effective search space used:  1002336
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: 58 (26.9 bits)

Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_013417717.1 RVAN_RS00095 5-methyltetrahydrofolate--homocysteine methyltransferase

Query= CharProtDB::CH_090726
         (1227 letters)



>NCBI__GCF_000166055.1:WP_013417717.1
          Length = 353

 Score =  455 bits (1171), Expect = e-132
 Identities = 221/345 (64%), Positives = 272/345 (78%)

Query: 2   SSKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKP 61
           + ++  L+A   ERIL+LDGGMGTMIQ ++  EAD+RGERF DWP DLKGNNDLLVL++P
Sbjct: 4   TDRIAALKAAAKERILILDGGMGTMIQRHKPTEADYRGERFKDWPSDLKGNNDLLVLTQP 63

Query: 62  EVIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTAR 121
            +I  +H AYFEAGADIIETN+FN+  I+MADY ME+LSAEIN AAAKLAR  AD +TA+
Sbjct: 64  AIIKGVHEAYFEAGADIIETNSFNAQRISMADYGMEALSAEINLAAAKLAREAADAYTAK 123

Query: 122 TPEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIE 181
           TPEKPR+VAG +GPTNRTAS+SPDVN+P FRNI+FD LV AY E T+AL+EGG D ILIE
Sbjct: 124 TPEKPRFVAGSIGPTNRTASLSPDVNNPGFRNISFDELVDAYGEQTRALIEGGVDAILIE 183

Query: 182 TVFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEAL 241
           T+FDTLNAKAA FAVK  F+  GVELP+M+SGT+TD SGR LSGQT EAF+ SLRH +  
Sbjct: 184 TIFDTLNAKAAGFAVKKAFDETGVELPLMLSGTVTDLSGRNLSGQTPEAFWYSLRHLKPF 243

Query: 242 TFGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQA 301
           + G+NCA G ++LR  V  LS++A+ Y++ + NAGLPN  GEYD   + MA+ +  WA  
Sbjct: 244 SVGMNCAFGAEQLRPPVALLSKVADTYMSVYANAGLPNEMGEYDETPEDMARAMASWAAD 303

Query: 302 GFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLE 346
           G LNIVGGCCGTTP HIAA+++AV    PR++PE+    RLSGLE
Sbjct: 304 GLLNIVGGCCGTTPDHIAAIAKAVAPYPPRRIPELEPRLRLSGLE 348


Lambda     K      H
   0.318    0.134    0.391 

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: 1125
Number of extensions: 44
Number of successful extensions: 1
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: 1227
Length of database: 353
Length adjustment: 38
Effective length of query: 1189
Effective length of database: 315
Effective search space:   374535
Effective search space used:   374535
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: 54 (25.4 bits)

Align candidate WP_013420197.1 RVAN_RS13110 (methionine synthase)
to HMM TIGR02082 (metH: methionine synthase (EC 2.1.1.13))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR02082.hmm
# target sequence database:        /tmp/gapView.611.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02082  [M=1182]
Accession:   TIGR02082
Description: metH: methionine synthase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                 Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
          0 1204.6   0.0          0 1204.3   0.0    1.0  1  lcl|NCBI__GCF_000166055.1:WP_013420197.1  RVAN_RS13110 methionine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000166055.1:WP_013420197.1  RVAN_RS13110 methionine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1204.3   0.0         0         0     341    1182 .]       6     849 ..       2     849 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1204.3 bits;  conditional E-value: 0
                                 TIGR02082  341 ssfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmkkllsll 407 
                                                ++f+++GeRtnv+Gs+kfrkli+a+dy++al++a++qve+Ga++lD+n+De+llD+e++m+++l+l+
  lcl|NCBI__GCF_000166055.1:WP_013420197.1    6 QQFIIVGERTNVTGSAKFRKLIEAGDYDAALSVAREQVESGANVLDVNMDEGLLDSEKAMTTFLHLI 72  
                                                68***************************************************************** PP

                                 TIGR02082  408 asepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavvvmafDe 474 
                                                asepdi++vP+m+Dss++ v+eaGLk++qGk ivnsislk+Gee Fl++ak++ +yGaa+vvmafDe
  lcl|NCBI__GCF_000166055.1:WP_013420197.1   73 ASEPDISRVPVMIDSSKWTVIEAGLKCVQGKPIVNSISLKEGEEPFLDHAKKVMRYGAAAVVMAFDE 139 
                                                ******************************************************************* PP

                                 TIGR02082  475 eGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieaireikeelP 541 
                                                 Gqa+t ++k+ i++Ra+klltek+gf pediifDpn+++++tGi++h++y++dfiea+r+i++e+P
  lcl|NCBI__GCF_000166055.1:WP_013420197.1  140 VGQADTEERKVSICRRAFKLLTEKIGFSPEDIIFDPNVFAVGTGIDDHNNYGVDFIEATRRIRQEMP 206 
                                                ******************************************************************* PP

                                 TIGR02082  542 dakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrevvedlil 608 
                                                ++++sgGvsn+sFs+rgn++vR+a+h+vFLy+aikaG+Dmgivnag+l vydd+++elre++ed++l
  lcl|NCBI__GCF_000166055.1:WP_013420197.1  207 HCHVSGGVSNLSFSFRGNEPVRQAMHTVFLYHAIKAGMDMGIVNAGQLGVYDDLNPELRELAEDVVL 273 
                                                ******************************************************************* PP

                                 TIGR02082  609 drrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleearkklka 675 
                                                +rr +at++Lle a+++kg  +k  k a    wr+ +v +RL++al++G++++i++d+eear  l +
  lcl|NCBI__GCF_000166055.1:WP_013420197.1  274 NRRADATDRLLEAADRFKGGGSK--KAAPDLTWRERSVADRLKHALIHGITDYIDADTEEARASLGR 338 
                                                ********************999..778999************************************ PP

                                 TIGR02082  676 pleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeed....kskGkivl 738 
                                                p+++iegpL+ Gm+ vGdLFG+GkmfLPqvvksarvmkkavayL+P++e+ek++     +++G+i++
  lcl|NCBI__GCF_000166055.1:WP_013420197.1  339 PMHVIEGPLMGGMNAVGDLFGAGKMFLPQVVKSARVMKKAVAYLMPFMEEEKAAGggeaQAAGRIIM 405 
                                                ****************************************************988888899****** PP

                                 TIGR02082  739 atvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksldemveva 805 
                                                atvkGDvhDiGkniv+vvL+cn+yev+dlGv+vP ++il+aa+++kaDviglsGLi++sldemv+va
  lcl|NCBI__GCF_000166055.1:WP_013420197.1  406 ATVKGDVHDIGKNIVGVVLQCNNYEVIDLGVMVPPQQILDAAREHKADVIGLSGLITPSLDEMVFVA 472 
                                                ******************************************************************* PP

                                 TIGR02082  806 eemerrgvkiPlllGGaalskahvavkiaekY.kgevvyvkdaseavkvvdkllsekkkaeelekik 871 
                                                 emer+g+++Pll+GGa++s+ h+avkia++Y +g+ vyv+das+av vv++ll  + ++++++k++
  lcl|NCBI__GCF_000166055.1:WP_013420197.1  473 SEMERQGFEVPLLIGGATTSQVHTAVKIAPNYaRGQAVYVTDASRAVGVVSSLLGGE-RDTYVGKLR 538 
                                                ********************************558********************99.5******** PP

                                 TIGR02082  872 eeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieellkyiDwka 937 
                                                e+y ++   +++ +  ++ l++++ar ++f++ ++  + +p+p f+G + le++ +++l++yiDw++
  lcl|NCBI__GCF_000166055.1:WP_013420197.1  539 ETYTKVALAHERGRAAKMRLTLAQARANRFDPGWH-GYVPPKPSFIGARALENYdLATLVPYIDWTP 604 
                                                ***********************************.9****************************** PP

                                 TIGR02082  938 lFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaq.svgddieiyt 1003
                                                +F +We++g+yp il+d+++g  a  l++da+++l ++++e+  ra++v+G++Pa+  ++ddi+iy+
  lcl|NCBI__GCF_000166055.1:WP_013420197.1  605 FFSAWEMKGTYPGILTDNKYGDAASSLYRDAQAMLAQIVEERWFRANAVYGFWPANaLEDDDIAIYA 671 
                                                ********************************************************456789***** PP

                                 TIGR02082 1004 detvsqetkpiatvrekleqlrqqsdr.ylclaDfiaskesGikDylgallvtaglgaeelakklea 1069
                                                d+++   t++iat+r+ ++q+ ++s+r +++l+Dfia+ ++ i+Dy+g ++vtag+g++ +a+++  
  lcl|NCBI__GCF_000166055.1:WP_013420197.1  672 DDSR---TETIATFRTLRQQIARDSGRaNIALSDFIAPEATNIADYIGGFAVTAGIGEDVIAERFSR 735 
                                                9988...9*******************99************************************** PP

                                 TIGR02082 1070 keddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafGYpacPdh 1136
                                                 +ddy+ ilvkaladrlaea+ae+lh rvR+e+wgya++e+l+ ++ll e YrGirpa+GYpa+Pdh
  lcl|NCBI__GCF_000166055.1:WP_013420197.1  736 ANDDYSRILVKALADRLAEAFAEHLHARVRREFWGYAADEALAPHELLAETYRGIRPAPGYPAQPDH 802 
                                                ******************************************************************* PP

                                 TIGR02082 1137 tekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfav 1182
                                                tek+ l++Ll+a r +G+ ltes+a++P asvsglyf+hpe+ Yf v
  lcl|NCBI__GCF_000166055.1:WP_013420197.1  803 TEKTPLFDLLDATRaTGIALTESYAMTPPASVSGLYFSHPESYYFGV 849 
                                                **************9******************************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (893 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.06u 0.02s 00:00:00.08 Elapsed: 00:00:00.08
# Mc/sec: 12.60
//
[ok]

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