GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metH in Thioalkalivibrio halophilus HL17

Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_077243567.1 B1A74_RS01430 methionine synthase

Query= CharProtDB::CH_090726
         (1227 letters)



>NCBI__GCF_001995255.1:WP_077243567.1
          Length = 1263

 Score = 1655 bits (4287), Expect = 0.0
 Identities = 820/1247 (65%), Positives = 988/1247 (79%), Gaps = 24/1247 (1%)

Query: 1    MSSKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSK 60
            M++  + +   L ERIL+LDGGMGT IQ Y L EAD+RGERF DW  DLKGNNDLL L++
Sbjct: 1    MTATRQDIENALKERILILDGGMGTTIQLYELGEADYRGERFKDWESDLKGNNDLLSLTR 60

Query: 61   PEVIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTA 120
            P++I  IHN Y EAGADIIE NTFN T IAMADY ME L  E+N  +AKLAR  AD WTA
Sbjct: 61   PDIIEQIHNDYLEAGADIIEANTFNGTRIAMADYHMEDLVPELNRESAKLARKAADAWTA 120

Query: 121  RTPEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILI 180
            +TP+KPR+VAG+LGPTNRTASISPDVNDP  RN+ FD LVAAY+E+ +AL+EGG DL+LI
Sbjct: 121  KTPDKPRFVAGILGPTNRTASISPDVNDPGARNVDFDTLVAAYKEAAEALIEGGVDLLLI 180

Query: 181  ETVFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEA 240
            ETVFDTLNAKAA+FAVKT  + LG +LPIMISGTITDASGRTLSGQTTEAF+NS+RHA  
Sbjct: 181  ETVFDTLNAKAAIFAVKTLEDELGKDLPIMISGTITDASGRTLSGQTTEAFWNSVRHANP 240

Query: 241  LTFGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQ 300
            ++ GLNCALG  E+RQYV+ELSRIA+ +V+AHPNAGLPN FG+YD   + MA  +  WA+
Sbjct: 241  VSIGLNCALGAKEMRQYVEELSRIADTHVSAHPNAGLPNEFGDYDESPEQMAADVGPWAE 300

Query: 301  AGFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVG 360
             G LNI+GGCCGT P+HI AM  AVE   PRK+PE+  ACRLSGLEP NI +DSLFVNVG
Sbjct: 301  QGMLNIIGGCCGTLPEHIRAMREAVEKFPPRKVPEVSPACRLSGLEPCNITDDSLFVNVG 360

Query: 361  ERTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLI 420
            ERTNVTGS KF RLI+ E+Y  AL+VA  QVE GAQIID+NMDEGML+++ AMVRFLNL+
Sbjct: 361  ERTNVTGSRKFLRLIQNEEYDVALEVALNQVEGGAQIIDVNMDEGMLESQDAMVRFLNLL 420

Query: 421  AGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAV 480
            AGEPDIARVP+MIDSSK+++IE GLKC+QGK +VNSISMKEG + FI  A+L RRYGAA+
Sbjct: 421  AGEPDIARVPVMIDSSKFEIIEAGLKCVQGKPVVNSISMKEGEENFIKQAELCRRYGAAI 480

Query: 481  VVMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQ 540
            VVMAFDE GQAD   R++EIC RAYK+LTE+VGFP EDIIFDPNIFAVATGIEEHNNY  
Sbjct: 481  VVMAFDEDGQADNEQRRVEICTRAYKLLTEKVGFPAEDIIFDPNIFAVATGIEEHNNYGV 540

Query: 541  DFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAG 600
            DFI A   IK +LPHALISGGVSNVSFSFRGN+PVREAIHAVFLY+AI+ GMDMGIVNAG
Sbjct: 541  DFIEATRRIKNDLPHALISGGVSNVSFSFRGNEPVREAIHAVFLYHAIKAGMDMGIVNAG 600

Query: 601  QLAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVN 660
            QLA+YDD+  +L++AVEDV+LNRRDD T+RLLEL+E+Y+G         +  EWR WEV+
Sbjct: 601  QLAVYDDIDEKLKEAVEDVVLNRRDDATDRLLELSEEYKGQ--GGGKKEENLEWREWEVS 658

Query: 661  KRLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVK 720
            KRLE+SLVKGI  ++  DTEEARQ   RPI+VIEGPLMDGMNVVGDLFGEGKMFLPQVVK
Sbjct: 659  KRLEHSLVKGIDTYVVDDTEEARQAYDRPIQVIEGPLMDGMNVVGDLFGEGKMFLPQVVK 718

Query: 721  SARVMKQAVAYLEPFIEASKEQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDL 780
            SARVMK+AVA+L P+IEA K   + NGK+++ATVKGDVHDIGKNIVGVVLQCNN+E++D+
Sbjct: 719  SARVMKKAVAHLIPYIEAEKTGTENNGKILMATVKGDVHDIGKNIVGVVLQCNNFEVIDI 778

Query: 781  GVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKA 840
            GVM P  +IL+ AKE + D+IGLSGLITPSL+EM N A ++ER+G T PL+IGGATTS+A
Sbjct: 779  GVMQPGAEILKAAKEHDVDVIGLSGLITPSLEEMANFAADLEREGMTTPLMIGGATTSRA 838

Query: 841  HTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPR 900
            HTAVKIE NYSGP V+V++ASR VGV  +L+S   R+++ A  R+EYE +R+Q+  +K +
Sbjct: 839  HTAVKIEPNYSGPVVWVKDASRAVGVAQSLISPELRENYAAEIREEYEKLRVQNAGRKKK 898

Query: 901  TPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEV--------------------EASIET 940
               ++LE AR N    DW AY P     L  +++                    +  +  
Sbjct: 899  VQWLSLEKARANKPEIDWSAYAPAKPKALETEDLPGEPTVLHPHGDGSVLLRFDDFDLNK 958

Query: 941  LRNYIDWTPFFMTWSLAGKYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVG 1000
            ++ YIDWTPFF +W L   YPRILEDE VG EA++LFKD  +ML ++  EK +  RGVVG
Sbjct: 959  VKEYIDWTPFFHSWQLHAAYPRILEDEKVGEEARKLFKDGQEMLQRMIDEKWVTCRGVVG 1018

Query: 1001 LFPANRVG-DDIEIYRDETRTHVINVSHHLRQQTEK-TGFANYCLADFVAPKLSGKADYI 1058
             FPAN V  DDIE+Y DE R+ V+   HHLRQQTEK  G  ++ LADFV PK +G  DYI
Sbjct: 1019 FFPANSVDHDDIEVYTDENRSQVLKKLHHLRQQTEKRRGQPSHSLADFVMPKEAGGPDYI 1078

Query: 1059 GAFAVTGGLEEDALADAFEAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNE 1118
            GAFAV+ G + DA A+ +E  +DDY+ I+VK+LADRLAEAFAE +HE VRK YWGY  +E
Sbjct: 1079 GAFAVSAGGDVDAKAEEYEKANDDYHAILVKSLADRLAEAFAECMHEYVRKYYWGYVADE 1138

Query: 1119 NLSNEELIRENYQGIRPAPGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVS 1178
             L NE+LI E YQGIRPAPGYPACPEHTEKAT+WELL+ E++  M LTES+AM P ++VS
Sbjct: 1139 QLENEDLIEEKYQGIRPAPGYPACPEHTEKATLWELLQAEENADMTLTESYAMLPVSAVS 1198

Query: 1179 GWYFSHPDSKYYAVAQIQRDQVEDYARRKGMSVTEVERWLAPNLGYD 1225
            GWYF+HP+S+Y+ + ++ RDQVEDYA+RKGMS  E ERWLAPN+GYD
Sbjct: 1199 GWYFAHPESRYFGLGKVNRDQVEDYAKRKGMSFEEAERWLAPNIGYD 1245


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: 3925
Number of extensions: 158
Number of successful extensions: 5
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: 1263
Length adjustment: 48
Effective length of query: 1179
Effective length of database: 1215
Effective search space:  1432485
Effective search space used:  1432485
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: 59 (27.3 bits)

Align candidate WP_077243567.1 B1A74_RS01430 (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.3022210.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 1765.7   0.0          0 1765.4   0.0    1.0  1  NCBI__GCF_001995255.1:WP_077243567.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001995255.1:WP_077243567.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1765.4   0.0         0         0       1    1181 [.      12    1211 ..      12    1212 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1765.4 bits;  conditional E-value: 0
                             TIGR02082    1 lnkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDivetn 70  
                                            l++ril+lDG+mGt++q ++L ead+rge ++d++++lkGnndlL+lt+P++i++ih++y+eaGaDi+e n
  NCBI__GCF_001995255.1:WP_077243567.1   12 LKERILILDGGMGTTIQLYELGEADYRGErFKDWESDLKGNNDLLSLTRPDIIEQIHNDYLEAGADIIEAN 82  
                                            579******************************************************************** PP

                             TIGR02082   71 tFnsteialadYdledkayelnkkaaklarevadeft.ltpekkRfvaGslGPtnklatlspdverpefrn 140 
                                            tFn+t ia+adY++ed++ eln+++aklar++ad +t +tp+k+RfvaG lGPtn++a++spdv++p+ rn
  NCBI__GCF_001995255.1:WP_077243567.1   83 TFNGTRIAMADYHMEDLVPELNRESAKLARKAADAWTaKTPDKPRFVAGILGPTNRTASISPDVNDPGARN 153 
                                            *********************************************************************** PP

                             TIGR02082  141 vtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgvivdksGrtLs 211 
                                            v++d+lv+aYke++++l++GGvDllLietvfDtlnakaa+fav+++ +e g++lPi+isg+i+d+sGrtLs
  NCBI__GCF_001995255.1:WP_077243567.1  154 VDFDTLVAAYKEAAEALIEGGVDLLLIETVFDTLNAKAAIFAVKTLEDELGKDLPIMISGTITDASGRTLS 224 
                                            *********************************************************************** PP

                             TIGR02082  212 GqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnalgeYdltpeelakal 282 
                                            Gqt+eaf +s++ha+ +++GLnCalGa+e+r++v+els++a++ vs++PnaGLPn++g+Yd+ pe++a+ +
  NCBI__GCF_001995255.1:WP_077243567.1  225 GQTTEAFWNSVRHANPVSIGLNCALGAKEMRQYVEELSRIADTHVSAHPNAGLPNEFGDYDESPEQMAADV 295 
                                            *********************************************************************** PP

                             TIGR02082  283 kefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsglealkiaqessfvniGeRtnva 353 
                                              +ae+g+lni+GGCCGt Pehira+ eav++  prk++e+ ++++lsgle+ +i+++s fvn+GeRtnv+
  NCBI__GCF_001995255.1:WP_077243567.1  296 GPWAEQGMLNIIGGCCGTLPEHIRAMREAVEKFPPRKVPEVSPACRLSGLEPCNITDDSLFVNVGERTNVT 366 
                                            *********************************************************************** PP

                             TIGR02082  354 GskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmkkllsllasepdiakvPlmlDsse 424 
                                            Gs+kf +li++e+y+ al++a +qve Gaqi+D+n+De++l+++ +m+++l+lla+epdia+vP+m+Dss+
  NCBI__GCF_001995255.1:WP_077243567.1  367 GSRKFLRLIQNEEYDVALEVALNQVEGGAQIIDVNMDEGMLESQDAMVRFLNLLAGEPDIARVPVMIDSSK 437 
                                            *********************************************************************** PP

                             TIGR02082  425 fevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavvvmafDeeGqartadkkieiakRaykll 495 
                                            fe++eaGLk++qGk +vnsis+k+Gee+F+++a+l ++yGaa+vvmafDe+Gqa++ ++++ei++Raykll
  NCBI__GCF_001995255.1:WP_077243567.1  438 FEIIEAGLKCVQGKPVVNSISMKEGEENFIKQAELCRRYGAAIVVMAFDEDGQADNEQRRVEICTRAYKLL 508 
                                            *********************************************************************** PP

                             TIGR02082  496 tekvgfppediifDpniltiatGieehdryaidfieaireikeelPdakisgGvsnvsFslrgndavReal 566 
                                            tekvgfp+ediifDpni+++atGieeh++y++dfiea+r+ik++lP+a isgGvsnvsFs+rgn++vRea+
  NCBI__GCF_001995255.1:WP_077243567.1  509 TEKVGFPAEDIIFDPNIFAVATGIEEHNNYGVDFIEATRRIKNDLPHALISGGVSNVSFSFRGNEPVREAI 579 
                                            *********************************************************************** PP

                             TIGR02082  567 hsvFLyeaikaGlDmgivnagklavyddidkelrevvedlildrrreatekLlelaelykgtkeksskeaq 637 
                                            h+vFLy+aikaG+Dmgivnag+lavyddid+ l+e+ved++l+rr++at++Llel e ykg+     k+++
  NCBI__GCF_001995255.1:WP_077243567.1  580 HAVFLYHAIKAGMDMGIVNAGQLAVYDDIDEKLKEAVEDVVLNRRDDATDRLLELSEEYKGQGGG--KKEE 648 
                                            **************************************************************999..7789 PP

                             TIGR02082  638 eaewrnlpveeRLeralvkGeregieedleearkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvks 708 
                                            + ewr+++v++RLe++lvkG+  ++ +d+eear+ + +p+++iegpL+dGm+vvGdLFG+GkmfLPqvvks
  NCBI__GCF_001995255.1:WP_077243567.1  649 NLEWREWEVSKRLEHSLVKGIDTYVVDDTEEARQAYDRPIQVIEGPLMDGMNVVGDLFGEGKMFLPQVVKS 719 
                                            99********************************************************************* PP

                             TIGR02082  709 arvmkkavayLePylekekeedkskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekilea 779 
                                            arvmkkava+L+Py+e+ek+ ++++Gki++atvkGDvhDiGkniv+vvL+cn++ev+d+Gv++P ++il+a
  NCBI__GCF_001995255.1:WP_077243567.1  720 ARVMKKAVAHLIPYIEAEKTGTENNGKILMATVKGDVHDIGKNIVGVVLQCNNFEVIDIGVMQPGAEILKA 790 
                                            *********************************************************************** PP

                             TIGR02082  780 akkkkaDviglsGLivksldemvevaeemerrgvkiPlllGGaalskahvavkiaekYkgevvyvkdasea 850 
                                            ak+++ DviglsGLi++sl+em++ a ++er+g+++Pl++GGa++s+ah+avki+++Y+g+vv+vkdas+a
  NCBI__GCF_001995255.1:WP_077243567.1  791 AKEHDVDVIGLSGLITPSLEEMANFAADLEREGMTTPLMIGGATTSRAHTAVKIEPNYSGPVVWVKDASRA 861 
                                            *********************************************************************** PP

                             TIGR02082  851 vkvvdkllsekkkaeelekikeeyeeirekfgekkeklialsekaarkevfaldrse.............. 907 
                                            v v+++l+s + +++++++i+eeye++r +   +k+k++ ls+++ar ++ ++d+s               
  NCBI__GCF_001995255.1:WP_077243567.1  862 VGVAQSLISPELRENYAAEIREEYEKLRVQNAGRKKKVQWLSLEKARANKPEIDWSAyapakpkaletedl 932 
                                            ********************************************************999999999999988 PP

                             TIGR02082  908 ..dlevpapkflGtkvleas...ieellkyiDwkalFvqWelrgkypkilkdeleglearklfkdakelld 973 
                                              + +v +p+  G+  l+     ++++ +yiDw+++F +W+l+  yp+il+de++g+earklfkd +e+l+
  NCBI__GCF_001995255.1:WP_077243567.1  933 pgEPTVLHPHGDGSVLLRFDdfdLNKVKEYIDWTPFFHSWQLHAAYPRILEDEKVGEEARKLFKDGQEMLQ 1003
                                            88888888999998877644459************************************************ PP

                             TIGR02082  974 klsaekllrargvvGlfPaqsv.gddieiytdetvsqetkpiatvrekleqlrqqsdr.ylclaDfiaske 1042
                                            +++ ek +++rgvvG+fPa+sv +ddie+ytde +sq  k++  +r   +q+++ +++   +laDf+ +ke
  NCBI__GCF_001995255.1:WP_077243567.1 1004 RMIDEKWVTCRGVVGFFPANSVdHDDIEVYTDENRSQVLKKLHHLR---QQTEKRRGQpSHSLADFVMPKE 1071
                                            ********************873699*********88777777765...666666666689********** PP

                             TIGR02082 1043 sGikDylgallvtaglgaeelakkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldk 1113
                                            +G  Dy+ga++v+ag  +++ a+++e+ +ddy++ilvk+ladrlaea+ae +he vRk +wgy ++e+l++
  NCBI__GCF_001995255.1:WP_077243567.1 1072 AGGPDYIGAFAVSAGGDVDAKAEEYEKANDDYHAILVKSLADRLAEAFAECMHEYVRKYYWGYVADEQLEN 1142
                                            *********************************************************************** PP

                             TIGR02082 1114 edllkerYrGirpafGYpacPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfa 1181
                                            edl+ e+Y+Girpa+GYpacP+htekatl+eLl+ae+   ++ltes+a+ P ++vsg+yfahpe++Yf 
  NCBI__GCF_001995255.1:WP_077243567.1 1143 EDLIEEKYQGIRPAPGYPACPEHTEKATLWELLQAEEnADMTLTESYAMLPVSAVSGWYFAHPESRYFG 1211
                                            ***********************************999******************************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (1263 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.05
# Mc/sec: 27.64
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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:

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:

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:

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:

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