GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metH in Pseudomonas putida KT2440

Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate PP_2375 PP_2375 cobalamin-dependent methionine synthase

Query= CharProtDB::CH_090726
         (1227 letters)



>FitnessBrowser__Putida:PP_2375
          Length = 1235

 Score = 1607 bits (4160), Expect = 0.0
 Identities = 821/1235 (66%), Positives = 978/1235 (79%), Gaps = 14/1235 (1%)

Query: 2    SSKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKP 61
            S++++ L+  L ERIL+LDGGMGTMIQSYRL E D+RG RFADWP D+KGNNDLL+LS+P
Sbjct: 5    SARLQALQNALKERILILDGGMGTMIQSYRLEEHDYRGTRFADWPSDVKGNNDLLLLSRP 64

Query: 62   EVIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTAR 121
            +VIAAI  AY +AGADI+ETNTFN+T I+ ADY MESL  E+N   A++AR  AD  T  
Sbjct: 65   DVIAAIEKAYLDAGADILETNTFNATQISQADYGMESLVYELNVEGARIARQVADAKTLE 124

Query: 122  TPEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIE 181
            TP+KPR+VAGVLGPT+RT SISPDVNDP FRN+TFD LV  Y E+T+ L+EGGADLILIE
Sbjct: 125  TPDKPRFVAGVLGPTSRTCSISPDVNDPGFRNVTFDELVENYIEATRGLIEGGADLILIE 184

Query: 182  TVFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEAL 241
            T+FDTLNAKAA+FAV+  FE   VELPIMISGTITDASGRTLSGQTTEAF+NS+RHA+ +
Sbjct: 185  TIFDTLNAKAAIFAVQQVFEDDNVELPIMISGTITDASGRTLSGQTTEAFWNSVRHAKPI 244

Query: 242  TFGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQA 301
            + GLNCALG  +LR Y++EL+  A+ +V+AHPNAGLPNAFGEYD     MA  + E+A +
Sbjct: 245  SVGLNCALGAKDLRPYLEELATKADTHVSAHPNAGLPNAFGEYDETPAEMAAVVEEFAAS 304

Query: 302  GFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGE 361
            GFLNI+GGCCGTTP HI A++ AV    PR++PEI  ACRLSGLEP  I   SLFVNVGE
Sbjct: 305  GFLNIIGGCCGTTPGHIQAIAEAVAKYKPREIPEIAKACRLSGLEPFTIDRQSLFVNVGE 364

Query: 362  RTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIA 421
            RTN+TGSAKF RLI+EE Y+EAL+VA QQVE GAQ+IDINMDEGMLD++AAMVRFLNLIA
Sbjct: 365  RTNITGSAKFARLIREENYTEALEVALQQVEAGAQVIDINMDEGMLDSQAAMVRFLNLIA 424

Query: 422  GEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVV 481
            GEPDI+RVPIMIDSSKW+VIE GLKCIQGKGIVNSISMKEGV+ F HHA+L +RYGAAVV
Sbjct: 425  GEPDISRVPIMIDSSKWEVIEAGLKCIQGKGIVNSISMKEGVEQFKHHARLCKRYGAAVV 484

Query: 482  VMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQD 541
            VMAFDE GQADT ARK EIC+R+Y IL  EVGFPPEDIIFDPNIFAVATGIEEHNNYA D
Sbjct: 485  VMAFDEVGQADTAARKKEICQRSYDILVNEVGFPPEDIIFDPNIFAVATGIEEHNNYAVD 544

Query: 542  FIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQ 601
            FI AC  I+  LPHAL SGGVSNVSFSFRGN+PVREAIH+VFLY+AI+NG+ MGIVNAGQ
Sbjct: 545  FIEACAYIRDHLPHALSSGGVSNVSFSFRGNNPVREAIHSVFLYHAIQNGLTMGIVNAGQ 604

Query: 602  LAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNK 661
            L IYD++PA+LR+ VEDV+LNR   GT+ LL +A+ Y+G     T   +  EWRS  V K
Sbjct: 605  LEIYDEIPAQLREKVEDVVLNRTPHGTDALLAIADDYKGGGA--TKEVENEEWRSLPVEK 662

Query: 662  RLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKS 721
            RLE++LVKGIT FI +DTE  RQQ  RPIEVIEGPLM+GMNVVGDLFG GKMFLPQVVKS
Sbjct: 663  RLEHALVKGITAFIVEDTEACRQQCARPIEVIEGPLMNGMNVVGDLFGAGKMFLPQVVKS 722

Query: 722  ARVMKQAVAYLEPFIEASK-EQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDL 780
            ARVMKQAVA+L PFIEA K ++ +  GK+++ATVKGDVHDIGKNIVGVVL CN Y+IVDL
Sbjct: 723  ARVMKQAVAHLIPFIEAEKGDKPEAKGKILMATVKGDVHDIGKNIVGVVLGCNGYDIVDL 782

Query: 781  GVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKA 840
            GVMVPAEKIL+TA+E   D+IGLSGLITPSLDEMV+VA+EM+RQGF +PL+IGGATTSKA
Sbjct: 783  GVMVPAEKILQTAREQKCDIIGLSGLITPSLDEMVHVAREMQRQGFELPLMIGGATTSKA 842

Query: 841  HTAVKIEQNYSGPTV-YVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKP 899
            HTAVKIE  YS   V YV +ASR VGV   LLS   +  FV +TR EY  VR +   +  
Sbjct: 843  HTAVKIEPKYSNDAVIYVTDASRAVGVATQLLSKELKPGFVEKTRLEYVDVRERTANRSA 902

Query: 900  RTPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVE-ASIETLRNYIDWTPFFMTWSLAG 958
            RT  ++   A      +DW  Y P      GV+ +E   + TL  YIDWTPFF++W LAG
Sbjct: 903  RTERLSYAQAIAAKPQYDWAGYQPTAPSFTGVKVLEDIDLRTLAEYIDWTPFFISWDLAG 962

Query: 959  KYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRV-GDDIEIYRDE 1017
            K+PRIL DEVVG  A  L+KDA +MLDKL  EK ++ R V G +PAN+V  DDIE+Y ++
Sbjct: 963  KFPRILTDEVVGEAATALYKDAREMLDKLIDEKLISARAVFGFWPANQVDDDDIEVYGED 1022

Query: 1018 TRTHVINVSHHLRQQTEK-TGFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAF 1076
             +   +   HHLRQQT K  G  N+ LADFVAPK SG  DY+G F  T G+  + +A A+
Sbjct: 1023 GQ--ALATLHHLRQQTIKPDGKPNWSLADFVAPKDSGVTDYVGGFITTAGIGAEEVAKAY 1080

Query: 1077 EAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPA 1136
            + + DDY+ IMVKALADRLAEA AE+LHE+VRK +WGYA +E+L NE LI+E Y GIRPA
Sbjct: 1081 QDKGDDYSSIMVKALADRLAEACAEWLHEQVRKEHWGYARDEHLDNEALIKEQYSGIRPA 1140

Query: 1137 PGYPACPEHTEKATIWELLE-----VEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYA 1191
            PGYPACP+HTEK T++ LL+         +G+ LTE FAM+P A+VSGWYF+HP +KY+A
Sbjct: 1141 PGYPACPDHTEKETLFRLLDGTAIGETGPSGVYLTEHFAMFPAAAVSGWYFAHPQAKYFA 1200

Query: 1192 VAQIQRDQVEDYARRKGMSVTEVERWLAPNLGYDA 1226
            V ++ +DQ+E Y+ RKG  ++  ERWLAPNLGYD+
Sbjct: 1201 VGKVDKDQIERYSARKGQDISVSERWLAPNLGYDS 1235


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: 3851
Number of extensions: 160
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: 1235
Length adjustment: 47
Effective length of query: 1180
Effective length of database: 1188
Effective search space:  1401840
Effective search space used:  1401840
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 PP_2375 PP_2375 (cobalamin-dependent 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.17539.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 1766.9   0.0          0 1766.7   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_2375  PP_2375 cobalamin-dependent meth


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_2375  PP_2375 cobalamin-dependent methionine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1766.7   0.0         0         0       1    1182 []      15    1201 ..      15    1201 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1766.7 bits;  conditional E-value: 0
                           TIGR02082    1 lnkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDivetntF 72  
                                          l++ril+lDG+mGt++qs++L+e+d+rg  +ad+++++kGnndlL l++P+viaai +ay++aGaDi+etntF
  lcl|FitnessBrowser__Putida:PP_2375   15 LKERILILDGGMGTMIQSYRLEEHDYRGTrFADWPSDVKGNNDLLLLSRPDVIAAIEKAYLDAGADILETNTF 87  
                                          579********************************************************************** PP

                           TIGR02082   73 nsteialadYdledkayelnkkaaklarevadeft.ltpekkRfvaGslGPtnklatlspdverpefrnvtyd 144 
                                          n+t+i++adY++e+++yeln ++a++ar+vad  t  tp+k+RfvaG+lGPt+++ ++spdv++p+frnvt+d
  lcl|FitnessBrowser__Putida:PP_2375   88 NATQISQADYGMESLVYELNVEGARIARQVADAKTlETPDKPRFVAGVLGPTSRTCSISPDVNDPGFRNVTFD 160 
                                          *********************************99899*********************************** PP

                           TIGR02082  145 elvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgvivdksGrtLsGqtlea 217 
                                          elv+ Y e+++gl++GG+Dl+Liet+fDtlnakaa+fav++vfe+ ++elPi+isg+i+d+sGrtLsGqt+ea
  lcl|FitnessBrowser__Putida:PP_2375  161 ELVENYIEATRGLIEGGADLILIETIFDTLNAKAAIFAVQQVFEDDNVELPIMISGTITDASGRTLSGQTTEA 233 
                                          ************************************************************************* PP

                           TIGR02082  218 flaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnalgeYdltpeelakalkefaeegl 290 
                                          f +s++ha+ +++GLnCalGa++lr++++el+ +a++ vs++PnaGLPna+geYd+tp e+a++++efa+ g+
  lcl|FitnessBrowser__Putida:PP_2375  234 FWNSVRHAKPISVGLNCALGAKDLRPYLEELATKADTHVSAHPNAGLPNAFGEYDETPAEMAAVVEEFAASGF 306 
                                          ************************************************************************* PP

                           TIGR02082  291 lnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsglealkiaqessfvniGeRtnvaGskkfrklik 363 
                                          lni+GGCCGttP hi+aiaeav++ kpr+ +e+ ++++lsgle+++i+++s fvn+GeRtn++Gs+kf++li+
  lcl|FitnessBrowser__Putida:PP_2375  307 LNIIGGCCGTTPGHIQAIAEAVAKYKPREIPEIAKACRLSGLEPFTIDRQSLFVNVGERTNITGSAKFARLIR 379 
                                          ************************************************************************* PP

                           TIGR02082  364 aedyeealkiakqqveeGaqilDinvDevllDgeadmkkllsllasepdiakvPlmlDssefevleaGLkviq 436 
                                          +e+y eal++a qqve Gaq++Din+De++lD++a+m+++l+l+a+epdi++vP+m+Dss++ev+eaGLk+iq
  lcl|FitnessBrowser__Putida:PP_2375  380 EENYTEALEVALQQVEAGAQVIDINMDEGMLDSQAAMVRFLNLIAGEPDISRVPIMIDSSKWEVIEAGLKCIQ 452 
                                          ************************************************************************* PP

                           TIGR02082  437 GkaivnsislkdGeerFlekaklikeyGaavvvmafDeeGqartadkkieiakRayklltekvgfppediifD 509 
                                          Gk+ivnsis+k+G+e+F ++a+l k+yGaavvvmafDe Gqa+ta++k ei++R y++l+++vgfppediifD
  lcl|FitnessBrowser__Putida:PP_2375  453 GKGIVNSISMKEGVEQFKHHARLCKRYGAAVVVMAFDEVGQADTAARKKEICQRSYDILVNEVGFPPEDIIFD 525 
                                          ************************************************************************* PP

                           TIGR02082  510 pniltiatGieehdryaidfieaireikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmg 582 
                                          pni+++atGieeh++ya+dfiea+  i+ +lP+a  sgGvsnvsFs+rgn++vRea+hsvFLy+ai++Gl mg
  lcl|FitnessBrowser__Putida:PP_2375  526 PNIFAVATGIEEHNNYAVDFIEACAYIRDHLPHALSSGGVSNVSFSFRGNNPVREAIHSVFLYHAIQNGLTMG 598 
                                          ************************************************************************* PP

                           TIGR02082  583 ivnagklavyddidkelrevvedlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralv 655 
                                          ivnag+l++yd+i+++lre+ved++l+r ++ t+ Ll +a+ ykg  ++  ke +++ewr+lpve+RLe+alv
  lcl|FitnessBrowser__Putida:PP_2375  599 IVNAGQLEIYDEIPAQLREKVEDVVLNRTPHGTDALLAIADDYKGGGAT--KEVENEEWRSLPVEKRLEHALV 669 
                                          *********************************************9999..8999****************** PP

                           TIGR02082  656 kGeregieedleearkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekeke 728 
                                          kG++ +i ed+e+ r++  +p+e+iegpL++Gm+vvGdLFG+GkmfLPqvvksarvmk+ava+L+P++e+ek 
  lcl|FitnessBrowser__Putida:PP_2375  670 KGITAFIVEDTEACRQQCARPIEVIEGPLMNGMNVVGDLFGAGKMFLPQVVKSARVMKQAVAHLIPFIEAEKG 742 
                                          ************************************************************************8 PP

                           TIGR02082  729 ed.kskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivkslde 800 
                                          ++ ++kGki++atvkGDvhDiGkniv+vvL+cngy++vdlGv+vP+ekil++a+++k D+iglsGLi++slde
  lcl|FitnessBrowser__Putida:PP_2375  743 DKpEAKGKILMATVKGDVHDIGKNIVGVVLGCNGYDIVDLGVMVPAEKILQTAREQKCDIIGLSGLITPSLDE 815 
                                          87689******************************************************************** PP

                           TIGR02082  801 mvevaeemerrgvkiPlllGGaalskahvavkiaekYkg.evvyvkdaseavkvvdkllsekkkaeelekike 872 
                                          mv+va+em+r+g+++Pl++GGa++skah+avki++kY+   v+yv+das+av v+ +lls++ k  ++ek++ 
  lcl|FitnessBrowser__Putida:PP_2375  816 MVHVAREMQRQGFELPLMIGGATTSKAHTAVKIEPKYSNdAVIYVTDASRAVGVATQLLSKELKPGFVEKTRL 888 
                                          *************************************872599****************************** PP

                           TIGR02082  873 eyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieellkyiDwkalFvqWel 944 
                                          ey ++re+  ++  +++ ls ++a   + + d+   ++++ap f G+kvle++ + +l +yiDw+++F++W+l
  lcl|FitnessBrowser__Putida:PP_2375  889 EYVDVRERTANRSARTERLSYAQAIAAKPQYDWA-GYQPTAPSFTGVKVLEDIdLRTLAEYIDWTPFFISWDL 960 
                                          **********************************.9************************************* PP

                           TIGR02082  945 rgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvg.ddieiytdetvsqetkpiat 1016
                                          +gk+p+il+de++g+ a+ l+kda+e+ldkl+ ekl+ ar+v+G++Pa++v+ ddie+y +++       +at
  lcl|FitnessBrowser__Putida:PP_2375  961 AGKFPRILTDEVVGEAATALYKDAREMLDKLIDEKLISARAVFGFWPANQVDdDDIEVYGEDGQ-----ALAT 1028
                                          ************************************************9875268*****8776.....6677 PP

                           TIGR02082 1017 vrekleqlrqqsdr.ylclaDfiaskesGikDylgallvtaglgaeelakkleakeddydsilvkaladrlae 1088
                                          +++ ++q+ +  ++ + +laDf+a+k+sG +Dy+g +++tag+gaee ak++++k ddy+si+vkaladrlae
  lcl|FitnessBrowser__Putida:PP_2375 1029 LHHLRQQTIKPDGKpNWSLADFVAPKDSGVTDYVGGFITTAGIGAEEVAKAYQDKGDDYSSIMVKALADRLAE 1101
                                          666555555555556********************************************************** PP

                           TIGR02082 1089 alaellhervRkelwgyaeeenldkedllkerYrGirpafGYpacPdhtekatlleLleaeri......Glkl 1155
                                          a ae+lhe+vRke+wgya++e+ld+e l+ke+Y Girpa+GYpacPdhtek tl++Ll+   i      G++l
  lcl|FitnessBrowser__Putida:PP_2375 1102 ACAEWLHEQVRKEHWGYARDEHLDNEALIKEQYSGIRPAPGYPACPDHTEKETLFRLLDGTAIgetgpsGVYL 1174
                                          **********************************************************987663333337*** PP

                           TIGR02082 1156 teslalaPeasvsglyfahpeakYfav 1182
                                          te +a+ P+a+vsg+yfahp+akYfav
  lcl|FitnessBrowser__Putida:PP_2375 1175 TEHFAMFPAAAVSGWYFAHPQAKYFAV 1201
                                          *************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (1235 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: 0.11u 0.06s 00:00:00.17 Elapsed: 00:00:00.17
# Mc/sec: 8.51
//
[ok]

This GapMind analysis is from Apr 09 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:

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