GapMind for Amino acid biosynthesis

 

Aligments for a candidate for metH in Shewanella sp. ANA-3

Align methionine synthase (EC 2.1.1.13) (characterized)
to candidate 7026140 Shewana3_3282 B12-dependent methionine synthase (RefSeq)

Query= BRENDA::P13009
         (1227 letters)



>lcl|FitnessBrowser__ANA3:7026140 Shewana3_3282 B12-dependent
            methionine synthase (RefSeq)
          Length = 1244

 Score = 1624 bits (4206), Expect = 0.0
 Identities = 819/1238 (66%), Positives = 974/1238 (78%), Gaps = 14/1238 (1%)

Query: 2    SSKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKP 61
            S  +  +R QL++RIL+LDG MGTMIQ Y+L E D+RGERF DW  D+KGNNDLLVL++P
Sbjct: 9    SQTLADIRNQLSKRILILDGAMGTMIQGYKLEEEDYRGERFKDWHTDVKGNNDLLVLTQP 68

Query: 62   EVIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTAR 121
             +I  IH  Y +AGADIIETNTFN+TTIAMADY M+SLSAEIN   A+LAR   DE    
Sbjct: 69   HIIKQIHIDYLKAGADIIETNTFNATTIAMADYDMQSLSAEINREGARLAREACDEIEQA 128

Query: 122  TPEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIE 181
            T  KPRYVAGVLGPTNRT SISPDVNDP +RNI FD LV AY EST+AL+EGGAD+I++E
Sbjct: 129  TG-KPRYVAGVLGPTNRTCSISPDVNDPGYRNIHFDELVTAYCESTRALIEGGADIIMVE 187

Query: 182  TVFDTLNAKAAVFAVKTEFEAL-----GVELPIMISGTITDASGRTLSGQTTEAFYNSLR 236
            T+FDTLNAKAA+FA++T F+ L        LP+MISGTITDASGRTL+GQTTEAFYNSLR
Sbjct: 188  TIFDTLNAKAALFAIETVFDELFGPNSPARLPVMISGTITDASGRTLTGQTTEAFYNSLR 247

Query: 237  HAEALTFGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIR 296
            H + L+ GLNCALGP ELR YV+ELSRIAECYV+AHPNAGLPN FG YD   + MA  I+
Sbjct: 248  HIKPLSIGLNCALGPKELRPYVEELSRIAECYVSAHPNAGLPNEFGGYDETPEDMASVIQ 307

Query: 297  EWAQAGFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLF 356
            EWA+ G LNI+GGCCG+TP+HI  +  AVE  APR LPEIPVACRLSGLEPL I   +LF
Sbjct: 308  EWAREGMLNIIGGCCGSTPEHIKVIREAVEPFAPRVLPEIPVACRLSGLEPLTIDAQTLF 367

Query: 357  VNVGERTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRF 416
            VNVGERTNVTGSAKF +LIKE K+ +ALDVAR+QVE+GAQIIDINMDEGMLD    M +F
Sbjct: 368  VNVGERTNVTGSAKFLKLIKEGKFEQALDVAREQVESGAQIIDINMDEGMLDGVEVMHKF 427

Query: 417  LNLIAGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRY 476
            LNLIA EPDI+RVPIMIDSSKW+VIE GLKCIQGKGIVNSIS+KEG + FI  A L++RY
Sbjct: 428  LNLIASEPDISRVPIMIDSSKWEVIEAGLKCIQGKGIVNSISLKEGEEKFIEQATLVKRY 487

Query: 477  GAAVVVMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHN 536
            GAA ++MAFDEQGQADT+ARK+EIC RAY++L ++VGFPPEDIIFDPNIFA+ATGI+EH+
Sbjct: 488  GAAAIIMAFDEQGQADTKARKVEICTRAYRVLVDKVGFPPEDIIFDPNIFAIATGIDEHD 547

Query: 537  NYAQDFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGI 596
            NYA DFI A ++IK  LPHA+ISGGVSNVSFSFRGN+PVREAIHAVFLY+AI+ GMDMGI
Sbjct: 548  NYAVDFIEAIKEIKATLPHAMISGGVSNVSFSFRGNNPVREAIHAVFLYHAIKVGMDMGI 607

Query: 597  VNAGQLAIYDDLPAELRDAVEDVILN-----RRDDGTERLLELAEKYRGSKTDDTANAQQ 651
            VNAGQLAIYDD+  EL+D VE+V+LN        + TE+LLE+AEK+RG  +  +A  + 
Sbjct: 608  VNAGQLAIYDDIDPELKDKVENVVLNLHCPVEDSNNTEQLLEIAEKFRGDGS-SSAKKED 666

Query: 652  AEWRSWEVNKRLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEG 711
             EWRSW VN+RL ++LVKGITEFI++DTE ARQ A+RP++VIEGPLMDGMN+VGDLFG G
Sbjct: 667  LEWRSWPVNQRLAHALVKGITEFIDEDTEAARQLASRPLDVIEGPLMDGMNIVGDLFGSG 726

Query: 712  KMFLPQVVKSARVMKQAVAYLEPFIEASKEQGKTNGKMVIATVKGDVHDIGKNIVGVVLQ 771
            KMFLPQVVKSARVMK+AVAYL PFIE  K +G++NG++++ TVKGDVHDIGKNIVGVVL 
Sbjct: 727  KMFLPQVVKSARVMKKAVAYLNPFIEQEKVEGQSNGRILMVTVKGDVHDIGKNIVGVVLA 786

Query: 772  CNNYEIVDLGVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLL 831
            CN +E+ DLGVMV  E+IL   KE N D+IG+SGLITPSLDEMV+  K   R+G TIP +
Sbjct: 787  CNGFEVFDLGVMVSVERILEAVKEHNIDIIGMSGLITPSLDEMVHNVKTFHREGLTIPAI 846

Query: 832  IGGATTSKAHTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVR 891
            IGGAT SK HTAVKI  +Y    +Y+ +ASR V +V+ L+S+  R   +  T  EYE +R
Sbjct: 847  IGGATCSKIHTAVKIAPHYPHGAIYIADASRAVPMVSKLVSNETRQATIDETYAEYEEMR 906

Query: 892  IQHGRKKPRTPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEV-EASIETLRNYIDWTPF 950
            I+   +  R   V+LEAAR+N    DW  YTP   + LG Q   +  +  L + IDWTPF
Sbjct: 907  IKRLSQTKRKEIVSLEAARENRCQHDWANYTPFKPNVLGRQVFDDYPLTDLVDRIDWTPF 966

Query: 951  FMTWSLAGKYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVG-D 1009
            F  W L G YP IL D+VVGVEAQ+LF D   ML K+  EK L  +GV+GLFPAN VG D
Sbjct: 967  FRAWELHGHYPEILTDKVVGVEAQKLFADGQAMLKKIIDEKWLTAKGVIGLFPANTVGFD 1026

Query: 1010 DIEIYRDETRTHVINVSHHLRQQTEKTGFANYCLADFVAPKLSGKADYIGAFAVTGGLEE 1069
            DIE+Y DETRT V   +HHLR Q E+ G  N+CLADFVAPK SG ADY+G FAVT G   
Sbjct: 1027 DIELYTDETRTEVEMTTHHLRMQLERVGNDNFCLADFVAPKDSGVADYMGGFAVTAGHGI 1086

Query: 1070 DALADAFEAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIREN 1129
            D     FEA HDDYN IM+K LADRLAEAFAE +HERVRK +WGYA +E L NE LIRE 
Sbjct: 1087 DEHIARFEANHDDYNAIMLKCLADRLAEAFAERMHERVRKEFWGYAADEQLDNEALIREK 1146

Query: 1130 YQGIRPAPGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKY 1189
            Y+GIRPAPGYPACP+HTEK  +W+LL+  +   + +TES+AM+P A+VSGWYF+HP S+Y
Sbjct: 1147 YKGIRPAPGYPACPDHTEKGLLWDLLKPNETIDLNITESYAMFPTAAVSGWYFAHPKSRY 1206

Query: 1190 YAVAQIQRDQVEDYARRKGMSVTEVERWLAPNLGYDAD 1227
            + V  I RDQVEDYA+RKGM+V E E+WLAP L YD +
Sbjct: 1207 FGVTNIGRDQVEDYAKRKGMTVAETEKWLAPVLDYDPE 1244


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: 3805
Number of extensions: 150
Number of successful extensions: 7
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: 1244
Length adjustment: 48
Effective length of query: 1179
Effective length of database: 1196
Effective search space:  1410084
Effective search space used:  1410084
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 7026140 Shewana3_3282 (B12-dependent methionine synthase (RefSeq))
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.12967.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 1770.9   0.0          0 1770.7   0.0    1.0  1  lcl|FitnessBrowser__ANA3:7026140  Shewana3_3282 B12-dependent meth


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7026140  Shewana3_3282 B12-dependent methionine synthase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1770.7   0.0         0         0       1    1182 []      19    1209 ..      19    1209 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1770.7 bits;  conditional E-value: 0
                         TIGR02082    1 lnkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDivetntFns 74  
                                        l+kril+lDGamGt++q ++L+e+d+rge ++d+++++kGnndlL+lt+P +i++ih +y++aGaDi+etntFn+
  lcl|FitnessBrowser__ANA3:7026140   19 LSKRILILDGAMGTMIQGYKLEEEDYRGErFKDWHTDVKGNNDLLVLTQPHIIKQIHIDYLKAGADIIETNTFNA 93  
                                        579************************************************************************ PP

                         TIGR02082   75 teialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdverpefrnvtydelvda 149 
                                        t+ia+adYd++++++e+n+++a+lare++de+++ + k+R+vaG+lGPtn++ ++spdv++p++rn+++delv a
  lcl|FitnessBrowser__ANA3:7026140   94 TTIAMADYDMQSLSAEINREGARLAREACDEIEQATGKPRYVAGVLGPTNRTCSISPDVNDPGYRNIHFDELVTA 168 
                                        *************************************************************************** PP

                         TIGR02082  150 YkeqvkglldGGvDllLietvfDtlnakaalfaveevfee.....kgrelPilisgvivdksGrtLsGqtleafl 219 
                                        Y e++++l++GG+D++++et+fDtlnakaalfa+e+vf+e       ++lP++isg+i+d+sGrtL+Gqt+eaf+
  lcl|FitnessBrowser__ANA3:7026140  169 YCESTRALIEGGADIIMVETIFDTLNAKAALFAIETVFDElfgpnSPARLPVMISGTITDASGRTLTGQTTEAFY 243 
                                        **************************************97222224689************************** PP

                         TIGR02082  220 aslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnalgeYdltpeelakalkefaeegllniv 294 
                                        +sl+h + l++GLnCalG++elr++v+els++ae++vs++PnaGLPn++g Yd+tpe +a++++e+a+eg+lni+
  lcl|FitnessBrowser__ANA3:7026140  244 NSLRHIKPLSIGLNCALGPKELRPYVEELSRIAECYVSAHPNAGLPNEFGGYDETPEDMASVIQEWAREGMLNII 318 
                                        *************************************************************************** PP

                         TIGR02082  295 GGCCGttPehiraiaeavkdikprkrqeleeksvlsglealkiaqessfvniGeRtnvaGskkfrklikaedyee 369 
                                        GGCCG+tPehi+ i eav+  +pr  +e++ +++lsgle+l+i+ ++ fvn+GeRtnv+Gs+kf klik++++e+
  lcl|FitnessBrowser__ANA3:7026140  319 GGCCGSTPEHIKVIREAVEPFAPRVLPEIPVACRLSGLEPLTIDAQTLFVNVGERTNVTGSAKFLKLIKEGKFEQ 393 
                                        *************************************************************************** PP

                         TIGR02082  370 alkiakqqveeGaqilDinvDevllDgeadmkkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsi 444 
                                        al++a++qve+Gaqi+Din+De++lDg++ m+k+l+l+asepdi++vP+m+Dss++ev+eaGLk+iqGk+ivnsi
  lcl|FitnessBrowser__ANA3:7026140  394 ALDVAREQVESGAQIIDINMDEGMLDGVEVMHKFLNLIASEPDISRVPIMIDSSKWEVIEAGLKCIQGKGIVNSI 468 
                                        *************************************************************************** PP

                         TIGR02082  445 slkdGeerFlekaklikeyGaavvvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGi 519 
                                        slk+Gee+F+e+a l+k+yGaa+++mafDe+Gqa+t+++k+ei++Ray++l++kvgfppediifDpni++iatGi
  lcl|FitnessBrowser__ANA3:7026140  469 SLKEGEEKFIEQATLVKRYGAAAIIMAFDEQGQADTKARKVEICTRAYRVLVDKVGFPPEDIIFDPNIFAIATGI 543 
                                        *************************************************************************** PP

                         TIGR02082  520 eehdryaidfieaireikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavydd 594 
                                        +ehd+ya+dfieai+eik +lP+a isgGvsnvsFs+rgn++vRea+h+vFLy+aik+G+Dmgivnag+la+ydd
  lcl|FitnessBrowser__ANA3:7026140  544 DEHDNYAVDFIEAIKEIKATLPHAMISGGVSNVSFSFRGNNPVREAIHAVFLYHAIKVGMDMGIVNAGQLAIYDD 618 
                                        *************************************************************************** PP

                         TIGR02082  595 idkelrevvedlildrr.....reatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregiee 664 
                                        id+el+++ve+++l+ +     +++te+Lle+ae+++g  ++s ++++  ewr++pv++RL++alvkG++e+i+e
  lcl|FitnessBrowser__ANA3:7026140  619 IDPELKDKVENVVLNLHcpvedSNNTEQLLEIAEKFRGDGSSS-AKKEDLEWRSWPVNQRLAHALVKGITEFIDE 692 
                                        ***************888887799***************9995.558899************************* PP

                         TIGR02082  665 dleearkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeedkskGkivla 739 
                                        d+e+ar+ +++pl++iegpL+dGm++vGdLFGsGkmfLPqvvksarvmkkavayL+P++e+ek e +s+G+i++ 
  lcl|FitnessBrowser__ANA3:7026140  693 DTEAARQLASRPLDVIEGPLMDGMNIVGDLFGSGKMFLPQVVKSARVMKKAVAYLNPFIEQEKVEGQSNGRILMV 767 
                                        *************************************************************************** PP

                         TIGR02082  740 tvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksldemvevaeemerrgvk 814 
                                        tvkGDvhDiGkniv+vvL+cng+ev dlGv+v ve+ilea k+++ D+ig+sGLi++sldemv++++ ++r+g++
  lcl|FitnessBrowser__ANA3:7026140  768 TVKGDVHDIGKNIVGVVLACNGFEVFDLGVMVSVERILEAVKEHNIDIIGMSGLITPSLDEMVHNVKTFHREGLT 842 
                                        *************************************************************************** PP

                         TIGR02082  815 iPlllGGaalskahvavkiaekYkgevvyvkdaseavkvvdkllsekkkaeelekikeeyeeirekfgekkekli 889 
                                        iP ++GGa+ sk h+avkia++Y    +y  das+av +v+kl+s++++++ ++++ +eyee+r k  ++ ++++
  lcl|FitnessBrowser__ANA3:7026140  843 IPAIIGGATCSKIHTAVKIAPHYPHGAIYIADASRAVPMVSKLVSNETRQATIDETYAEYEEMRIKRLSQTKRKE 917 
                                        *************************************************************************** PP

                         TIGR02082  890 alsekaarkevfaldrsedlevpapkflGtkvleas.ieellkyiDwkalFvqWelrgkypkilkdelegleark 963 
                                         +s++aar+++ + d+  ++++ +p+ lG++v++++ + +l++ iDw+++F +Wel+g+yp+il+d+++g+ea+k
  lcl|FitnessBrowser__ANA3:7026140  918 IVSLEAARENRCQHDWA-NYTPFKPNVLGRQVFDDYpLTDLVDRIDWTPFFRAWELHGHYPEILTDKVVGVEAQK 991 
                                        *****************.9******************************************************** PP

                         TIGR02082  964 lfkdakelldklsaekllrargvvGlfPaqsvg.ddieiytdetvsqetkpiatvrekleqlrqqsdrylclaDf 1037
                                        lf+d +++l+k++ ek l+a+gv+GlfPa++vg ddie+ytdet+   t++  t+++ + ql++  + + claDf
  lcl|FitnessBrowser__ANA3:7026140  992 LFADGQAMLKKIIDEKWLTAKGVIGLFPANTVGfDDIELYTDETR---TEVEMTTHHLRMQLERVGNDNFCLADF 1063
                                        ******************************98769*********9...55555555556666666666******* PP

                         TIGR02082 1038 iaskesGikDylgallvtaglgaeelakkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenld 1112
                                        +a+k+sG +Dy+g ++vtag g++e   ++ea++ddy++i++k ladrlaea+ae +hervRke+wgya++e+ld
  lcl|FitnessBrowser__ANA3:7026140 1064 VAPKDSGVADYMGGFAVTAGHGIDEHIARFEANHDDYNAIMLKCLADRLAEAFAERMHERVRKEFWGYAADEQLD 1138
                                        *************************************************************************** PP

                         TIGR02082 1113 kedllkerYrGirpafGYpacPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfav 1182
                                        +e l++e+Y+Girpa+GYpacPdhtek  l++Ll++++ i l++tes+a+ P+a+vsg+yfahp+++Yf v
  lcl|FitnessBrowser__ANA3:7026140 1139 NEALIREKYKGIRPAPGYPACPDHTEKGLLWDLLKPNEtIDLNITESYAMFPTAAVSGWYFAHPKSRYFGV 1209
                                        ***********************************9887******************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (1244 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: 0.12u 0.04s 00:00:00.16 Elapsed: 00:00:00.15
# Mc/sec: 9.46
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see 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