Alignments for a candidate for metH in Cupriavidus basilensis 4G11

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Cupriavidus basilensis 4G11

Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate RR42_RS00775 RR42_RS00775 methionine synthase

Query= CharProtDB::CH_090726
         (1227 letters)



>FitnessBrowser__Cup4G11:RR42_RS00775
          Length = 915

 Score = 1068 bits (2761), Expect = 0.0
 Identities = 572/913 (62%), Positives = 671/913 (73%), Gaps = 32/913 (3%)

Query: 337  PVACRLSGLEPLNIGEDSLFVNVGERTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQ 396
            P   RLSGLEP  I ED+LFVNVGERTNVTGS  F R+I   ++ +AL VARQQVENGAQ
Sbjct: 8    PRPMRLSGLEPFTIDEDTLFVNVGERTNVTGSKAFARMILNGQFDDALVVARQQVENGAQ 67

Query: 397  IIDINMDEGMLDAEAAMVRFLNLIAGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNS 456
            IIDINMDE MLD++AAMVRFLNLIA EPDIARVPIM+DSSKW+VIE GLKC+QGK +VNS
Sbjct: 68   IIDINMDEAMLDSKAAMVRFLNLIASEPDIARVPIMLDSSKWEVIEAGLKCVQGKPVVNS 127

Query: 457  ISMKEGVDAFIHHAKLLRRYGAAVVVMAFDEQGQADTRARKIEICRRAYKILTEEVGFPP 516
            IS+KEG + F HHA+L+RRYGAA VVMAFDEQGQADT ARK EIC+R+Y IL  EVGFPP
Sbjct: 128  ISLKEGEEQFRHHAELIRRYGAASVVMAFDEQGQADTFARKTEICKRSYDILVNEVGFPP 187

Query: 517  EDIIFDPNIFAVATGIEEHNNYAQDFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVR 576
            EDIIFDPNIFAVATGIEEHNNYA DFI A   IK+ LP+A +SGGVSNVSFSFRGND VR
Sbjct: 188  EDIIFDPNIFAVATGIEEHNNYAVDFIEATAWIKQNLPYAKVSGGVSNVSFSFRGNDAVR 247

Query: 577  EAIHAVFLYYAIRNGMDMGIVNAGQLAIYDDLPAELRDAVEDVILNRRDDGTERLLELAE 636
            EAIH VFLY+AI+ GMDMGIVNAGQL +YD L AELR+ VEDV+LNRR+D T+RLLE+A+
Sbjct: 248  EAIHTVFLYHAIKAGMDMGIVNAGQLGVYDQLDAELRERVEDVVLNRREDSTDRLLEIAD 307

Query: 637  KYRGSKTDDTANAQQAEWRSWEVN-----KRLEYSLVKGITEFIEQDTEEARQQAT---- 687
            +Y+G       N     WR    N      RL ++LV G+T FI +DTEE RQQ      
Sbjct: 308  RYKGGGAKKEENLL---WRGTPENPVPVADRLSHALVHGLTTFIVEDTEEVRQQVEARGG 364

Query: 688  RPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSARVMKQAVAYLEPFIEASK----EQG 743
            R IEVIEGPLMDGMN+VGDLFG GKMFLPQVVKSARVMKQAVA+L P+IE  K    E G
Sbjct: 365  RTIEVIEGPLMDGMNIVGDLFGAGKMFLPQVVKSARVMKQAVAHLLPYIEEEKRLLAEAG 424

Query: 744  ---KTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLGVMVPAEKILRTAKEVNADL 800
               K  GK+VIATVKGDVHDIGKNIV VVLQCNN+E+V++GVMVP  +IL  AK   AD+
Sbjct: 425  GDVKARGKIVIATVKGDVHDIGKNIVSVVLQCNNFEVVNMGVMVPCNEILARAKVEGADI 484

Query: 801  IGLSGLITPSLDEMVNVAKEMERQGF----TIPLLIGGATTSKAHTAVKIEQNYSGPTVY 856
            +GLSGLITPSL+EM  VA EM+R  +     IPLLIGGATTS+ HTAVKI  +Y GP VY
Sbjct: 485  VGLSGLITPSLEEMAYVASEMQRDDYFRIKKIPLLIGGATTSRVHTAVKIAPHYEGPVVY 544

Query: 857  VQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPRTPPVTLEAARDNDFAF 916
            V +ASR+V V ++LLSD     ++   + +YE +R QH  KK  TP V+L  AR N    
Sbjct: 545  VPDASRSVSVASSLLSDDGAARYLDELKTDYERIRHQHANKK-ATPMVSLAKARANKTPV 603

Query: 917  DWQAYTPPVAHRLGVQEV-EASIETLRNYIDWTPFFMTWSLAGKYPRILEDEVVGVEAQR 975
            DW AY PP    +G +      +  L NYIDW PFF TW LAGK+P IL DE+VG  A+R
Sbjct: 604  DWSAYVPPKPKFIGRRIFRNYDLTELANYIDWAPFFQTWDLAGKFPDILNDEIVGESARR 663

Query: 976  LFKDANDMLDKLSAEKTLNPRGVVGLFPANRVG-DDIEIYRDETRTHVINVSHHLRQQTE 1034
            +F D   ML +L   + L   GV+ L PAN V  DDIEIY DETR+ V    H+LRQQ+E
Sbjct: 664  VFSDGKAMLSRLIQGRWLTANGVLALLPANAVNDDDIEIYTDETRSQVALTWHNLRQQSE 723

Query: 1035 KTGF-----ANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEAQHDDYNKIMVK 1089
            +         N CLADFVAPK SG ADYIG FAVT G+  D     FEA HDDY+ IM+K
Sbjct: 724  RPVIDGVMRPNRCLADFVAPKDSGIADYIGVFAVTAGIGVDKKEAQFEADHDDYSAIMLK 783

Query: 1090 ALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGYPACPEHTEKA 1149
            +LADRLAEAFAE LHERVR+  WGY   E L+NE+LI E Y+GIRPAPGYPACPEHT KA
Sbjct: 784  SLADRLAEAFAECLHERVRRDLWGYDAGEVLTNEQLIAETYRGIRPAPGYPACPEHTVKA 843

Query: 1150 TIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQVEDYARRKGM 1209
             ++E L   +  GM +T+S AM P ASVSG+Y +HP+S Y++V +I  DQ++D   R+G 
Sbjct: 844  PMFEFLNAAE-IGMGITDSLAMTPAASVSGFYLAHPESTYFSVGKIGEDQLDDMVARRGE 902

Query: 1210 SVTEVERWLAPNL 1222
              + +ER LAPNL
Sbjct: 903  ERSVLERALAPNL 915


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: 2701
Number of extensions: 123
Number of successful extensions: 11
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 1227
Length of database: 915
Length adjustment: 45
Effective length of query: 1182
Effective length of database: 870
Effective search space:  1028340
Effective search space used:  1028340
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 RR42_RS00770 RR42_RS00770 5-methyltetrahydrofolate--homocysteine methyltransferase

Query= CharProtDB::CH_090726
         (1227 letters)



>FitnessBrowser__Cup4G11:RR42_RS00770
          Length = 355

 Score =  386 bits (992), Expect = e-111
 Identities = 190/334 (56%), Positives = 246/334 (73%), Gaps = 4/334 (1%)

Query: 3   SKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPE 62
           ++   L A L ERIL+LDG MGTMIQ Y+L EAD+RGERFA    D+KGNN+LL+LS+P+
Sbjct: 17  TRAANLPALLRERILILDGAMGTMIQRYKLTEADYRGERFAGHHVDVKGNNELLLLSRPQ 76

Query: 63  VIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTART 122
           VI+ IH  Y  AGAD+IETNTF +T +A  DY+M  L+ E+N  AA+LAR   D+++  T
Sbjct: 77  VISEIHEQYLAAGADLIETNTFGATGVAQEDYKMADLAYEMNVVAARLAREACDKYS--T 134

Query: 123 PEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIET 182
           P+KPR+VAG  GPT +TASISPDVNDP  RN+TF+ L  +Y E  K L+EGGAD+ L+ET
Sbjct: 135 PDKPRFVAGAFGPTPKTASISPDVNDPGARNVTFEELRCSYYEQGKGLLEGGADVFLVET 194

Query: 183 VFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALT 242
           +FDTLNAKAA+FA+   FE  G  LP+MISGT+TDASGR LSGQT EAF+NSLRHA  +T
Sbjct: 195 IFDTLNAKAALFAIDQLFEDTGERLPVMISGTVTDASGRILSGQTVEAFWNSLRHARPIT 254

Query: 243 FGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGE--YDLDADTMAKQIREWAQ 300
           FGLNCALG   +R Y+ EL++I +  V+ +PNAGLPN   +  +D   +  +  + E+A 
Sbjct: 255 FGLNCALGATLMRPYIAELAKICDAAVSCYPNAGLPNPMSDTGFDETPEVTSSLVEEFAA 314

Query: 301 AGFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLP 334
           +G +N+VGGCCGTTP+HIAA++  V    PR  P
Sbjct: 315 SGLVNLVGGCCGTTPEHIAAIAERVASKKPRTWP 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: 1056
Number of extensions: 37
Number of successful extensions: 3
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: 355
Length adjustment: 38
Effective length of query: 1189
Effective length of database: 317
Effective search space:   376913
Effective search space used:   376913
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 RR42_RS00775 RR42_RS00775 (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.14366.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 1204.5   0.0          0 1204.3   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS00775  RR42_RS00775 methionine synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS00775  RR42_RS00775 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     325    1182 .]       9     885 ..       3     885 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1204.3 bits;  conditional E-value: 0
                                 TIGR02082  325 eksvlsglealkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDe 391 
                                                 +++lsgle+++i++++ fvn+GeRtnv+Gsk f+++i ++++++al +a+qqve+Gaqi+Din+De
  lcl|FitnessBrowser__Cup4G11:RR42_RS00775    9 RPMRLSGLEPFTIDEDTLFVNVGERTNVTGSKAFARMILNGQFDDALVVARQQVENGAQIIDINMDE 75  
                                                6899*************************************************************** PP

                                 TIGR02082  392 vllDgeadmkkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekak 458 
                                                ++lD++a+m+++l+l+asepdia+vP+mlDss++ev+eaGLk++qGk +vnsislk+Gee+F ++a+
  lcl|FitnessBrowser__Cup4G11:RR42_RS00775   76 AMLDSKAAMVRFLNLIASEPDIARVPIMLDSSKWEVIEAGLKCVQGKPVVNSISLKEGEEQFRHHAE 142 
                                                ******************************************************************* PP

                                 TIGR02082  459 likeyGaavvvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdry 525 
                                                li++yGaa vvmafDe+Gqa+t ++k ei+kR y++l+++vgfppediifDpni+++atGieeh++y
  lcl|FitnessBrowser__Cup4G11:RR42_RS00775  143 LIRRYGAASVVMAFDEQGQADTFARKTEICKRSYDILVNEVGFPPEDIIFDPNIFAVATGIEEHNNY 209 
                                                ******************************************************************* PP

                                 TIGR02082  526 aidfieaireikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavy 592 
                                                a+dfiea+ +ik++lP+ak+sgGvsnvsFs+rgndavRea+h+vFLy+aikaG+Dmgivnag+l vy
  lcl|FitnessBrowser__Cup4G11:RR42_RS00775  210 AVDFIEATAWIKQNLPYAKVSGGVSNVSFSFRGNDAVREAIHTVFLYHAIKAGMDMGIVNAGQLGVY 276 
                                                ******************************************************************* PP

                                 TIGR02082  593 ddidkelrevvedlildrrreatekLlelaelykgtkeksskea..qeaewrnlpveeRLeralvkG 657 
                                                d++d+elre ved++l+rr+++t++Lle+a++ykg  +k++++   +      +pv +RL++alv+G
  lcl|FitnessBrowser__Cup4G11:RR42_RS00775  277 DQLDAELRERVEDVVLNRREDSTDRLLEIADRYKGGGAKKEENLlwRGTPENPVPVADRLSHALVHG 343 
                                                **********************************9988865554114455566789*********** PP

                                 TIGR02082  658 eregieedleearkklk....apleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLe 720 
                                                 + +i ed+ee r++++    +++e+iegpL+dGm++vGdLFG+GkmfLPqvvksarvmk+ava+L 
  lcl|FitnessBrowser__Cup4G11:RR42_RS00775  344 LTTFIVEDTEEVRQQVEarggRTIEVIEGPLMDGMNIVGDLFGAGKMFLPQVVKSARVMKQAVAHLL 410 
                                                *************8775333379******************************************** PP

                                 TIGR02082  721 Pylekekeed.......kskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaa 780 
                                                Py+e+ek          k++Gkiv+atvkGDvhDiGkniv+vvL+cn++evv++Gv+vP+++il  a
  lcl|FitnessBrowser__Cup4G11:RR42_RS00775  411 PYIEEEKRLLaeaggdvKARGKIVIATVKGDVHDIGKNIVSVVLQCNNFEVVNMGVMVPCNEILARA 477 
                                                ******96446678999************************************************** PP

                                 TIGR02082  781 kkkkaDviglsGLivksldemvevaeemerrgvk....iPlllGGaalskahvavkiaekYkgevvy 843 
                                                k + aD++glsGLi++sl+em++va em+r        iPll+GGa++s+ h+avkia++Y+g+vvy
  lcl|FitnessBrowser__Cup4G11:RR42_RS00775  478 KVEGADIVGLSGLITPSLEEMAYVASEMQRDDYFrikkIPLLIGGATTSRVHTAVKIAPHYEGPVVY 544 
                                                ******************************87422446***************************** PP

                                 TIGR02082  844 vkdaseavkvvdkllsekkkaeelekikeeyeeirekfgekkeklialsekaarkevfaldrsedle 910 
                                                v das++v+v+++lls++  a +l+++k++ye ir+++ + k+ +  +s+++ar ++  +d+s ++ 
  lcl|FitnessBrowser__Cup4G11:RR42_RS00775  545 VPDASRSVSVASSLLSDDGAARYLDELKTDYERIRHQHAN-KKATPMVSLAKARANKTPVDWS-AYV 609 
                                                **************************************98.778999****************.*** PP

                                 TIGR02082  911 vpapkflGtkvleas.ieellkyiDwkalFvqWelrgkypkilkdeleglearklfkdakelldkls 976 
                                                +p+pkf+G+++++++ + el +yiDw ++F +W+l+gk+p il+de++g+ ar++f+d k++l +l+
  lcl|FitnessBrowser__Cup4G11:RR42_RS00775  610 PPKPKFIGRRIFRNYdLTELANYIDWAPFFQTWDLAGKFPDILNDEIVGESARRVFSDGKAMLSRLI 676 
                                                ******************************************************************* PP

                                 TIGR02082  977 aekllrargvvGlfPaqsvg.ddieiytdetvsqetkpiatvrekleqlrqqsdr.........ylc 1033
                                                + + l+a+gv+ l Pa+ v+ ddieiytdet+sq + +        ++lrqqs+r         + c
  lcl|FitnessBrowser__Cup4G11:RR42_RS00775  677 QGRWLTANGVLALLPANAVNdDDIEIYTDETRSQVALTW-------HNLRQQSERpvidgvmrpNRC 736 
                                                *****************876268********96554444.......555555555555566689*** PP

                                 TIGR02082 1034 laDfiaskesGikDylgallvtaglgaeelakkleakeddydsilvkaladrlaealaellhervRk 1100
                                                laDf+a+k+sGi+Dy+g+++vtag+g+++   ++ea++ddy++i++k+ladrlaea+ae lhervR+
  lcl|FitnessBrowser__Cup4G11:RR42_RS00775  737 LADFVAPKDSGIADYIGVFAVTAGIGVDKKEAQFEADHDDYSAIMLKSLADRLAEAFAECLHERVRR 803 
                                                ******************************************************************* PP

                                 TIGR02082 1101 elwgyaeeenldkedllkerYrGirpafGYpacPdhtekatlleLleaeriGlklteslalaPeasv 1167
                                                +lwgy + e l +e+l+ e YrGirpa+GYpacP+ht ka ++e l+a +iG+ +t+sla++P+asv
  lcl|FitnessBrowser__Cup4G11:RR42_RS00775  804 DLWGYDAGEVLTNEQLIAETYRGIRPAPGYPACPEHTVKAPMFEFLNAAEIGMGITDSLAMTPAASV 870 
                                                ******************************************************************* PP

                                 TIGR02082 1168 sglyfahpeakYfav 1182
                                                sg+y+ahpe+ Yf+v
  lcl|FitnessBrowser__Cup4G11:RR42_RS00775  871 SGFYLAHPESTYFSV 885 
                                                *************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (915 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: 13.41
//
[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:

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