Alignments for a candidate for metH in Rhodospirillum centenum SW; ATCC 51521

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Rhodospirillum centenum SW; ATCC 51521

Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_083759290.1 RC1_RS09810 methionine synthase

Query= CharProtDB::CH_090726
         (1227 letters)



>NCBI__GCF_000016185.1:WP_083759290.1
          Length = 953

 Score = 1108 bits (2866), Expect = 0.0
 Identities = 570/885 (64%), Positives = 676/885 (76%), Gaps = 15/885 (1%)

Query: 354  SLFVNVGERTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAM 413
            +LFVNVGERTNVTGSA+FK+LI E  +  ALDVAR+QV NGAQ+ID+NMDE MLD+EAAM
Sbjct: 61   ALFVNVGERTNVTGSARFKKLILEGNFEAALDVAREQVANGAQVIDVNMDEAMLDSEAAM 120

Query: 414  VRFLNLIAGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLL 473
            VRFL LIA EPDIARVP+MIDSSKW VIE GLK +QGK IVNSIS+KEG + FI HA+ +
Sbjct: 121  VRFLRLIASEPDIARVPVMIDSSKWSVIEAGLKNVQGKPIVNSISLKEGEEPFIEHARKI 180

Query: 474  RRYGAAVVVMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIE 533
            RRYGAAVVVMAFDE+GQADTR RK+EICRR+Y IL   VGFP EDIIFDPN+FAVATGIE
Sbjct: 181  RRYGAAVVVMAFDEKGQADTRDRKVEICRRSYDILVNRVGFPAEDIIFDPNVFAVATGIE 240

Query: 534  EHNNYAQDFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMD 593
            EHNNYA DFI A   I+R  P   ISGG+SNVSFSFRGN+ VR A+H+VFLY+AI  GMD
Sbjct: 241  EHNNYAVDFIEAARLIRRACPGCHISGGLSNVSFSFRGNNAVRAAMHSVFLYHAIPAGMD 300

Query: 594  MGIVNAGQLAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAE 653
            MGIVNAG+L +YD++PAELR+ VEDVILNRR D T+RLLE+A+KY+G      A+     
Sbjct: 301  MGIVNAGELPVYDEIPAELRERVEDVILNRRPDATDRLLEVADKYKGGAAKKEAD---LS 357

Query: 654  WRSWEVNKRLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKM 713
            WR  +V  RL ++LV GI E+I+ D EEAR+QA RP+ VIEGPLMDGMNVVGDLFG GKM
Sbjct: 358  WRQQDVRARLTHALVHGIDEYIDTDVEEARRQADRPLSVIEGPLMDGMNVVGDLFGAGKM 417

Query: 714  FLPQVVKSARVMKQAVAYLEPFIEASKEQ------GKTNGKMVIATVKGDVHDIGKNIVG 767
            FLPQVVKSARVMK+AVAYL PFIE  K          + G++++ATVKGDVHDIGKNIVG
Sbjct: 418  FLPQVVKSARVMKKAVAYLLPFIEEEKAAAGGGGGSDSAGRVLMATVKGDVHDIGKNIVG 477

Query: 768  VVLQCNNYEIVDLGVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFT 827
            VVLQCNN+E+VDLGVMVP  KIL  A+    D+IGLSGLITPSLDEMV VAKEM R+GF 
Sbjct: 478  VVLQCNNFEVVDLGVMVPCAKILEEARRHKVDIIGLSGLITPSLDEMVFVAKEMAREGFD 537

Query: 828  IPLLIGGATTSKAHTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEY 887
            IPLLIGGATTSK HTAVKI+ +Y+GP V+V +ASR VGV   LLS   +  +    + +Y
Sbjct: 538  IPLLIGGATTSKVHTAVKIDPHYAGPVVHVLDASRAVGVAQNLLSADAKTGYAGGIKADY 597

Query: 888  ETVRIQHGRKKPRTPPVTLEAARDNDFAFDWQAYTP--PVAHRLGVQEVEASIETLRNYI 945
              +R  H R +     ++L  AR N F+ DW AY P  P A  + V E +  +  L   I
Sbjct: 598  ARMREAHERNQYGRARLSLADARANRFSPDWSAYAPVRPAAPGVTVFE-DYDLAELATRI 656

Query: 946  DWTPFFMTWSLAGKYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPAN 1005
            DW  FF  W LAG +P IL+DE+VG  A+ LFKDA  ML ++  EK L  RGV+GLFPAN
Sbjct: 657  DWKFFFEAWELAGSFPAILDDEIVGESARGLFKDAQVMLQRIIGEKWLTARGVIGLFPAN 716

Query: 1006 RVGDDIEIYRDETRTHVINVSHHLRQQTEK---TGFANYCLADFVAPKLSGKADYIGAFA 1062
             VGDD+EIY DE+RT V+   H LRQQ  +      A+ CLADF+APK SG  D+IG+FA
Sbjct: 717  SVGDDVEIYTDESRTTVLTRLHFLRQQMAREPGRERAHLCLADFIAPKQSGVPDWIGSFA 776

Query: 1063 VTGGLEEDALADAFEAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSN 1122
            VT G   +  A AFEA HDDYN I++KAL DRLAEAFAE +HERVR+ +W YAP+E LSN
Sbjct: 777  VTAGHGLEERARAFEAAHDDYNAILLKALGDRLAEAFAERMHERVRREFWAYAPDETLSN 836

Query: 1123 EELIRENYQGIRPAPGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYF 1182
            EELI E Y+GIRPAPGYPACP+HTEKAT+W LL+ EK  G+ LTE+FAM P A+VSGWY 
Sbjct: 837  EELIAEAYRGIRPAPGYPACPDHTEKATLWRLLDAEKAAGISLTETFAMMPTAAVSGWYI 896

Query: 1183 SHPDSKYYAVAQIQRDQVEDYARRKGMSVTEVERWLAPNLGYDAD 1227
            +HP++KY+ + +I+RDQV DYARRKGM V  +ERWLAPNL YD D
Sbjct: 897  AHPEAKYFGLGKIERDQVADYARRKGMEVAAMERWLAPNLNYDPD 941


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: 2805
Number of extensions: 107
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: 953
Length adjustment: 46
Effective length of query: 1181
Effective length of database: 907
Effective search space:  1071167
Effective search space used:  1071167
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_041786279.1 RC1_RS09795 5-methyltetrahydrofolate--homocysteine methyltransferase

Query= CharProtDB::CH_090726
         (1227 letters)



>NCBI__GCF_000016185.1:WP_041786279.1
          Length = 355

 Score =  432 bits (1112), Expect = e-125
 Identities = 215/347 (61%), Positives = 262/347 (75%)

Query: 4   KVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPEV 63
           ++ +LR     RILV+DG MGTMIQ + L+EA +RGERF DWP D+KGNNDLL L++P++
Sbjct: 6   RLAKLRGIAARRILVIDGAMGTMIQRHHLDEAGYRGERFKDWPRDVKGNNDLLSLTRPDI 65

Query: 64  IAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTARTP 123
           I  IH  Y  AGADIIETNTFNST+I++ADY ME+L+ E+N A AKLAR  AD   A  P
Sbjct: 66  IRDIHAQYLAAGADIIETNTFNSTSISLADYGMEALAYELNVAGAKLAREAADAAEAADP 125

Query: 124 EKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIETV 183
            +PRYVAG LGPTNRTASISP V DP FRN+ FD L  AY E T+ L++GGAD++L+ETV
Sbjct: 126 SRPRYVAGALGPTNRTASISPVVTDPGFRNVDFDELRGAYAEQTRGLIDGGADVLLVETV 185

Query: 184 FDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALTF 243
           FDTLNAKAA+FAV+   E  G++LP+MISGTITD SGRTLSGQTTEAF+NSLRH    + 
Sbjct: 186 FDTLNAKAALFAVEEVLEERGLDLPVMISGTITDRSGRTLSGQTTEAFWNSLRHVRPFSI 245

Query: 244 GLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAGF 303
           GLNCALG D +R YVQEL+R+A+  V+A+PNAGLPN FG YD     MA+ +  WA  G 
Sbjct: 246 GLNCALGADLMRPYVQELARVADVPVSAYPNAGLPNEFGGYDETPAQMAQSLHSWAADGL 305

Query: 304 LNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNI 350
           +NIVGGCCGTTP HI A++ AV+ + PR  P    A RLSGLEP  +
Sbjct: 306 VNIVGGCCGTTPDHIRAIAEAVKDVTPRVPPVPDRAMRLSGLEPFTM 352


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: 1051
Number of extensions: 37
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: 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 WP_083759290.1 RC1_RS09810 (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.26311.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 1242.5   0.0          0 1242.2   0.0    1.0  1  lcl|NCBI__GCF_000016185.1:WP_083759290.1  RC1_RS09810 methionine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016185.1:WP_083759290.1  RC1_RS09810 methionine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1242.2   0.0         0         0     338    1181 ..      58     905 ..      41     906 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1242.2 bits;  conditional E-value: 0
                                 TIGR02082  338 aqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmkkll 404 
                                                 + + fvn+GeRtnv+Gs++f+kli ++++e+al++a++qv +Gaq++D+n+De++lD+ea+m+++l
  lcl|NCBI__GCF_000016185.1:WP_083759290.1   58 PRTALFVNVGERTNVTGSARFKKLILEGNFEAALDVAREQVANGAQVIDVNMDEAMLDSEAAMVRFL 124 
                                                56789************************************************************** PP

                                 TIGR02082  405 sllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavvvma 471 
                                                +l+asepdia+vP+m+Dss++ v+eaGLk +qGk ivnsislk+Gee F+e+a++i++yGaavvvma
  lcl|NCBI__GCF_000016185.1:WP_083759290.1  125 RLIASEPDIARVPVMIDSSKWSVIEAGLKNVQGKPIVNSISLKEGEEPFIEHARKIRRYGAAVVVMA 191 
                                                ******************************************************************* PP

                                 TIGR02082  472 fDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieaireike 538 
                                                fDe+Gqa+t+d+k+ei++R y++l+++vgfp+ediifDpn++++atGieeh++ya+dfiea r i++
  lcl|NCBI__GCF_000016185.1:WP_083759290.1  192 FDEKGQADTRDRKVEICRRSYDILVNRVGFPAEDIIFDPNVFAVATGIEEHNNYAVDFIEAARLIRR 258 
                                                ******************************************************************* PP

                                 TIGR02082  539 elPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrevved 605 
                                                  P ++isgG+snvsFs+rgn+avR a+hsvFLy+ai aG+Dmgivnag+l vyd+i++elre ved
  lcl|NCBI__GCF_000016185.1:WP_083759290.1  259 ACPGCHISGGLSNVSFSFRGNNAVRAAMHSVFLYHAIPAGMDMGIVNAGELPVYDEIPAELRERVED 325 
                                                ******************************************************************* PP

                                 TIGR02082  606 lildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleearkk 672 
                                                +il+rr++at++Lle+a++ykg  +k   +++   wr+++v+ RL++alv+G+ e+i+ d+eear++
  lcl|NCBI__GCF_000016185.1:WP_083759290.1  326 VILNRRPDATDRLLEVADKYKGGAAK---KEADLSWRQQDVRARLTHALVHGIDEYIDTDVEEARRQ 389 
                                                **********************9999...456778******************************** PP

                                 TIGR02082  673 lkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeed......ksk 733 
                                                + +pl +iegpL+dGm+vvGdLFG+GkmfLPqvvksarvmkkavayL P++e+ek++       +s+
  lcl|NCBI__GCF_000016185.1:WP_083759290.1  390 ADRPLSVIEGPLMDGMNVVGDLFGAGKMFLPQVVKSARVMKKAVAYLLPFIEEEKAAAgggggsDSA 456 
                                                *******************************************************9989999999** PP

                                 TIGR02082  734 GkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivkslde 800 
                                                G++++atvkGDvhDiGkniv+vvL+cn++evvdlGv+vP++kile+a+++k D+iglsGLi++slde
  lcl|NCBI__GCF_000016185.1:WP_083759290.1  457 GRVLMATVKGDVHDIGKNIVGVVLQCNNFEVVDLGVMVPCAKILEEARRHKVDIIGLSGLITPSLDE 523 
                                                ******************************************************************* PP

                                 TIGR02082  801 mvevaeemerrgvkiPlllGGaalskahvavkiaekYkgevvyvkdaseavkvvdkllsekkkaeel 867 
                                                mv+va+em r+g++iPll+GGa++sk h+avki+++Y g+vv+v das+av v+++lls+++k+ ++
  lcl|NCBI__GCF_000016185.1:WP_083759290.1  524 MVFVAKEMAREGFDIPLLIGGATTSKVHTAVKIDPHYAGPVVHVLDASRAVGVAQNLLSADAKTGYA 590 
                                                ******************************************************************* PP

                                 TIGR02082  868 ekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieellkyi 933 
                                                + ik++y  +re +++++  +  ls+++ar ++f++d+s ++ ++ p   G+ v+e++ ++el   i
  lcl|NCBI__GCF_000016185.1:WP_083759290.1  591 GGIKADYARMREAHERNQYGRARLSLADARANRFSPDWS-AYAPVRPAAPGVTVFEDYdLAELATRI 656 
                                                ***************************************.*************************** PP

                                 TIGR02082  934 DwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvgddie 1000
                                                Dwk++F +Wel+g++p il+de++g+ ar lfkda+ +l++++ ek l+argv+GlfPa+svgdd+e
  lcl|NCBI__GCF_000016185.1:WP_083759290.1  657 DWKFFFEAWELAGSFPAILDDEIVGESARGLFKDAQVMLQRIIGEKWLTARGVIGLFPANSVGDDVE 723 
                                                ******************************************************************* PP

                                 TIGR02082 1001 iytdetvsqetkpiatvrekleqlrqqsdr.......ylclaDfiaskesGikDylgallvtaglga 1060
                                                iytde++       +tv ++l++lrqq +r       +lclaDfia+k+sG  D++g ++vtag g 
  lcl|NCBI__GCF_000016185.1:WP_083759290.1  724 IYTDESR-------TTVLTRLHFLRQQMARepgreraHLCLADFIAPKQSGVPDWIGSFAVTAGHGL 783 
                                                ***9999.......344455566666665555557789***************************** PP

                                 TIGR02082 1061 eelakkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpa 1127
                                                ee a+++ea +ddy++il+kal+drlaea+ae +hervR+e+w+ya +e l++e+l+ e YrGirpa
  lcl|NCBI__GCF_000016185.1:WP_083759290.1  784 EERARAFEAAHDDYNAILLKALGDRLAEAFAERMHERVRREFWAYAPDETLSNEELIAEAYRGIRPA 850 
                                                ******************************************************************* PP

                                 TIGR02082 1128 fGYpacPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfa 1181
                                                +GYpacPdhtekatl++Ll+ae+  G+ lte +a++P+a+vsg+y+ahpeakYf 
  lcl|NCBI__GCF_000016185.1:WP_083759290.1  851 PGYPACPDHTEKATLWRLLDAEKaAGISLTETFAMMPTAAVSGWYIAHPEAKYFG 905 
                                                ***********************9******************************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (953 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: 0.08u 0.03s 00:00:00.11 Elapsed: 00:00:00.10
# Mc/sec: 10.74
//
[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