Alignments for a candidate for metH in Stenotrophomonas chelatiphaga DSM 21508

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Stenotrophomonas chelatiphaga DSM 21508

Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_057507948.1 ABB28_RS06945 methionine synthase

Query= CharProtDB::CH_090726
         (1227 letters)



>NCBI__GCF_001431535.1:WP_057507948.1
          Length = 894

 Score = 1119 bits (2894), Expect = 0.0
 Identities = 558/893 (62%), Positives = 692/893 (77%), Gaps = 12/893 (1%)

Query: 341  RLSGLEPLNIGEDSLFVNVGERTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDI 400
            RLSGLEPL I  D LF+N+GERTNVTGSA+F++L+KEE+Y EA+DVARQQV +GAQI+D+
Sbjct: 8    RLSGLEPLVITPDLLFINIGERTNVTGSAQFRKLVKEERYEEAVDVARQQVASGAQILDV 67

Query: 401  NMDEGMLDAEAAMVRFLNLIAGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMK 460
            NMDEG++D+EAAM R+LNLI  EPDIAR+P+M+DSSKW VIE GLKC+QGK +VNSIS+K
Sbjct: 68   NMDEGLIDSEAAMTRYLNLIMSEPDIARIPVMVDSSKWSVIEAGLKCLQGKSVVNSISLK 127

Query: 461  EGVDAFIHHAKLLRRYGAAVVVMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDII 520
            EG D F  HA+ + RYGAA VVMAFDE GQADT ARK+EIC RAY+IL +E+GFPP+DII
Sbjct: 128  EGEDLFREHARKVLRYGAAAVVMAFDEAGQADTCARKVEICTRAYRILVDEIGFPPQDII 187

Query: 521  FDPNIFAVATGIEEHNNYAQDFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIH 580
            FDPNIFAVATGIEEH+NYA DFI A   IKR LPH  +SGGVSNVSFSFRGN+ VR+AIH
Sbjct: 188  FDPNIFAVATGIEEHDNYAVDFIEATRIIKRTLPHCHVSGGVSNVSFSFRGNETVRQAIH 247

Query: 581  AVFLYYAIRNGMDMGIVNAGQLAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRG 640
            +VFLY+AI  GMDMGIVNAG + IYDDL AELR+ VEDVILNRR DGTERLLE+AE+Y+G
Sbjct: 248  SVFLYHAIAAGMDMGIVNAGAMPIYDDLDAELRERVEDVILNRRADGTERLLEIAERYKG 307

Query: 641  SKTDDTANAQQAEWRSWEVNKRLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDG 700
            SK    A  +   WR   V  RL ++LV G+  ++EQDTEEARQ +TRP++VIEGPLM+G
Sbjct: 308  SK--GAARVEDLAWREKPVTDRLAHALVHGLDAWVEQDTEEARQASTRPLDVIEGPLMNG 365

Query: 701  MNVVGDLFGEGKMFLPQVVKSARVMKQAVAYLEPFIEASK----EQGKTNGKMVIATVKG 756
            MNVVGDLFG GKMFLPQVVKSARVMK+AVAYL P+IEA K    +  ++NGK+++ATVKG
Sbjct: 366  MNVVGDLFGAGKMFLPQVVKSARVMKKAVAYLLPYIEAEKLRSGDTARSNGKIIMATVKG 425

Query: 757  DVHDIGKNIVGVVLQCNNYEIVDLGVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVN 816
            DVHDIGKNIVGVVL CNN+E++DLGVMVPA+KIL  A+  NAD+IGLSGLITPSL+EM +
Sbjct: 426  DVHDIGKNIVGVVLACNNFEVIDLGVMVPAQKILDAARAENADIIGLSGLITPSLEEMSH 485

Query: 817  VAKEMERQGFTIPLLIGGATTSKAHTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQR 876
            VA+EM+RQGF +PL+IGGATTS+AHTA+KI+ +Y  PTV+V++ASR VGV  +L+S   R
Sbjct: 486  VAREMQRQGFELPLMIGGATTSRAHTALKIDPHYKAPTVWVKDASRAVGVAQSLISHDLR 545

Query: 877  DDFVARTRKEYETVRIQHGRKKPRTPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEV-E 935
              FVA    +Y  +R++H  +      V+L  AR   F   W  Y PP  ++ G+    +
Sbjct: 546  AAFVAANEADYADIRLRHRNRGDAKRLVSLAHARGQRFDGGWADYVPPAPNQPGLHVFDD 605

Query: 936  ASIETLRNYIDWTPFFMTWSLAGKYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNP 995
              +  L +YIDWTPFF  W LAGKYP IL DE+VG +A  L++DA  MLD++  E+ L  
Sbjct: 606  YPLAELVDYIDWTPFFQAWELAGKYPAILTDEIVGSQASELYRDARQMLDRIVKERWLQA 665

Query: 996  RGVVGLFPANRVGDDIEIYRDETRTHVINVSHHLRQQTEKTG-FANYCLADFVAPKLSGK 1054
            R V GL+PAN VGDD+ +   +    +    H LRQQ +K     ++CLADF+AP  SG+
Sbjct: 666  RAVFGLWPANSVGDDVRVQHPDGEATL----HFLRQQVDKPAERPDFCLADFIAPADSGR 721

Query: 1055 ADYIGAFAVTGGLEEDALADAFEAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGY 1114
             D+IGAFAVT G+  DA    FEA HDDYN I++KALADR AEA AE LH+RVRK +WG+
Sbjct: 722  QDWIGAFAVTAGIGIDAHVARFEAAHDDYNAILLKALADRFAEALAERLHQRVRKEFWGH 781

Query: 1115 APNENLSNEELIRENYQGIRPAPGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPG 1174
            A +E L N+ LI E Y GIRPAPGYPACPEH+EK T++ LL+ + + GM+LTESFAM P 
Sbjct: 782  ANDETLDNDALIAEKYSGIRPAPGYPACPEHSEKDTLFRLLDAQGNAGMQLTESFAMLPT 841

Query: 1175 ASVSGWYFSHPDSKYYAVAQIQRDQVEDYARRKGMSVTEVERWLAPNLGYDAD 1227
            A+VSG+YFSHP S+Y+ V ++ R+QV DYA+RKG+   + ERWLA NL YD +
Sbjct: 842  AAVSGYYFSHPQSQYFVVGRVSREQVTDYAKRKGVDRVQAERWLASNLDYDPE 894


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: 2638
Number of extensions: 114
Number of successful extensions: 6
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: 894
Length adjustment: 45
Effective length of query: 1182
Effective length of database: 849
Effective search space:  1003518
Effective search space used:  1003518
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_057507947.1 ABB28_RS06940 5-methyltetrahydrofolate--homocysteine methyltransferase

Query= CharProtDB::CH_090726
         (1227 letters)



>NCBI__GCF_001431535.1:WP_057507947.1
          Length = 368

 Score =  411 bits (1056), Expect = e-119
 Identities = 204/347 (58%), Positives = 253/347 (72%), Gaps = 20/347 (5%)

Query: 8   LRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFAD--------------------WPC 47
           L + L ERIL++DG MGTMIQ + L E D+RGERF                         
Sbjct: 15  LLSALRERILIIDGAMGTMIQRHGLQEDDYRGERFIGGVDTRAAGHVHGAGCDHGPVQEQ 74

Query: 48  DLKGNNDLLVLSKPEVIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAA 107
           DLKGNNDLL+L++PE+IA IH  Y +AGAD++ETNTFN+T+++ ADY +E L  E+N A 
Sbjct: 75  DLKGNNDLLLLTRPEIIAGIHTEYLQAGADLVETNTFNATSVSQADYHLEHLVYELNKAG 134

Query: 108 AKLARACADEWTARTPEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYREST 167
           A +ARAC D   A TP+KPR+V GVLGPT+RTASISPDVNDP FRN +FD L   YRE+ 
Sbjct: 135 AAVARACCDAMEATTPDKPRFVIGVLGPTSRTASISPDVNDPGFRNTSFDELRGTYREAI 194

Query: 168 KALVEGGADLILIETVFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQT 227
             L++GGAD +++ET+FDTLNAKAA+FAV+  F+A G  LP+MISGTITDASGRTLSGQT
Sbjct: 195 DGLIDGGADTLMVETIFDTLNAKAALFAVEEAFDARGARLPVMISGTITDASGRTLSGQT 254

Query: 228 TEAFYNSLRHAEALTFGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLD 287
            EAF+ SL HA  L+ GLNCALG D +R +V+ LS++A CYV+AHPNAGLPNAFGEYD  
Sbjct: 255 AEAFHASLAHARPLSIGLNCALGADAMRPHVETLSQVAGCYVSAHPNAGLPNAFGEYDET 314

Query: 288 ADTMAKQIREWAQAGFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLP 334
            + MA  +  +A  G LN+VGGCCG+TP HI A++ AV GL PR LP
Sbjct: 315 PEEMAATLHGFATDGLLNLVGGCCGSTPAHIRAIAEAVAGLPPRALP 361


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: 1109
Number of extensions: 44
Number of successful extensions: 2
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: 368
Length adjustment: 38
Effective length of query: 1189
Effective length of database: 330
Effective search space:   392370
Effective search space used:   392370
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_057507948.1 ABB28_RS06945 (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.14206.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 1222.0   0.0          0 1221.9   0.0    1.0  1  lcl|NCBI__GCF_001431535.1:WP_057507948.1  ABB28_RS06945 methionine synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057507948.1  ABB28_RS06945 methionine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1221.9   0.0         0         0     324    1182 .]       4     859 ..       1     859 [. 0.98

  Alignments for each domain:
  == domain 1  score: 1221.9 bits;  conditional E-value: 0
                                 TIGR02082  324 eeksvlsglealkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvD 390 
                                                 ++++lsgle+l i+++  f+niGeRtnv+Gs++frkl+k+e yeea+++a+qqv +GaqilD+n+D
  lcl|NCBI__GCF_001431535.1:WP_057507948.1    4 APHTRLSGLEPLVITPDLLFINIGERTNVTGSAQFRKLVKEERYEEAVDVARQQVASGAQILDVNMD 70  
                                                57899************************************************************** PP

                                 TIGR02082  391 evllDgeadmkkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFleka 457 
                                                e+l D+ea+m+++l+l+ sepdia++P+m+Dss++ v+eaGLk++qGk++vnsislk+Ge+ F e+a
  lcl|NCBI__GCF_001431535.1:WP_057507948.1   71 EGLIDSEAAMTRYLNLIMSEPDIARIPVMVDSSKWSVIEAGLKCLQGKSVVNSISLKEGEDLFREHA 137 
                                                ******************************************************************* PP

                                 TIGR02082  458 klikeyGaavvvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdr 524 
                                                +++ +yGaa+vvmafDe Gqa+t ++k+ei++Ray++l++++gfpp+diifDpni+++atGieehd+
  lcl|NCBI__GCF_001431535.1:WP_057507948.1  138 RKVLRYGAAAVVMAFDEAGQADTCARKVEICTRAYRILVDEIGFPPQDIIFDPNIFAVATGIEEHDN 204 
                                                ******************************************************************* PP

                                 TIGR02082  525 yaidfieaireikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklav 591 
                                                ya+dfiea+r ik++lP++++sgGvsnvsFs+rgn++vR+a+hsvFLy+ai aG+Dmgivnag + +
  lcl|NCBI__GCF_001431535.1:WP_057507948.1  205 YAVDFIEATRIIKRTLPHCHVSGGVSNVSFSFRGNETVRQAIHSVFLYHAIAAGMDMGIVNAGAMPI 271 
                                                ******************************************************************* PP

                                 TIGR02082  592 yddidkelrevvedlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGe 658 
                                                ydd+d+elre ved+il+rr + te+Lle+ae+ykg k +  +  +  +wr++pv++RL++alv+G 
  lcl|NCBI__GCF_001431535.1:WP_057507948.1  272 YDDLDAELRERVEDVILNRRADGTERLLEIAERYKGSKGA--ARVEDLAWREKPVTDRLAHALVHGL 336 
                                                **************************************99..6678889****************** PP

                                 TIGR02082  659 regieedleearkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylek 725 
                                                   +e+d+eear+  ++pl++iegpL++Gm+vvGdLFG+GkmfLPqvvksarvmkkavayL Py+e+
  lcl|NCBI__GCF_001431535.1:WP_057507948.1  337 DAWVEQDTEEARQASTRPLDVIEGPLMNGMNVVGDLFGAGKMFLPQVVKSARVMKKAVAYLLPYIEA 403 
                                                ******************************************************************* PP

                                 TIGR02082  726 ekeed....kskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDvi 788 
                                                ek  +    +s+Gki++atvkGDvhDiGkniv+vvL+cn++ev+dlGv+vP++kil+aa+ ++aD+i
  lcl|NCBI__GCF_001431535.1:WP_057507948.1  404 EKLRSgdtaRSNGKIIMATVKGDVHDIGKNIVGVVLACNNFEVIDLGVMVPAQKILDAARAENADII 470 
                                                *987777889********************************************************* PP

                                 TIGR02082  789 glsGLivksldemvevaeemerrgvkiPlllGGaalskahvavkiaekYkgevvyvkdaseavkvvd 855 
                                                glsGLi++sl+em +va+em+r+g+++Pl++GGa++s+ah+a ki+++Yk+++v+vkdas+av v++
  lcl|NCBI__GCF_001431535.1:WP_057507948.1  471 GLSGLITPSLEEMSHVAREMQRQGFELPLMIGGATTSRAHTALKIDPHYKAPTVWVKDASRAVGVAQ 537 
                                                ******************************************************************* PP

                                 TIGR02082  856 kllsekkkaeelekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvl 922 
                                                +l+s++ +a+++++++++y +ir +++++ + ++ +s+++ar ++f+  +  d+ +pap++ G +v+
  lcl|NCBI__GCF_001431535.1:WP_057507948.1  538 SLISHDLRAAFVAANEADYADIRLRHRNRGDAKRLVSLAHARGQRFDGGWA-DYVPPAPNQPGLHVF 603 
                                                ***************************************************.*************** PP

                                 TIGR02082  923 eas.ieellkyiDwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvG 988 
                                                +++ ++el++yiDw+++F +Wel+gkyp il+de++g +a +l++da+++ld++++e+ l+ar+v+G
  lcl|NCBI__GCF_001431535.1:WP_057507948.1  604 DDYpLAELVDYIDWTPFFQAWELAGKYPAILTDEIVGSQASELYRDARQMLDRIVKERWLQARAVFG 670 
                                                ******************************************************************* PP

                                 TIGR02082  989 lfPaqsvgddieiytdetvsqetkpiatvrekleqlrqqsdr.ylclaDfiaskesGikDylgallv 1054
                                                l+Pa+svgdd+ + ++++        at++  ++q+ +  +r   claDfia+ +sG +D++ga++v
  lcl|NCBI__GCF_001431535.1:WP_057507948.1  671 LWPANSVGDDVRVQHPDGE-------ATLHFLRQQVDKPAERpDFCLADFIAPADSGRQDWIGAFAV 730 
                                                *************996665.......777666666666666689*********************** PP

                                 TIGR02082 1055 taglgaeelakkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerY 1121
                                                tag+g+++   ++ea +ddy++il+kaladr+aealae lh+rvRke+wg a++e ld++ l+ e+Y
  lcl|NCBI__GCF_001431535.1:WP_057507948.1  731 TAGIGIDAHVARFEAAHDDYNAILLKALADRFAEALAERLHQRVRKEFWGHANDETLDNDALIAEKY 797 
                                                ******************************************************************* PP

                                 TIGR02082 1122 rGirpafGYpacPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfav 1182
                                                 Girpa+GYpacP+h+ek tl++Ll+a+   G++ltes+a+ P+a+vsg+yf+hp+++Yf v
  lcl|NCBI__GCF_001431535.1:WP_057507948.1  798 SGIRPAPGYPACPEHSEKDTLFRLLDAQGnAGMQLTESFAMLPTAAVSGYYFSHPQSQYFVV 859 
                                                ***************************998******************************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (894 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: 13.01
//
[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