Alignments for a candidate for metH in Dyella japonica UNC79MFTsu3.2

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Dyella japonica UNC79MFTsu3.2

Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate N515DRAFT_0495 N515DRAFT_0495 methionine synthase (B12-dependent)

Query= CharProtDB::CH_090726
         (1227 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0495
          Length = 895

 Score = 1150 bits (2974), Expect = 0.0
 Identities = 572/893 (64%), Positives = 709/893 (79%), Gaps = 10/893 (1%)

Query: 341  RLSGLEPLNIGEDSLFVNVGERTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDI 400
            RLSGLEPL I  D LFVNVGERTNVTGSA+F++LIKE++Y EA+DVARQQV +GAQIID+
Sbjct: 7    RLSGLEPLVITPDLLFVNVGERTNVTGSAQFRKLIKEDRYEEAVDVARQQVASGAQIIDV 66

Query: 401  NMDEGMLDAEAAMVRFLNLIAGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMK 460
            NMDEG++D+EAAM RFLNLIA EPDIARVP+M+DSSKW V+E GL+C+QGKGIVNSISMK
Sbjct: 67   NMDEGLIDSEAAMTRFLNLIAAEPDIARVPVMVDSSKWTVLEAGLRCLQGKGIVNSISMK 126

Query: 461  EGVDAFIHHAKLLRRYGAAVVVMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDII 520
            EG + F+ HA+ +++YGAAVVVMAFDEQGQADT  RK+EIC RAY +LTE++ FPPEDI+
Sbjct: 127  EGEELFLEHARKVQQYGAAVVVMAFDEQGQADTCERKVEICSRAYALLTEQLDFPPEDIV 186

Query: 521  FDPNIFAVATGIEEHNNYAQDFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIH 580
            FDPNIFA+ATGIEEHNNYA DFI A  ++KR  P + ISGGVSNVSFSFRGN+ VREAIH
Sbjct: 187  FDPNIFAIATGIEEHNNYAVDFIEATRELKRRFPLSHISGGVSNVSFSFRGNNTVREAIH 246

Query: 581  AVFLYYAIRNGMDMGIVNAGQLAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRG 640
            +VFLY+AI+ GMDMGIVNAG L IYDD+PAELR+ VEDV+LNRR D TERLLE+A+ Y+ 
Sbjct: 247  SVFLYHAIKAGMDMGIVNAGALMIYDDVPAELRERVEDVVLNRRPDATERLLEIADNYKA 306

Query: 641  SKTDDTANAQQAEWRSWEVNKRLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDG 700
             K +     +   WR   V +RL ++LV GI  F++ DTEEARQ ATRP++VIEGPLMDG
Sbjct: 307  RKGE--VVVENLAWREKPVRERLSHALVHGIDAFVDADTEEARQLATRPLDVIEGPLMDG 364

Query: 701  MNVVGDLFGEGKMFLPQVVKSARVMKQAVAYLEPFIEASK----EQGKTNGKMVIATVKG 756
            MNVVGDLFG GKMFLPQVVKSARVMK+AVAYL P+IE  K    + GK NG +V+ATVKG
Sbjct: 365  MNVVGDLFGAGKMFLPQVVKSARVMKKAVAYLLPYIEEEKARTGDVGKNNGTIVMATVKG 424

Query: 757  DVHDIGKNIVGVVLQCNNYEIVDLGVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVN 816
            DVHDIGKNIVGVVL+CNN++++DLGVMVPA+KIL  A+E NADLIGLSGLITPSL+EM +
Sbjct: 425  DVHDIGKNIVGVVLRCNNFDVIDLGVMVPAQKILDAAREHNADLIGLSGLITPSLEEMSH 484

Query: 817  VAKEMERQGFTIPLLIGGATTSKAHTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQR 876
            VA+EM+RQ F+IPLLIGGATTS+AHTA+KI+ +Y  PTV+V++ASR VGV  +L+S    
Sbjct: 485  VAREMQRQEFSIPLLIGGATTSRAHTALKIDPHYKAPTVWVKDASRAVGVAQSLVSKDLV 544

Query: 877  DDFVARTRKEYETVRIQHGRKKPRTPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVEA 936
            D F+A+ R +YE VR +H  + P    V LE AR   +  DW  Y PP   + GV   +A
Sbjct: 545  DAFMAKVRADYEEVRERHRNRGPGKSLVPLEKARAQRYTCDWAGYAPPQPRQPGVTVFDA 604

Query: 937  -SIETLRNYIDWTPFFMTWSLAGKYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNP 995
              +  LR YIDWTPFF  W LAG+YP IL+DE+VG +A  LF+DA  MLD++ AE+ L  
Sbjct: 605  YDLAELREYIDWTPFFQAWELAGRYPAILKDEIVGTQASELFRDAQAMLDRIVAERWLTA 664

Query: 996  RGVVGLFPANRVGDDIEIYRDETRTHVINVSHHLRQQTEK-TGFANYCLADFVAPKLSGK 1054
            R V+G + A +VGDD E+Y ++ R   + V  HLRQQ +K     ++ L DF+APK +GK
Sbjct: 665  RAVIGFWRAAQVGDDTEVYGEDGRK--LAVLRHLRQQADKPADRPDFSLGDFIAPKEAGK 722

Query: 1055 ADYIGAFAVTGGLEEDALADAFEAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGY 1114
             D++GAFAVT G+  +     FEA HDDY+ I++KALADRLAEAFAE +H+RVR+ +WGY
Sbjct: 723  QDWVGAFAVTAGIGIEEHVARFEAAHDDYSSILLKALADRLAEAFAERMHQRVRREFWGY 782

Query: 1115 APNENLSNEELIRENYQGIRPAPGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPG 1174
            AP+E L NE LI E Y+GIRPAPGYPACP+HTEK+T+++LL+   + G++LTE +AM+P 
Sbjct: 783  APDEALDNEALIDEKYRGIRPAPGYPACPDHTEKSTLFKLLDATANAGIELTEGYAMYPT 842

Query: 1175 ASVSGWYFSHPDSKYYAVAQIQRDQVEDYARRKGMSVTEVERWLAPNLGYDAD 1227
            A+VSGWYFSHPDS+Y+ V ++ R+QVEDYA+RKG +  E ERWLAPNL YD D
Sbjct: 843  AAVSGWYFSHPDSQYFVVGRLTREQVEDYAKRKGWTREEAERWLAPNLDYDPD 895


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: 2658
Number of extensions: 96
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: 895
Length adjustment: 45
Effective length of query: 1182
Effective length of database: 850
Effective search space:  1004700
Effective search space used:  1004700
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 N515DRAFT_0494 N515DRAFT_0494 5-methyltetrahydrofolate--homocysteine methyltransferase

Query= CharProtDB::CH_090726
         (1227 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0494
          Length = 361

 Score =  427 bits (1099), Expect = e-124
 Identities = 211/345 (61%), Positives = 257/345 (74%), Gaps = 12/345 (3%)

Query: 4   KVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFA-----------DWP-CDLKG 51
           +V  L A L ERIL+LDGGMGTM+Q +RL E  FRGERF            D P CDLKG
Sbjct: 11  RVALLEAALRERILILDGGMGTMLQGHRLEEEGFRGERFVEGRDHAHEAHHDHPGCDLKG 70

Query: 52  NNDLLVLSKPEVIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLA 111
           NNDLL L++P +I  +H AY EAGAD++ETNTFNST I+ ADY +E L+ E+N   A+LA
Sbjct: 71  NNDLLTLTQPAIIRGVHEAYLEAGADLVETNTFNSTRISQADYHLEHLAHELNLEGARLA 130

Query: 112 RACADEWTARTPEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALV 171
           RA  D WTA+TPE+PR+V GVLGPT+RTAS+SPDVNDP FRN+TF+ L A Y E+   LV
Sbjct: 131 RAACDAWTAKTPEQPRFVIGVLGPTSRTASLSPDVNDPGFRNVTFEELAANYTEAAAGLV 190

Query: 172 EGGADLILIETVFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAF 231
           +GGADLI++ET+FDTLNAKAA+FA+   F   G  LP+MISGTITD SGRTLSGQT EAF
Sbjct: 191 DGGADLIMVETIFDTLNAKAALFAISELFRERGARLPVMISGTITDRSGRTLSGQTAEAF 250

Query: 232 YNSLRHAEALTFGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTM 291
           Y S+ HA  L+ GLNCALG  +LR +VQ L+++A C+V+ HPNAGLPNAFGEYD   + M
Sbjct: 251 YYSVAHARPLSVGLNCALGAADLRPHVQTLAQVAGCFVSTHPNAGLPNAFGEYDETPEQM 310

Query: 292 AKQIREWAQAGFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEI 336
           A  I  +A+ G LN+VGGCCGTTP HI A++ AV   APR LP +
Sbjct: 311 AAVIGGFARDGLLNLVGGCCGTTPAHIKAIAEAVRDCAPRALPSL 355


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: 1134
Number of extensions: 41
Number of successful extensions: 2
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: 361
Length adjustment: 38
Effective length of query: 1189
Effective length of database: 323
Effective search space:   384047
Effective search space used:   384047
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 N515DRAFT_0495 N515DRAFT_0495 (methionine synthase (B12-dependent))
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.12809.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 1239.2   0.0          0 1239.0   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_0495  N515DRAFT_0495 methionine syntha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_0495  N515DRAFT_0495 methionine synthase (B12-dependent)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1239.0   0.0         0         0     325    1182 .]       4     860 ..       1     860 [. 0.99

  Alignments for each domain:
  == domain 1  score: 1239.0 bits;  conditional E-value: 0
                                    TIGR02082  325 eksvlsglealkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDin 388 
                                                    +++lsgle+l i+++  fvn+GeRtnv+Gs++frklik++ yeea+++a+qqv +Gaqi+D+n
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0495    4 RHTRLSGLEPLVITPDLLFVNVGERTNVTGSAQFRKLIKEDRYEEAVDVARQQVASGAQIIDVN 67  
                                                   6899************************************************************ PP

                                    TIGR02082  389 vDevllDgeadmkkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeer 452 
                                                   +De+l D+ea+m+++l+l+a+epdia+vP+m+Dss++ vleaGL+++qGk+ivnsis+k+Gee 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0495   68 MDEGLIDSEAAMTRFLNLIAAEPDIARVPVMVDSSKWTVLEAGLRCLQGKGIVNSISMKEGEEL 131 
                                                   **************************************************************** PP

                                    TIGR02082  453 FlekaklikeyGaavvvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltia 516 
                                                   Fle+a+++++yGaavvvmafDe+Gqa+t ++k+ei++Ray llte+++fppedi+fDpni++ia
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0495  132 FLEHARKVQQYGAAVVVMAFDEQGQADTCERKVEICSRAYALLTEQLDFPPEDIVFDPNIFAIA 195 
                                                   **************************************************************** PP

                                    TIGR02082  517 tGieehdryaidfieaireikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlD 580 
                                                   tGieeh++ya+dfiea+re+k+++P  +isgGvsnvsFs+rgn++vRea+hsvFLy+aikaG+D
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0495  196 TGIEEHNNYAVDFIEATRELKRRFPLSHISGGVSNVSFSFRGNNTVREAIHSVFLYHAIKAGMD 259 
                                                   **************************************************************** PP

                                    TIGR02082  581 mgivnagklavyddidkelrevvedlildrrreatekLlelaelykgtkeksskeaqeaewrnl 644 
                                                   mgivnag l +ydd+++elre ved++l+rr++ate+Lle+a++yk  k +   + ++ +wr++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0495  260 MGIVNAGALMIYDDVPAELRERVEDVVLNRRPDATERLLEIADNYKARKGE--VVVENLAWREK 321 
                                                   ***********************************************9999..778999***** PP

                                    TIGR02082  645 pveeRLeralvkGeregieedleearkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvks 708 
                                                   pv+eRL++alv+G+  ++++d+eear+ +++pl++iegpL+dGm+vvGdLFG+GkmfLPqvvks
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0495  322 PVRERLSHALVHGIDAFVDADTEEARQLATRPLDVIEGPLMDGMNVVGDLFGAGKMFLPQVVKS 385 
                                                   **************************************************************** PP

                                    TIGR02082  709 arvmkkavayLePylekekeed....kskGkivlatvkGDvhDiGknivdvvLscngyevvdlG 768 
                                                   arvmkkavayL Py+e+ek+ +    k++G+iv+atvkGDvhDiGkniv+vvL cn+++v+dlG
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0495  386 ARVMKKAVAYLLPYIEEEKARTgdvgKNNGTIVMATVKGDVHDIGKNIVGVVLRCNNFDVIDLG 449 
                                                   *******************9999999************************************** PP

                                    TIGR02082  769 vkvPvekileaakkkkaDviglsGLivksldemvevaeemerrgvkiPlllGGaalskahvavk 832 
                                                   v+vP++kil+aa++++aD+iglsGLi++sl+em +va+em+r+ ++iPll+GGa++s+ah+a k
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0495  450 VMVPAQKILDAAREHNADLIGLSGLITPSLEEMSHVAREMQRQEFSIPLLIGGATTSRAHTALK 513 
                                                   **************************************************************** PP

                                    TIGR02082  833 iaekYkgevvyvkdaseavkvvdkllsekkkaeelekikeeyeeirekfgekkeklialsekaa 896 
                                                   i+++Yk+++v+vkdas+av v+++l+s++  +++++k++++yee+re+++++   +  +++++a
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0495  514 IDPHYKAPTVWVKDASRAVGVAQSLVSKDLVDAFMAKVRADYEEVRERHRNRGPGKSLVPLEKA 577 
                                                   **************************************************************** PP

                                    TIGR02082  897 rkevfaldrsedlevpapkflGtkvleas.ieellkyiDwkalFvqWelrgkypkilkdelegl 959 
                                                   r ++++ d+   + +p+p++ G+ v++a+ ++el++yiDw+++F +Wel+g+yp ilkde++g+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0495  578 RAQRYTCDWA-GYAPPQPRQPGVTVFDAYdLAELREYIDWTPFFQAWELAGRYPAILKDEIVGT 640 
                                                   **********.9**************************************************** PP

                                    TIGR02082  960 earklfkdakelldklsaekllrargvvGlfPaqsvgddieiytdetvsqetkpiatvrekleq 1023
                                                   +a +lf+da+++ld+++ae+ l+ar+v+G++ a +vgdd e+y ++++     ++a++r+ ++q
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0495  641 QASELFRDAQAMLDRIVAERWLTARAVIGFWRAAQVGDDTEVYGEDGR-----KLAVLRHLRQQ 699 
                                                   ********************************************8887.....89999999999 PP

                                    TIGR02082 1024 lrqqsdr.ylclaDfiaskesGikDylgallvtaglgaeelakkleakeddydsilvkaladrl 1086
                                                   + +  dr   +l Dfia+ke+G++D++ga++vtag+g+ee   ++ea +ddy+sil+kaladrl
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0495  700 ADKPADRpDFSLGDFIAPKEAGKQDWVGAFAVTAGIGIEEHVARFEAAHDDYSSILLKALADRL 763 
                                                   9999999999****************************************************** PP

                                    TIGR02082 1087 aealaellhervRkelwgyaeeenldkedllkerYrGirpafGYpacPdhtekatlleLleaer 1150
                                                   aea+ae +h+rvR+e+wgya +e+ld+e l+ e+YrGirpa+GYpacPdhtek tl++Ll+a  
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0495  764 AEAFAERMHQRVRREFWGYAPDEALDNEALIDEKYRGIRPAPGYPACPDHTEKSTLFKLLDATA 827 
                                                   *************************************************************999 PP

                                    TIGR02082 1151 .iGlklteslalaPeasvsglyfahpeakYfav 1182
                                                     G++lte +a++P+a+vsg+yf+hp+++Yf v
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0495  828 nAGIELTEGYAMYPTAAVSGWYFSHPDSQYFVV 860 
                                                   8******************************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (895 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: 9.97
//
[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