Alignments for a candidate for metH in Nocardiopsis lucentensis DSM 44048

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Nocardiopsis lucentensis DSM 44048

Align cobalamin-dependent methionine synthase (EC 2.1.1.13) (characterized)
to candidate WP_083924073.1 D471_RS0104310 methionine synthase

Query= metacyc::G18NG-11090-MONOMER
         (1221 letters)



>NCBI__GCF_000341125.1:WP_083924073.1
          Length = 1157

 Score = 1442 bits (3734), Expect = 0.0
 Identities = 745/1205 (61%), Positives = 912/1205 (75%), Gaps = 55/1205 (4%)

Query: 18   FLDALANHVLIGDGAMGTQLQGFDLDVEKDFLDLEGCNEILNDTRPDVLRQIHRAYFEAG 77
            F +AL+  V++ DGAMGT LQ  DLD+++ F   EGCN+ILN TRPD++   H A+   G
Sbjct: 7    FREALSQRVIVADGAMGTMLQAHDLDLDQ-FEGHEGCNDILNITRPDIVHDTHAAFLAVG 65

Query: 78   ADLVETNTFGCNLPNLADYDIADRCRELAYKGTAVAREVADEMGPGRNGMRRFVVGSLGP 137
            +D VETNTF  N   LA+Y I DR  E+A  G  VARE AD      +   R+V+GS+GP
Sbjct: 66   SDCVETNTFSANYGGLAEYGIEDRAYEIAEAGARVAREAADAYSTPDHP--RYVLGSVGP 123

Query: 138  GTKLPSLGHAPYADLRGHYKEAALGIIDGGGDAFLIETAQDLLQVKAAVHGVQDAMAELD 197
            GTKLPSLGHAPYA LR HY++   G+IDGG DA LIET QDLLQVKAAV G Q A   L 
Sbjct: 124  GTKLPSLGHAPYALLRDHYEQCHRGLIDGGADAILIETCQDLLQVKAAVVGAQRARKALG 183

Query: 198  TFLPIICHVTVETTGTMLMGSEIGAALTALQPLGIDMIGLNCATGPDEMSEHLRYLSKHA 257
              +PII  VT+ETTGTMLMGSEIGAALT+L PLGID+IGLNCATGP EMSEHLRYLS H+
Sbjct: 184  RDVPIIAQVTIETTGTMLMGSEIGAALTSLAPLGIDVIGLNCATGPAEMSEHLRYLSHHS 243

Query: 258  DIPVSVMPNAGLPVLGKNGAEYPLEAEDLAQALAGFVSEYGLSMVGGCCGTTPEHIRAVR 317
             IP+S MPNAGLP LG +GA YPL   +LA A   F SE+GLS+VGGCCGTTPEH+R V 
Sbjct: 244  PIPISCMPNAGLPQLGADGAVYPLTPAELADAHDTFTSEFGLSVVGGCCGTTPEHLRQVV 303

Query: 318  DAVVGVPEQETSTLTKIPAGPVEQASREVEKEDSVASLYTSVPLSQETGISMIGERTNSN 377
            + V G   ++   L                 E + +SLY SVP  Q+     +GERTN+N
Sbjct: 304  ERVQGRGIKDRKPLV----------------EAAASSLYQSVPFRQDASYLAVGERTNAN 347

Query: 378  GSKAFREAMLSGDWEKCVDIAKQQTRDGAHMLDLCVDYVGRDGTADMATLAALLATSSTL 437
            GSK FR AML   W+ CV++A+ Q RDGAH+LDL +DYVGRDG  DM  LA+  ATSSTL
Sbjct: 348  GSKKFRTAMLEERWDDCVEMARDQIRDGAHLLDLNIDYVGRDGVRDMRELASRFATSSTL 407

Query: 438  PIMIDSTEPEVIRTGLEHLGGRSIVNSVNFEDGDGPESRYQRIMKLVKQHGAAVVALTID 497
            PIM+DSTEP V+  GLE LGGR+++NSVN+EDGDGP+SR+ RIM+LV +HGAAVV L ID
Sbjct: 408  PIMLDSTEPAVLEAGLEALGGRAVINSVNYEDGDGPDSRFTRIMELVSEHGAAVVGLCID 467

Query: 498  EEGQARTAEHKVRIAKRLIDDITGSYGLDIKDIVVDCLTFPISTGQEETRRDGIETIEAI 557
            EEGQARTAE K+R+A RLI+ ITG +GL   DIV+DCLTFPI+TGQEETRRDGIET++AI
Sbjct: 468  EEGQARTAEWKLRVATRLIEQITGEWGLRTGDIVIDCLTFPITTGQEETRRDGIETLDAI 527

Query: 558  RELKKLYPEIHTTLGLSNISFGLNPAARQVLNSVFLNECIEAGLDSAIAHSSKILPMNRI 617
            RELK+ YP++ TTLGLSN+SFG+NPAAR VLNSVFL+E +EAGLDSAI H+SKI+P+N+I
Sbjct: 528  RELKRRYPDVQTTLGLSNLSFGVNPAARIVLNSVFLHEAVEAGLDSAIVHASKIVPINQI 587

Query: 618  DDRQREVALDMVYDRRTEDYDPLQEFMQLFEGVSAADAKDARAEQLAAMPLFERLAQRII 677
             D QREVALD+VYDRR +DYDPL  F++LFEGV A   + +RAE+LAA+PL+ERL +RI+
Sbjct: 588  PDEQREVALDLVYDRRADDYDPLSRFIELFEGVDAKSMRASRAEELAALPLWERLERRIV 647

Query: 678  DGDKNGLEDDLEAGMKEKSPIAIINEDLLNGMKTVGELFGSGQMQLPFVLQSAETMKTAV 737
            DG+  G+E DLEA + E+  +AI+N+ LL GMKTVGELFGSGQMQLPFVL+SAE MK AV
Sbjct: 648  DGEMTGIEADLEAALAERPALAIVNDTLLEGMKTVGELFGSGQMQLPFVLKSAEVMKGAV 707

Query: 738  AYLEPFMEEEAEATGSAQAEGKGKIVVATVKGDVHDIGKNLVDIILSNNGYDVVNLGIKQ 797
            AYLEP ME+  +       +GKG+IV+ATVKGDVHDIGKNLVDIILSNNGYDVVN+GIKQ
Sbjct: 708  AYLEPHMEKTDD-------DGKGRIVLATVKGDVHDIGKNLVDIILSNNGYDVVNIGIKQ 760

Query: 798  PLSAMLEAAEEHKADVIGMSGLLVKSTVVMKENLEEMNNAGAS-NYPVILGGAALTRTYV 856
            P+SA+LEAAE+ +ADVIGMSGLLVKSTV+MKENLEEMN+ G S  +PV+LGGAALTR+YV
Sbjct: 761  PVSAILEAAEKERADVIGMSGLLVKSTVIMKENLEEMNSRGLSERFPVLLGGAALTRSYV 820

Query: 857  ENDLNEVYTGEVYYARDAFEGLRLMDEVMAEKRGEGLDPNSPEAIEQAKKKAERKARNER 916
            E DL E++ G+V YA+DAFEGLRLMD  MA KRGE          E A+  A R+ R  R
Sbjct: 821  EQDLAEMFEGQVRYAKDAFEGLRLMDSFMAVKRGE----------EGAELPALRQRRVRR 870

Query: 917  SRKIAAERKANAAPVIVPERSDVSTDTPTAAPPFWGTRIVKGLPLAEFLGNLDERALFMG 976
               +         P  +P RSDV+TD     PPFWG RI KG+PLA++   LDERA FMG
Sbjct: 871  GATLKV-----TEPEDMPARSDVATDNRVPVPPFWGDRISKGIPLADYSAFLDERATFMG 925

Query: 977  QWGLKSTRGNEGPSYEDLVETEGRPRLRYWLDRLKSEGILDHVALVYGYFPAVAEGDDVV 1036
            QWGLK++RG  GPSYE+LVETEGRPR+R WLDR++++G+L+  A+V+G+FP  +EGDD+V
Sbjct: 926  QWGLKASRGGNGPSYEELVETEGRPRMRMWLDRIQTDGLLE-AAVVHGHFPCYSEGDDLV 984

Query: 1037 ILESPDPHAAERMRFSFPRQQRGRFLCIADFIRPREQAVKDGQVDVMPFQLVTMGNPIAD 1096
            +L+  +    ER RF+FPRQ+R R LC+AD+ RP+E     G++DV+ FQ+VT+G+ I+ 
Sbjct: 985  VLD--EDGVTERTRFTFPRQRRDRHLCLADYFRPKE----SGELDVVSFQVVTVGSAISR 1038

Query: 1097 FANELFAANEYREYLEVHGIGVQLTEALAEYWHSRVRSELKLNDGGSVADFDPEDKTKFF 1156
               ELF  + YR+YLE+HG+ VQLTEALAEYWH+RVR+EL        A  DP +   FF
Sbjct: 1039 ATAELFERDAYRDYLELHGLSVQLTEALAEYWHTRVRAEL------GFAGEDPAELDAFF 1092

Query: 1157 DLDYRGARFSFGYGSCPDLEDRAKLVELLEPGRIGVELSEELQLHPEQSTDAFVLYHPEA 1216
             L YRGARFS GYG+CP+LEDRAK++ LLEP R+GV LSEE QL PEQ+TDA V++HPEA
Sbjct: 1093 KLGYRGARFSLGYGACPNLEDRAKIMRLLEPERVGVTLSEEFQLVPEQATDAIVIHHPEA 1152

Query: 1217 KYFNV 1221
             YFNV
Sbjct: 1153 TYFNV 1157


Lambda     K      H
   0.316    0.135    0.386 

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: 3534
Number of extensions: 157
Number of successful extensions: 13
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: 1221
Length of database: 1157
Length adjustment: 47
Effective length of query: 1174
Effective length of database: 1110
Effective search space:  1303140
Effective search space used:  1303140
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 (21.6 bits)
S2: 59 (27.3 bits)

Align candidate WP_083924073.1 D471_RS0104310 (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.1261048.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 1424.4   0.0          0 1424.2   0.0    1.0  1  NCBI__GCF_000341125.1:WP_083924073.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000341125.1:WP_083924073.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1424.2   0.0         0         0       1    1182 []      11    1157 .]      11    1157 .] 0.97

  Alignments for each domain:
  == domain 1  score: 1424.2 bits;  conditional E-value: 0
                             TIGR02082    1 lnkrilvlDGamGtqlqsanLteadFrgeeadlarelkGnndlLnltkPeviaaihrayfeaGaDivetnt 71  
                                            l++r++v DGamGt+lq+++L+ ++F+g         +G+nd+Ln+t+P+++++ h a++  G+D vetnt
  NCBI__GCF_000341125.1:WP_083924073.1   11 LSQRVIVADGAMGTMLQAHDLDLDQFEG--------HEGCNDILNITRPDIVHDTHAAFLAVGSDCVETNT 73  
                                            589*************************........5********************************** PP

                             TIGR02082   72 FnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdverpefrnvt 142 
                                            F+++   la+Y++ed+aye+ +++a++are+ad ++ tp+++R+v+Gs+GP++kl++l+         +  
  NCBI__GCF_000341125.1:WP_083924073.1   74 FSANYGGLAEYGIEDRAYEIAEAGARVAREAADAYS-TPDHPRYVLGSVGPGTKLPSLG---------HAP 134 
                                            ************************************.**********************.........9** PP

                             TIGR02082  143 ydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgvivdksGrtLsGq 213 
                                            y+ l+d Y++  +gl+dGG+D++Liet++D+l++kaa+++++++ ++ gr++Pi+++ v+++++G++L+G+
  NCBI__GCF_000341125.1:WP_083924073.1  135 YALLRDHYEQCHRGLIDGGADAILIETCQDLLQVKAAVVGAQRARKALGRDVPIIAQ-VTIETTGTMLMGS 204 
                                            ********************************************************9.************* PP

                             TIGR02082  214 tleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnalg...eYdltpeelaka 281 
                                            +++a+l+sl + +i+++GLnCa+G++e++e++++ls+++++++s++PnaGLP+  +    Y+ltp ela a
  NCBI__GCF_000341125.1:WP_083924073.1  205 EIGAALTSLAPLGIDVIGLNCATGPAEMSEHLRYLSHHSPIPISCMPNAGLPQLGAdgaVYPLTPAELADA 275 
                                            *****************************************************9987778*********** PP

                             TIGR02082  282 lkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsglealkiaqessfvniGeRtnv 352 
                                               f +e++l++vGGCCGttPeh+r++ e v++   ++r+ l e+ ++s+++++++ q++s++ +GeRtn+
  NCBI__GCF_000341125.1:WP_083924073.1  276 HDTFTSEFGLSVVGGCCGTTPEHLRQVVERVQGRGIKDRKPLVEAAASSLYQSVPFRQDASYLAVGERTNA 346 
                                            *********************************************************************** PP

                             TIGR02082  353 aGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmkkllsllasepdiakvPlmlDss 423 
                                            +Gskkfr ++ +e +++++++a++q+++Ga++lD+n+D+v++Dg++dm++l+s+ a++   +++P+mlDs+
  NCBI__GCF_000341125.1:WP_083924073.1  347 NGSKKFRTAMLEERWDDCVEMARDQIRDGAHLLDLNIDYVGRDGVRDMRELASRFATS---STLPIMLDST 414 
                                            **********************************************************...8********* PP

                             TIGR02082  424 efevleaGLkviqGkaivnsislkdG...eerFlekaklikeyGaavvvmafDeeGqartadkkieiakRa 491 
                                            e +vleaGL+ ++G+a++ns++++dG   ++rF + ++l+ e+Gaavv + +DeeGqarta+ k+++a+R+
  NCBI__GCF_000341125.1:WP_083924073.1  415 EPAVLEAGLEALGGRAVINSVNYEDGdgpDSRFTRIMELVSEHGAAVVGLCIDEEGQARTAEWKLRVATRL 485 
                                            **************************88889**************************************** PP

                             TIGR02082  492 yklltekvgfppediifDpniltiatGieehdryaidfieaireikeelPdakisgGvsnvsFslrgndav 562 
                                            ++++t ++g+   di++D ++++i+tG+ee +r++i++++aire+k+++Pd+++++G+sn+sF+++  +a+
  NCBI__GCF_000341125.1:WP_083924073.1  486 IEQITGEWGLRTGDIVIDCLTFPITTGQEETRRDGIETLDAIRELKRRYPDVQTTLGLSNLSFGVN--PAA 554 
                                            ******************************************************************..*** PP

                             TIGR02082  563 RealhsvFLyeaikaGlDmgivnagklavyddidkelrevvedlildrrreatekLlelaelykgtkekss 633 
                                            R +l+svFL+ea++aGlD++iv+a+k+ ++++i++e+rev++dl++drr +++++L +++el++g+ +ks 
  NCBI__GCF_000341125.1:WP_083924073.1  555 RIVLNSVFLHEAVEAGLDSAIVHASKIVPINQIPDEQREVALDLVYDRRADDYDPLSRFIELFEGVDAKSM 625 
                                            *********************************************************************** PP

                             TIGR02082  634 keaqeaewrnlpveeRLeralvkGeregieedleearkklkapleiiegpLldGmkvvGdLFGsGkmfLPq 704 
                                            + ++ +e++ lp+ eRLer++v+Ge  gie+dle+a+   +++l+i++  Ll+Gmk+vG+LFGsG+m+LP+
  NCBI__GCF_000341125.1:WP_083924073.1  626 RASRAEELAALPLWERLERRIVDGEMTGIEADLEAAL-AERPALAIVNDTLLEGMKTVGELFGSGQMQLPF 695 
                                            *************************************.88999**************************** PP

                             TIGR02082  705 vvksarvmkkavayLePylekekeedkskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvek 775 
                                            v+ksa+vmk avayLeP++ek +  d+ kG+ivlatvkGDvhDiGkn+vd++Ls+ngy+vv++G+k+Pv  
  NCBI__GCF_000341125.1:WP_083924073.1  696 VLKSAEVMKGAVAYLEPHMEKTD--DDGKGRIVLATVKGDVHDIGKNLVDIILSNNGYDVVNIGIKQPVSA 764 
                                            ********************988..889******************************************* PP

                             TIGR02082  776 ileaakkkkaDviglsGLivksldemvevaeemerrgvk..iPlllGGaalskahvavkiaekYkgevvyv 844 
                                            ileaa+k++aDvig+sGL+vks++ m+e++eem+ rg++  +P+llGGaal++++v++++ae ++g+v y+
  NCBI__GCF_000341125.1:WP_083924073.1  765 ILEAAEKERADVIGMSGLLVKSTVIMKENLEEMNSRGLSerFPVLLGGAALTRSYVEQDLAEMFEGQVRYA 835 
                                            **************************************888****************************** PP

                             TIGR02082  845 kdaseavkvvdkllsekkkaeelekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapk 915 
                                            kda+e+++++d+++  k+ +e +e    ++  +r+ ++         +  + ++     d   d +vp+p+
  NCBI__GCF_000341125.1:WP_083924073.1  836 KDAFEGLRLMDSFMAVKRGEEGAELPALRQRRVRRGATL--------KVTEPEDMPARSDVATDNRVPVPP 898 
                                            ****************98666655555555555544444........22233333333444556789**** PP

                             TIGR02082  916 flGtkvleas.ieellkyiDwkalFv.qWelrgkypkilkdeleglearklfkdakelldklsaekllrar 984 
                                            f+G ++ + + ++++  ++D++a F+ qW+l+ +++    +++e+l++++ +++++ +ld++++++ll+a+
  NCBI__GCF_000341125.1:WP_083924073.1  899 FWGDRISKGIpLADYSAFLDERATFMgQWGLKASRG-GNGPSYEELVETEGRPRMRMWLDRIQTDGLLEAA 968 
                                            ************************************.99******************************** PP

                             TIGR02082  985 gvvGlfPaqsvgddieiytdetvsqetkpiatvrekleqlrqqsdrylclaDfiaskesGikDylgallvt 1055
                                            +v G fP+ s+gdd++++++++v        t r+++ ++rq +dr+lclaD++++kesG+ D++++++vt
  NCBI__GCF_000341125.1:WP_083924073.1  969 VVHGHFPCYSEGDDLVVLDEDGV--------TERTRFTFPRQRRDRHLCLADYFRPKESGELDVVSFQVVT 1031
                                            *******************9999........778899********************************** PP

                             TIGR02082 1056 aglgaeelakkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirp 1126
                                            +g  ++  + +l+++++++d++++++l+++l+ealae++h rvR el +   e++ + + ++k+ YrG+r+
  NCBI__GCF_000341125.1:WP_083924073.1 1032 VGSAISRATAELFERDAYRDYLELHGLSVQLTEALAEYWHTRVRAELGFA-GEDPAELDAFFKLGYRGARF 1101
                                            ***********************************************998.899***************** PP

                             TIGR02082 1127 afGYpacPdhtekatlleLleaeriGlklteslalaPeasvsglyfahpeakYfav 1182
                                            ++GY+acP+++++a++++Lle+er+G++l+e+++l Pe+++++++++hpea Yf+v
  NCBI__GCF_000341125.1:WP_083924073.1 1102 SLGYGACPNLEDRAKIMRLLEPERVGVTLSEEFQLVPEQATDAIVIHHPEATYFNV 1157
                                            ******************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (1157 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: 0.04u 0.04s 00:00:00.08 Elapsed: 00:00:00.07
# Mc/sec: 17.57
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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 2024 update 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 original 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