Alignments for a candidate for metH in Clostridium kluyveri DSM 555

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Clostridium kluyveri DSM 555

Align methionine synthase (EC 2.1.1.13) (characterized)
to candidate WP_012101348.1 CKL_RS04800 homocysteine methyltransferase

Query= BRENDA::Q9WYA5
         (768 letters)



>NCBI__GCF_000016505.1:WP_012101348.1
          Length = 801

 Score =  526 bits (1354), Expect = e-153
 Identities = 294/800 (36%), Positives = 464/800 (58%), Gaps = 39/800 (4%)

Query: 3   NRREVSKLLSERVLLLDGAYGTEFMKYGYD--DLPEELNIKAPDVVLKVHRSYIESGSDV 60
           N + +    + R +  DGA GT   K G    +LPE LNI  P+++  +HR Y+++G+D+
Sbjct: 2   NFKNLVDKFNNRFIFFDGAMGTMLQKAGLKLGELPEVLNITNPEIISGIHRKYLDAGADI 61

Query: 61  ILTNTFGATRMKLRKHGLEDKLDPIVRNAVRIARRAAGEKLVFGDIGPTGELPYPLGSTL 120
           I TNTFGA  +K      +  ++ ++   V++A++ AG+KLV  DIGP G++  P G+  
Sbjct: 62  ITTNTFGANELKYDSS--DYTIEDVISAGVKLAKQEAGDKLVALDIGPIGKIMEPTGNLS 119

Query: 121 FEEFYENFRETVEIMVEEGVDGIIFETFSDILELKAAVLAAREVSRDVFLIAHMTFDEKG 180
           FE  Y+ F+  + I  + G D ++ ET +D+ E KAAVLAA+E S ++ +   MTF E G
Sbjct: 120 FESAYKLFKNQIVIGEKSGADVVLIETMTDLYEAKAAVLAAKENS-NIPIFCTMTFQEDG 178

Query: 181 RSLTGTDPANFAITFDELDIDALGINCSLGPEEILPIFQELSQYTDKFLVVEPNAGKPIV 240
           R+L GTD        + L +D LG+NCSLGP+E+  I +E+ +Y+   ++V+PNAG P  
Sbjct: 179 RTLMGTDAKTMVFVLEALGVDVLGVNCSLGPKELQGIVEEILKYSSIPVMVQPNAGLPRY 238

Query: 241 ENGKTVYPLKPHDFAVHIDSYYELGVNIFGGCCGTTPEHVKLFRKVLGNRKPLQRKKKRI 300
           +   T+Y + P DFA ++ +  + G+ + GGCCGTTPE +++ RK L    PL  ++K  
Sbjct: 239 DGENTIYDISPEDFAENVLTMAQKGIRVLGGCCGTTPEFIRMCRKDLEGLTPLNIEEKHY 298

Query: 301 FAV-SSPSKLVTFDHFVVIGERINPAGRKKLWAEMQKGNEEIVIKEAKTQVEKGAEVLDV 359
            AV S+   ++  +   +IGERINP GR     E+++G+   + KEA  Q E+GA +L V
Sbjct: 299 TAVCSATDTVIVGEKIKIIGERINPTGRSIYKKELKEGSINYIQKEAIMQKEEGANILGV 358

Query: 360 NFGIESQIDVRYVEKIVQTLPYVSNVPLSLDIQNVDLTERALRAYPGRSLFNSAKVDEEE 419
           N G+    +V  ++K ++ +  V  +PLS+D  +  + E  +R Y G+ + NS    ++ 
Sbjct: 359 NVGLPEINEVEIMKKAIRAVQKVVQLPLSIDSPDPQVLETGIRMYNGKPVINSVNGSKKS 418

Query: 420 LEMKINLLKKYGGTLIVLLMG-KDVPKSFEERKEYFEKALKILERHDFSDR-VIFDPGVL 477
           +E    ++KKYGG +I L +  K +P + E R +  EK +K    +  + + +I D   L
Sbjct: 419 MEEVFPIVKKYGGCVIALTIDEKGIPHTAEGRVKIAEKIIKTASIYGINKKNIIIDCLTL 478

Query: 478 PLGAEGKPV-EVLKTIEFISSK-GFNTTVGLSNLSFGLPDRSYYNTAFLVLGISKGLSSA 535
            + A+ K V E +K I+ ++ K G  T +G+SN+SFGLP+RS  N  FL + +  GL+  
Sbjct: 479 TVSAQQKEVLETIKAIKMVTEKFGVKTVLGVSNISFGLPNRSILNRTFLAMALQAGLNLP 538

Query: 536 IMNPLDETLMKTLNATLVILE----------------KKELPRAEVKE---------EKL 570
           IMNP DE++ + + A  V+                  K E P+ E            + L
Sbjct: 539 IMNPADESMKEVIAAFQVLTNIDKEGKEYVIKYGNKSKDEKPKGEGNSPLKNADNNLKDL 598

Query: 571 VEIILSGNRSELEKLVEDFLKEKDPLSVIEEHLRPAMERIGELYDKGKIFLPQLILAAQT 630
            ++I+ G   E E +  + LK K  L ++  ++ PA++ +G+ Y+   IFLPQLI +A+T
Sbjct: 599 KQLIIDGIEDEAEAMTTELLKNKKALEIVNSYIIPALDEVGKQYELQDIFLPQLIQSAET 658

Query: 631 VKPVFDKLTSMLPSDSQGE----TFVIATVKGDVHDIGKNIVASVIRSSGYRVVDLGKDV 686
           VK  F+ +   + S  Q      T V+ATVKGD+HDIGKNIV  ++ + G+ V+DLG+DV
Sbjct: 659 VKKSFEIIKDNMLSSGQKSLEKGTIVLATVKGDIHDIGKNIVKVLLENYGFEVIDLGRDV 718

Query: 687 DTSEIVEAVEKERPVALGLSAMMTTTVGRIKEVVEKLKEKNLKIPVIVGGASLNEKLAKE 746
           D   IV  +       +GLSA+MTTTV  +K+ +E ++E NL   ++VGGA LN+  A  
Sbjct: 719 DIDNIVNTIRDNNIKLVGLSALMTTTVASMKKTIEAIRENNLNCKIVVGGAVLNQNYADM 778

Query: 747 LGADYYAKNASEAVKILKSL 766
           +GADYYAK+A EAVKI + +
Sbjct: 779 IGADYYAKDAREAVKIAEEV 798


Lambda     K      H
   0.317    0.138    0.381 

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: 1543
Number of extensions: 77
Number of successful extensions: 8
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: 768
Length of database: 801
Length adjustment: 41
Effective length of query: 727
Effective length of database: 760
Effective search space:   552520
Effective search space used:   552520
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: 55 (25.8 bits)

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