Alignments for a candidate for metB in Methylobacterium sp. 4-46

GapMind for Amino acid biosynthesis

Alignments for a candidate for metB in Methylobacterium sp. 4-46

Align Cystathionine gamma-synthase; CGS; O-succinylhomoserine (thiol)-lyase; EC 2.5.1.48 (characterized)
to candidate WP_012333237.1 M446_RS16475 O-succinylhomoserine (thiol)-lyase

Query= SwissProt::P00935
         (386 letters)



>NCBI__GCF_000019365.1:WP_012333237.1
          Length = 388

 Score =  432 bits (1111), Expect = e-126
 Identities = 215/384 (55%), Positives = 278/384 (72%), Gaps = 1/384 (0%)

Query: 3   RKQATIAVRSGLNDDEQYGCVVPPIHLSSTYNFTGFNEPRAHDYSRRGNPTRDVVQRALA 62
           R   TIA  +G+  D  +G V PP++LS+TY F  F  PR +DY+R GNPTRD +   +A
Sbjct: 6   RAAETIAAANGIGADAAFGAVAPPLYLSTTYTFAEFETPRGYDYARLGNPTRDQLADTIA 65

Query: 63  ELEGGAGAVLTNTGMSAIHLVTTVFLKPGDLLVAPHDCYGGSYRLFDSLAKRGCYRVLFV 122
           +LEGGA AV+T +GM+A+ L  +  L PGDLLVAPHDCYGG++RL    A +G YRV FV
Sbjct: 66  KLEGGARAVVTASGMAALDLALSP-LSPGDLLVAPHDCYGGTHRLLSLRAAKGHYRVAFV 124

Query: 123 DQGDEQALRAALAEKPKLVLVESPSNPLLRVVDIAKICHLAREVGAVSVVDNTFLSPALQ 182
           DQ D  AL AALAE+P+++L E+PSNPL+R+VD+ +   LARE GA+ VVDNTFLSPALQ
Sbjct: 125 DQTDAAALSAALAERPRILLTETPSNPLMRIVDLGRTAALAREAGALFVVDNTFLSPALQ 184

Query: 183 NPLALGADLVLHSCTKYLNGHSDVVAGVVIAKDPDVVTELAWWANNIGVTGGAFDSYLLL 242
            P+A GADLV+HS TK++NGHSDV+ G V+A    +  ELA WAN IGVTG  FD+YL L
Sbjct: 185 QPIAHGADLVVHSTTKFINGHSDVIGGAVVAAQAALGEELANWANTIGVTGSPFDAYLTL 244

Query: 243 RGLRTLVPRMELAQRNAQAIVKYLQTQPLVKKLYHPSLPENQGHEIAARQQKGFGAMLSF 302
           RGLRTL  R+E  Q++A  +  +L   P V ++++P LP++ GH +A  QQ+GFGAMLSF
Sbjct: 245 RGLRTLFARLERQQQSAAVVASFLAAHPAVARVHYPGLPDHPGHAVARAQQRGFGAMLSF 304

Query: 303 ELDGDEQTLRRFLGGLSLFTLAESLGGVESLISHAATMTHAGMAPEARAAAGISETLLRI 362
           EL G  + +R  +G L +FTLAESLGG+ESLI+H  +MTHA MAPEAR AAG+ + LLR+
Sbjct: 305 ELAGGREAVRTLVGALRVFTLAESLGGIESLIAHPVSMTHAAMAPEARRAAGVGDGLLRL 364

Query: 363 STGIEDGEDLIADLENGFRAANKG 386
           S G+E   DL+ADL     AA +G
Sbjct: 365 SVGLEAESDLLADLAVALDAAARG 388


Lambda     K      H
   0.319    0.136    0.394 

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: 435
Number of extensions: 13
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: 386
Length of database: 388
Length adjustment: 30
Effective length of query: 356
Effective length of database: 358
Effective search space:   127448
Effective search space used:   127448
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_012333237.1 M446_RS16475 (O-succinylhomoserine (thiol)-lyase)
to HMM TIGR02080 (metB: O-succinylhomoserine (thiol)-lyase (EC 2.5.1.48))

# 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/TIGR02080.hmm
# target sequence database:        /tmp/gapView.27124.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02080  [M=382]
Accession:   TIGR02080
Description: O_succ_thio_ly: O-succinylhomoserine (thiol)-lyase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.2e-178  578.2   0.0   3.9e-178  577.9   0.0    1.0  1  lcl|NCBI__GCF_000019365.1:WP_012333237.1  M446_RS16475 O-succinylhomoserin


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000019365.1:WP_012333237.1  M446_RS16475 O-succinylhomoserine (thiol)-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  577.9   0.0  3.9e-178  3.9e-178       2     381 ..       6     384 ..       5     385 .. 0.99

  Alignments for each domain:
  == domain 1  score: 577.9 bits;  conditional E-value: 3.9e-178
                                 TIGR02080   2 rkkatiavrsGlesdkqygavvpPiylsttyefagfnepraydysrsgnPtrdllekalaelekGadav 70 
                                               r ++tia+++G+  d ++gav pP+ylstty fa+f++pr ydy+r gnPtrd l++++a+le+Ga av
  lcl|NCBI__GCF_000019365.1:WP_012333237.1   6 RAAETIAAANGIGADAAFGAVAPPLYLSTTYTFAEFETPRGYDYARLGNPTRDQLADTIAKLEGGARAV 74 
                                               5689***************************************************************** PP

                                 TIGR02080  71 vtssGmsaiellviallkpddllvaPhdcyGGtyrllkalakkgklkvqlvdqsdeealekalaekpkl 139
                                               vt+sGm+a++l + + l p+dllvaPhdcyGGt+rll+ +a kg+++v +vdq+d++al++alae+p++
  lcl|NCBI__GCF_000019365.1:WP_012333237.1  75 VTASGMAALDLAL-SPLSPGDLLVAPHDCYGGTHRLLSLRAAKGHYRVAFVDQTDAAALSAALAERPRI 142
                                               ************9.99***************************************************** PP

                                 TIGR02080 140 vlietPsnPllrvvdiaklcklakaagavvvvdntflsPilqkPlalGadlvlhsatkylnGhsdviaG 208
                                               +l etPsnPl+r+vd+ + + la++aga+ vvdntflsP+lq+P+a Gadlv+hs+tk++nGhsdvi+G
  lcl|NCBI__GCF_000019365.1:WP_012333237.1 143 LLTETPSNPLMRIVDLGRTAALAREAGALFVVDNTFLSPALQQPIAHGADLVVHSTTKFINGHSDVIGG 211
                                               ********************************************************************* PP

                                 TIGR02080 209 aviakdkqlaeelawwanalGvtgaafdsylllrGlrtlaarvreqernakkiveylqkqplvkkvyyp 277
                                               av+a++  l eela wan++Gvtg++fd+yl+lrGlrtl+ar+++q+++a  ++++l ++p+v +v+yp
  lcl|NCBI__GCF_000019365.1:WP_012333237.1 212 AVVAAQAALGEELANWANTIGVTGSPFDAYLTLRGLRTLFARLERQQQSAAVVASFLAAHPAVARVHYP 280
                                               ********************************************************************* PP

                                 TIGR02080 278 glpdhagheiaakqqkGfGallsfelkGgeeevkkflkklklftlaeslGGvesliahpatmthaamek 346
                                               glpdh+gh++a+ qq+GfGa+lsfel+Gg e+v++++++l++ftlaeslGG+esliahp +mthaam++
  lcl|NCBI__GCF_000019365.1:WP_012333237.1 281 GLPDHPGHAVARAQQRGFGAMLSFELAGGREAVRTLVGALRVFTLAESLGGIESLIAHPVSMTHAAMAP 349
                                               ********************************************************************* PP

                                 TIGR02080 347 eareeaGikdellrlsvGledaddliadleqalaa 381
                                               ear +aG+ d llrlsvGle  +dl+adl  al a
  lcl|NCBI__GCF_000019365.1:WP_012333237.1 350 EARRAAGVGDGLLRLSVGLEAESDLLADLAVALDA 384
                                               ******************************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (382 nodes)
Target sequences:                          1  (388 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.91
//
[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