Alignments for a candidate for metB in Sphingomonas wittichii RW1

GapMind for Amino acid biosynthesis

Alignments for a candidate for metB in Sphingomonas wittichii RW1

Align Cystathionine gamma-synthase; CGS; O-succinylhomoserine (thiol)-lyase; EC 2.5.1.48 (characterized)
to candidate WP_012049347.1 SWIT_RS15935 O-succinylhomoserine (thiol)-lyase

Query= SwissProt::P00935
         (386 letters)



>NCBI__GCF_000016765.1:WP_012049347.1
          Length = 390

 Score =  427 bits (1098), Expect = e-124
 Identities = 217/376 (57%), Positives = 273/376 (72%), Gaps = 1/376 (0%)

Query: 7   TIAVRSGLNDDEQYGCVVPPIHLSSTYNFTGFNEPRAHDYSRRGNPTRDVVQRALAELEG 66
           TI+   G+  D  +G V PP++LSSTY F G+++PR +DY R GNPTRD++  ALA+LEG
Sbjct: 13  TISAAHGVATDAGFGAVAPPLYLSSTYAFAGYDQPRHYDYGRAGNPTRDLLAEALAKLEG 72

Query: 67  GAGAVLTNTGMSAIHLVTTVFLKPGDLLVAPHDCYGGSYRLFDSLAKRGCYRVLFVDQGD 126
           GAGA++T++GM+A+ L+    L+P DL++APHDCYGG+ RL  + A RG   V FVDQ D
Sbjct: 73  GAGAIVTSSGMAALDLLVGR-LRPDDLVLAPHDCYGGTMRLLKARAGRGHCSVRFVDQTD 131

Query: 127 EQALRAALAEKPKLVLVESPSNPLLRVVDIAKICHLAREVGAVSVVDNTFLSPALQNPLA 186
            +A   AL E P LVL+E+PSNPL+RVVDIA +  LAR  GA   VDNTFLSPA+Q P+A
Sbjct: 132 MRAFAGALDEVPALVLIETPSNPLMRVVDIAALSALARAAGAEVAVDNTFLSPAIQRPIA 191

Query: 187 LGADLVLHSCTKYLNGHSDVVAGVVIAKDPDVVTELAWWANNIGVTGGAFDSYLLLRGLR 246
           LGAD  +HS TKYLNGHSDV+ G V+A DP  V  L  WAN +G  G  FDS+L LRGLR
Sbjct: 192 LGADYAIHSTTKYLNGHSDVIGGAVVAADPAQVEALRHWANVVGSAGAPFDSWLTLRGLR 251

Query: 247 TLVPRMELAQRNAQAIVKYLQTQPLVKKLYHPSLPENQGHEIAARQQKGFGAMLSFELDG 306
           TL PRME  Q NA A+  +L+  P V ++++P L  + GH IA+RQQ+GFGAMLSFEL G
Sbjct: 252 TLFPRMEQQQINAMAVANHLERHPAVARVHYPGLASHPGHAIASRQQRGFGAMLSFELAG 311

Query: 307 DEQTLRRFLGGLSLFTLAESLGGVESLISHAATMTHAGMAPEARAAAGISETLLRISTGI 366
               +RRF+  +  FTLAESLGGVESL++H ATMTHA M  EARAAAGIS++LLR+S G+
Sbjct: 312 GVAAVRRFIDAVRFFTLAESLGGVESLVAHPATMTHADMGEEARAAAGISDSLLRLSVGL 371

Query: 367 EDGEDLIADLENGFRA 382
           E   DLIA L+ G  A
Sbjct: 372 EAERDLIAGLDKGLAA 387


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: 423
Number of extensions: 15
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: 390
Length adjustment: 30
Effective length of query: 356
Effective length of database: 360
Effective search space:   128160
Effective search space used:   128160
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_012049347.1 SWIT_RS15935 (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.29424.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-189  615.8   0.0   1.4e-189  615.6   0.0    1.0  1  lcl|NCBI__GCF_000016765.1:WP_012049347.1  SWIT_RS15935 O-succinylhomoserin


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016765.1:WP_012049347.1  SWIT_RS15935 O-succinylhomoserine (thiol)-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  615.6   0.0  1.4e-189  1.4e-189       3     382 .]      10     388 ..       8     388 .. 0.99

  Alignments for each domain:
  == domain 1  score: 615.6 bits;  conditional E-value: 1.4e-189
                                 TIGR02080   3 kkatiavrsGlesdkqygavvpPiylsttyefagfnepraydysrsgnPtrdllekalaelekGadavv 71 
                                               + +ti++++G+++d  +gav pP+yls+ty+fag+++pr+ydy+r gnPtrdll++ala+le+Ga+a+v
  lcl|NCBI__GCF_000016765.1:WP_012049347.1  10 RPQTISAAHGVATDAGFGAVAPPLYLSSTYAFAGYDQPRHYDYGRAGNPTRDLLAEALAKLEGGAGAIV 78 
                                               578****************************************************************** PP

                                 TIGR02080  72 tssGmsaiellviallkpddllvaPhdcyGGtyrllkalakkgklkvqlvdqsdeealekalaekpklv 140
                                               tssGm+a++llv ++l+pddl++aPhdcyGGt+rllka+a +g++ v++vdq+d++a++ al e p+lv
  lcl|NCBI__GCF_000016765.1:WP_012049347.1  79 TSSGMAALDLLV-GRLRPDDLVLAPHDCYGGTMRLLKARAGRGHCSVRFVDQTDMRAFAGALDEVPALV 146
                                               ***********9.******************************************************** PP

                                 TIGR02080 141 lietPsnPllrvvdiaklcklakaagavvvvdntflsPilqkPlalGadlvlhsatkylnGhsdviaGa 209
                                               lietPsnPl+rvvdia+l+ la+aaga v+vdntflsP++q+P+alGad+++hs+tkylnGhsdvi+Ga
  lcl|NCBI__GCF_000016765.1:WP_012049347.1 147 LIETPSNPLMRVVDIAALSALARAAGAEVAVDNTFLSPAIQRPIALGADYAIHSTTKYLNGHSDVIGGA 215
                                               ********************************************************************* PP

                                 TIGR02080 210 viakdkqlaeelawwanalGvtgaafdsylllrGlrtlaarvreqernakkiveylqkqplvkkvyypg 278
                                               v+a+d+ ++e l++wan++G++ga+fds+l+lrGlrtl+ r+++q+ na++++++l+++p+v +v+ypg
  lcl|NCBI__GCF_000016765.1:WP_012049347.1 216 VVAADPAQVEALRHWANVVGSAGAPFDSWLTLRGLRTLFPRMEQQQINAMAVANHLERHPAVARVHYPG 284
                                               ********************************************************************* PP

                                 TIGR02080 279 lpdhagheiaakqqkGfGallsfelkGgeeevkkflkklklftlaeslGGvesliahpatmthaameke 347
                                               l++h+gh+ia +qq+GfGa+lsfel+Gg+++v++f+++++ ftlaeslGGvesl+ahpatmtha+m++e
  lcl|NCBI__GCF_000016765.1:WP_012049347.1 285 LASHPGHAIASRQQRGFGAMLSFELAGGVAAVRRFIDAVRFFTLAESLGGVESLVAHPATMTHADMGEE 353
                                               ********************************************************************* PP

                                 TIGR02080 348 areeaGikdellrlsvGledaddliadleqalaav 382
                                               ar++aGi+d+llrlsvGle   dlia+l+++laa+
  lcl|NCBI__GCF_000016765.1:WP_012049347.1 354 ARAAAGISDSLLRLSVGLEAERDLIAGLDKGLAAC 388
                                               ********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (382 nodes)
Target sequences:                          1  (390 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.12
//
[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