Alignments for a candidate for metB in Sinorhizobium meliloti 1021

GapMind for Amino acid biosynthesis

Alignments for a candidate for metB in Sinorhizobium meliloti 1021

Align Cystathionine gamma-synthase; CGS; O-succinylhomoserine (thiol)-lyase; EC 2.5.1.48 (characterized)
to candidate SMc02595 SMc02595 cystathionine gamma-synthase

Query= SwissProt::P00935
         (386 letters)



>FitnessBrowser__Smeli:SMc02595
          Length = 408

 Score =  395 bits (1014), Expect = e-114
 Identities = 202/376 (53%), Positives = 260/376 (69%), Gaps = 1/376 (0%)

Query: 7   TIAVRSGLNDDEQYGCVVPPIHLSSTYNFTGFNEPRAHDYSRRGNPTRDVVQRALAELEG 66
           T A   G+  D  +G VVPP++LSSTY F GF+ PRA+DY R GNPTRD++ +ALA+LEG
Sbjct: 33  TTAAAHGVATDPAFGSVVPPLYLSSTYEFAGFDTPRAYDYGRSGNPTRDLLAQALAKLEG 92

Query: 67  GAGAVLTNTGMSAIHLVTTVFLKPGDLLVAPHDCYGGSYRLFDSLAKRGCYRVLFVDQGD 126
           GA AV+T +GM+A+ L+    L+   L++APHDCYGG+ RL  + A  G       DQ D
Sbjct: 93  GADAVVTPSGMAALDLLLGR-LRRNHLVLAPHDCYGGTLRLLKARADLGHLTFRLTDQRD 151

Query: 127 EQALRAALAEKPKLVLVESPSNPLLRVVDIAKICHLAREVGAVSVVDNTFLSPALQNPLA 186
                AAL++ P LVL+ESPSNPL+RV DIA++  LA+  G+   VDNTFLSPALQ PL+
Sbjct: 152 FGGFEAALSDAPALVLIESPSNPLMRVTDIARLSTLAKAAGSAVAVDNTFLSPALQQPLS 211

Query: 187 LGADLVLHSCTKYLNGHSDVVAGVVIAKDPDVVTELAWWANNIGVTGGAFDSYLLLRGLR 246
           LGAD  +HS TK+LNGHSDV+AG VIA +P    +L  WAN  G     FD++L LRGLR
Sbjct: 212 LGADYAIHSATKFLNGHSDVIAGAVIAAEPQEAHDLKRWANVTGAVAAPFDAWLTLRGLR 271

Query: 247 TLVPRMELAQRNAQAIVKYLQTQPLVKKLYHPSLPENQGHEIAARQQKGFGAMLSFELDG 306
           TL  RM   +R+A  I +YL   P V+ +++  LP++  HE+A RQQ+GFGAM+SFEL+G
Sbjct: 272 TLFARMSSQERSAMTIAEYLDAHPAVRHVHYAGLPDHADHEVARRQQRGFGAMMSFELEG 331

Query: 307 DEQTLRRFLGGLSLFTLAESLGGVESLISHAATMTHAGMAPEARAAAGISETLLRISTGI 366
               +RRFL  +  FTLAESLGGVESL++H ATMTH  M PEAR  AGI + LLR+S G+
Sbjct: 332 GVPAVRRFLAHIRCFTLAESLGGVESLVAHPATMTHLDMGPEARERAGIRDELLRLSIGL 391

Query: 367 EDGEDLIADLENGFRA 382
           E  +DL+  LE G  A
Sbjct: 392 EHIDDLMEGLELGLGA 407


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: 452
Number of extensions: 10
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: 408
Length adjustment: 31
Effective length of query: 355
Effective length of database: 377
Effective search space:   133835
Effective search space used:   133835
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 SMc02595 SMc02595 (cystathionine gamma-synthase)
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.9879.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.1e-200  652.1   0.0   1.3e-200  651.9   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMc02595  SMc02595 cystathionine gamma-syn


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc02595  SMc02595 cystathionine gamma-synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  651.9   0.0  1.3e-200  1.3e-200       2     382 .]      29     408 .]      28     408 .] 0.99

  Alignments for each domain:
  == domain 1  score: 651.9 bits;  conditional E-value: 1.3e-200
                           TIGR02080   2 rkkatiavrsGlesdkqygavvpPiylsttyefagfnepraydysrsgnPtrdllekalaelekGadavvtssGm 76 
                                         ++++t+a+++G+++d+++g+vvpP+yls+tyefagf++praydy+rsgnPtrdll++ala+le+Gadavvt+sGm
  lcl|FitnessBrowser__Smeli:SMc02595  29 DRAETTAAAHGVATDPAFGSVVPPLYLSSTYEFAGFDTPRAYDYGRSGNPTRDLLAQALAKLEGGADAVVTPSGM 103
                                         7899*********************************************************************** PP

                           TIGR02080  77 saiellviallkpddllvaPhdcyGGtyrllkalakkgklkvqlvdqsdeealekalaekpklvlietPsnPllr 151
                                         +a++ll+ ++l++++l++aPhdcyGGt+rllka+a+ g+l+++l+dq+d+ ++e+al+++p+lvlie+PsnPl+r
  lcl|FitnessBrowser__Smeli:SMc02595 104 AALDLLL-GRLRRNHLVLAPHDCYGGTLRLLKARADLGHLTFRLTDQRDFGGFEAALSDAPALVLIESPSNPLMR 177
                                         ******9.******************************************************************* PP

                           TIGR02080 152 vvdiaklcklakaagavvvvdntflsPilqkPlalGadlvlhsatkylnGhsdviaGaviakdkqlaeelawwan 226
                                         v+dia+l++lakaag++v+vdntflsP+lq+Pl+lGad+++hsatk+lnGhsdviaGavia+++q+a++l++wan
  lcl|FitnessBrowser__Smeli:SMc02595 178 VTDIARLSTLAKAAGSAVAVDNTFLSPALQQPLSLGADYAIHSATKFLNGHSDVIAGAVIAAEPQEAHDLKRWAN 252
                                         *************************************************************************** PP

                           TIGR02080 227 alGvtgaafdsylllrGlrtlaarvreqernakkiveylqkqplvkkvyypglpdhagheiaakqqkGfGallsf 301
                                         ++G+++a+fd++l+lrGlrtl+ar+++qer+a++i+eyl+++p+v++v+y+glpdha+he+a++qq+GfGa++sf
  lcl|FitnessBrowser__Smeli:SMc02595 253 VTGAVAAPFDAWLTLRGLRTLFARMSSQERSAMTIAEYLDAHPAVRHVHYAGLPDHADHEVARRQQRGFGAMMSF 327
                                         *************************************************************************** PP

                           TIGR02080 302 elkGgeeevkkflkklklftlaeslGGvesliahpatmthaamekeareeaGikdellrlsvGledaddliadle 376
                                         el+Gg+++v++fl+++++ftlaeslGGvesl+ahpatmth +m++eare+aGi+dellrls+Gle++ddl+++le
  lcl|FitnessBrowser__Smeli:SMc02595 328 ELEGGVPAVRRFLAHIRCFTLAESLGGVESLVAHPATMTHLDMGPEARERAGIRDELLRLSIGLEHIDDLMEGLE 402
                                         *************************************************************************** PP

                           TIGR02080 377 qalaav 382
                                          +l a+
  lcl|FitnessBrowser__Smeli:SMc02595 403 LGLGAC 408
                                         **9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (382 nodes)
Target sequences:                          1  (408 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.95
//
[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