Alignments for a candidate for metB in Dyella japonica UNC79MFTsu3.2

GapMind for Amino acid biosynthesis

Alignments for a candidate for metB in Dyella japonica UNC79MFTsu3.2

Align Cystathionine gamma-synthase; CGS; O-succinylhomoserine (thiol)-lyase; EC 2.5.1.48 (characterized)
to candidate N515DRAFT_4363 N515DRAFT_4363 cystathionine gamma-synthase

Query= SwissProt::P00935
         (386 letters)



>FitnessBrowser__Dyella79:N515DRAFT_4363
          Length = 399

 Score =  424 bits (1089), Expect = e-123
 Identities = 213/374 (56%), Positives = 269/374 (71%), Gaps = 1/374 (0%)

Query: 6   ATIAVRSGLNDDEQYGCVVPPIHLSSTYNFTGFNEPRAHDYSRRGNPTRDVVQRALAELE 65
           +T AVR+G+  D Q+G VVPP+HLS+ Y F G    RA+DYSR GNPTRD++  ALAELE
Sbjct: 11  STCAVRAGIESDTQHGAVVPPLHLSTNYAFEGLGGKRAYDYSRSGNPTRDLLGNALAELE 70

Query: 66  GGAGAVLTNTGMSAIHLVTTVFLKPGDLLVAPHDCYGGSYRLFDSLAKRGCYRVLFVDQG 125
            GAGAV+T +GM+A+ L   + +  G  ++A HDCYGG++RL D+ AK+G + + F D  
Sbjct: 71  QGAGAVVTASGMAAVALALEL-VPAGGRVLAAHDCYGGTWRLLDAWAKKGRFTLEFADLT 129

Query: 126 DEQALRAALAEKPKLVLVESPSNPLLRVVDIAKICHLAREVGAVSVVDNTFLSPALQNPL 185
           D  AL A LA KP LV VE+PSNPLLR+ D+  +   A   GA+ VVDNTFLSPALQ PL
Sbjct: 130 DRVALAAGLASKPSLVWVETPSNPLLRITDVRHVAQAAHAAGALVVVDNTFLSPALQQPL 189

Query: 186 ALGADLVLHSCTKYLNGHSDVVAGVVIAKDPDVVTELAWWANNIGVTGGAFDSYLLLRGL 245
            LGAD+V+HS TKY+NGHSDVV G V+A+D  V  +L WW N  G+TG  FDS+L LRGL
Sbjct: 190 VLGADVVVHSTTKYINGHSDVVGGAVVARDQAVADQLKWWGNCNGLTGAPFDSFLTLRGL 249

Query: 246 RTLVPRMELAQRNAQAIVKYLQTQPLVKKLYHPSLPENQGHEIAARQQKGFGAMLSFELD 305
           RTL  R+   Q NAQ I   L     V+K+Y+P L  + GH +AARQQ GFGAMLSFEL+
Sbjct: 250 RTLSVRLRQHQENAQRIATLLDGHAAVRKVYYPGLESHPGHALAARQQAGFGAMLSFELE 309

Query: 306 GDEQTLRRFLGGLSLFTLAESLGGVESLISHAATMTHAGMAPEARAAAGISETLLRISTG 365
           GD   +  F+  L  F+LAESLGGVESL++H A+MTHA MAPEAR  AGI+++LLRIS G
Sbjct: 310 GDVAQIEAFVNELKYFSLAESLGGVESLVAHPASMTHASMAPEARRTAGIADSLLRISVG 369

Query: 366 IEDGEDLIADLENG 379
           IEDG+DL+ D++ G
Sbjct: 370 IEDGDDLVRDVDAG 383


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: 445
Number of extensions: 11
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: 399
Length adjustment: 31
Effective length of query: 355
Effective length of database: 368
Effective search space:   130640
Effective search space used:   130640
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 N515DRAFT_4363 N515DRAFT_4363 (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.28349.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   1.6e-184  598.9   0.0   1.9e-184  598.6   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_4363  N515DRAFT_4363 cystathionine gam


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_4363  N515DRAFT_4363 cystathionine gamma-synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  598.6   0.0  1.9e-184  1.9e-184       4     381 ..      10     386 ..       8     387 .. 0.99

  Alignments for each domain:
  == domain 1  score: 598.6 bits;  conditional E-value: 1.9e-184
                                    TIGR02080   4 katiavrsGlesdkqygavvpPiylsttyefagfnepraydysrsgnPtrdllekalaelekGada 69 
                                                  ++t avr G+esd+q+gavvpP++lst+y+f+g    raydysrsgnPtrdll +alaele+Ga+a
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4363  10 TSTCAVRAGIESDTQHGAVVPPLHLSTNYAFEGLGGKRAYDYSRSGNPTRDLLGNALAELEQGAGA 75 
                                                  589*************************************************************** PP

                                    TIGR02080  70 vvtssGmsaiellviallkpddllvaPhdcyGGtyrllkalakkgklkvqlvdqsdeealekalae 135
                                                  vvt+sGm+a+ l +  l+ ++  ++a hdcyGGt+rll+a akkg +++++ d +d  al++ la+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4363  76 VVTASGMAAVALAL-ELVPAGGRVLAAHDCYGGTWRLLDAWAKKGRFTLEFADLTDRVALAAGLAS 140
                                                  ************99.99999********************************************** PP

                                    TIGR02080 136 kpklvlietPsnPllrvvdiaklcklakaagavvvvdntflsPilqkPlalGadlvlhsatkylnG 201
                                                  kp lv++etPsnPllr++d+++++++a+aaga+vvvdntflsP+lq+Pl lGad+v+hs+tky+nG
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4363 141 KPSLVWVETPSNPLLRITDVRHVAQAAHAAGALVVVDNTFLSPALQQPLVLGADVVVHSTTKYING 206
                                                  ****************************************************************** PP

                                    TIGR02080 202 hsdviaGaviakdkqlaeelawwanalGvtgaafdsylllrGlrtlaarvreqernakkiveylqk 267
                                                  hsdv++Gav+a+d+ +a++l+ww+n+ G+tga+fds+l+lrGlrtl++r+r++++na++i+ +l+ 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4363 207 HSDVVGGAVVARDQAVADQLKWWGNCNGLTGAPFDSFLTLRGLRTLSVRLRQHQENAQRIATLLDG 272
                                                  ****************************************************************** PP

                                    TIGR02080 268 qplvkkvyypglpdhagheiaakqqkGfGallsfelkGgeeevkkflkklklftlaeslGGvesli 333
                                                  +++v+kvyypgl +h+gh++aa+qq GfGa+lsfel+G+++++++f+++lk f+laeslGGvesl+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4363 273 HAAVRKVYYPGLESHPGHALAARQQAGFGAMLSFELEGDVAQIEAFVNELKYFSLAESLGGVESLV 338
                                                  ****************************************************************** PP

                                    TIGR02080 334 ahpatmthaamekeareeaGikdellrlsvGledaddliadleqalaa 381
                                                  ahpa+mtha+m++ear +aGi d+llr+svG+ed+ddl+ d++++la 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4363 339 AHPASMTHASMAPEARRTAGIADSLLRISVGIEDGDDLVRDVDAGLAR 386
                                                  *********************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (382 nodes)
Target sequences:                          1  (399 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: 10.71
//
[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