Alignments for a candidate for metB in Stenotrophomonas chelatiphaga DSM 21508

GapMind for Amino acid biosynthesis

Alignments for a candidate for metB in Stenotrophomonas chelatiphaga DSM 21508

Align Cystathionine gamma-synthase; CGS; O-succinylhomoserine (thiol)-lyase; EC 2.5.1.48 (characterized)
to candidate WP_057508709.1 ABB28_RS11200 O-succinylhomoserine (thiol)-lyase

Query= SwissProt::P00935
         (386 letters)



>NCBI__GCF_001431535.1:WP_057508709.1
          Length = 412

 Score =  432 bits (1110), Expect = e-125
 Identities = 222/377 (58%), Positives = 273/377 (72%), Gaps = 5/377 (1%)

Query: 5   QATIAVRSGLNDDEQYGCVVPPIHLSSTYNFTGFNEPRAHDYSRRGNPTRDVVQRALAEL 64
           + T AVR+G++ D  YG V PPI LSS ++F GF   R +DY+R GNPTRD++  ALAEL
Sbjct: 13  RTTAAVRAGIDRDSAYGAVTPPIVLSSNFSFDGFGNKRQYDYTRSGNPTRDLLGEALAEL 72

Query: 65  EGGAGAVLTNTGMSAIHLVTTVFLKPGDLLVAPHDCYGGSYRLFDSLAKRGCYRVLFVDQ 124
           EGGAG V+T TGM AI LV    L P D LV PHD YGGS+RLF++LA +G ++++  D 
Sbjct: 73  EGGAGGVVTATGMGAISLVLQALLGPEDTLVVPHDAYGGSWRLFNALAGKGQFKLVTADL 132

Query: 125 GDEQALRAALAEKPKLVLVESPSNPLLRVVDIAKICHLAREVGAVSVVDNTFLSPALQNP 184
            D ++L  ALA  PKLVLVE+PSNPLLR+ D+  +   A + GA+ VVDNTFLSPALQ P
Sbjct: 133 TDPRSLAQALAGSPKLVLVETPSNPLLRITDLRFVIDAAHKAGALVVVDNTFLSPALQQP 192

Query: 185 LALGADLVLHSCTKYLNGHSDVVAGVVIAKDPDVVTELAWWANNIGVTGGAFDSYLLLRG 244
           LA GADLVLHS TKY+NGHSDVV G V+A+DP++  +L WWAN +G+TG  FD++L LRG
Sbjct: 193 LAFGADLVLHSTTKYINGHSDVVGGAVVARDPELAQQLTWWANALGLTGSPFDAFLTLRG 252

Query: 245 LRTLVPRMELAQRNAQAIVKYLQTQPLVKKLYHPSLPENQGHEIAARQQKGFGAMLSFEL 304
           LRTL  R+ + Q N  AIV  L     V  +Y+P L ++ GH IAARQQ GFGAMLSFEL
Sbjct: 253 LRTLDARLRVHQENTAAIVPLLAAHRAVSAVYYPGLADHPGHAIAARQQSGFGAMLSFEL 312

Query: 305 ---DGDE--QTLRRFLGGLSLFTLAESLGGVESLISHAATMTHAGMAPEARAAAGISETL 359
              DGD+    +R F+ GL  FTLAESLGGVESL++H ATMTHA M  +AR AAGISE L
Sbjct: 313 VTCDGDDPHAAVRAFVDGLQYFTLAESLGGVESLVAHPATMTHAAMTVQARQAAGISEGL 372

Query: 360 LRISTGIEDGEDLIADL 376
           LR+S GIE   DL+ADL
Sbjct: 373 LRLSVGIESERDLLADL 389


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: 469
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: 412
Length adjustment: 31
Effective length of query: 355
Effective length of database: 381
Effective search space:   135255
Effective search space used:   135255
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_057508709.1 ABB28_RS11200 (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.12198.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-177  576.1   0.0   1.6e-177  575.9   0.0    1.0  1  lcl|NCBI__GCF_001431535.1:WP_057508709.1  ABB28_RS11200 O-succinylhomoseri


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057508709.1  ABB28_RS11200 O-succinylhomoserine (thiol)-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  575.9   0.0  1.6e-177  1.6e-177       4     380 ..      13     394 ..      10     396 .. 0.98

  Alignments for each domain:
  == domain 1  score: 575.9 bits;  conditional E-value: 1.6e-177
                                 TIGR02080   4 katiavrsGlesdkqygavvpPiylsttyefagfnepraydysrsgnPtrdllekalaelekGadavvt 72 
                                               ++t avr G++ d++ygav pPi ls++++f+gf + r+ydy+rsgnPtrdll +alaele+Ga++vvt
  lcl|NCBI__GCF_001431535.1:WP_057508709.1  13 RTTAAVRAGIDRDSAYGAVTPPIVLSSNFSFDGFGNKRQYDYTRSGNPTRDLLGEALAELEGGAGGVVT 81 
                                               5799***************************************************************** PP

                                 TIGR02080  73 ssGmsaiellviallkpddllvaPhdcyGGtyrllkalakkgklkvqlvdqsdeealekalaekpklvl 141
                                               ++Gm ai+l++ all+p+d lv+Phd yGG++rl++ala kg++k+   d +d ++l++ala  pklvl
  lcl|NCBI__GCF_001431535.1:WP_057508709.1  82 ATGMGAISLVLQALLGPEDTLVVPHDAYGGSWRLFNALAGKGQFKLVTADLTDPRSLAQALAGSPKLVL 150
                                               ********************************************************************* PP

                                 TIGR02080 142 ietPsnPllrvvdiaklcklakaagavvvvdntflsPilqkPlalGadlvlhsatkylnGhsdviaGav 210
                                               +etPsnPllr++d++ + ++a++aga+vvvdntflsP+lq+Pla+Gadlvlhs+tky+nGhsdv++Gav
  lcl|NCBI__GCF_001431535.1:WP_057508709.1 151 VETPSNPLLRITDLRFVIDAAHKAGALVVVDNTFLSPALQQPLAFGADLVLHSTTKYINGHSDVVGGAV 219
                                               ********************************************************************* PP

                                 TIGR02080 211 iakdkqlaeelawwanalGvtgaafdsylllrGlrtlaarvreqernakkiveylqkqplvkkvyypgl 279
                                               +a+d++la++l+wwanalG+tg++fd++l+lrGlrtl ar+r++++n+ +iv +l ++ +v+ vyypgl
  lcl|NCBI__GCF_001431535.1:WP_057508709.1 220 VARDPELAQQLTWWANALGLTGSPFDAFLTLRGLRTLDARLRVHQENTAAIVPLLAAHRAVSAVYYPGL 288
                                               ********************************************************************* PP

                                 TIGR02080 280 pdhagheiaakqqkGfGallsfel...kGg..eeevkkflkklklftlaeslGGvesliahpatmthaa 343
                                               +dh+gh+iaa+qq+GfGa+lsfel   +G+   ++v++f++ l+ ftlaeslGGvesl+ahpatmthaa
  lcl|NCBI__GCF_001431535.1:WP_057508709.1 289 ADHPGHAIAARQQSGFGAMLSFELvtcDGDdpHAAVRAFVDGLQYFTLAESLGGVESLVAHPATMTHAA 357
                                               ***********************966656622578********************************** PP

                                 TIGR02080 344 mekeareeaGikdellrlsvGledaddliadleqala 380
                                               m+ +ar++aGi++ llrlsvG+e   dl+adl +al 
  lcl|NCBI__GCF_001431535.1:WP_057508709.1 358 MTVQARQAAGISEGLLRLSVGIESERDLLADLAAALD 394
                                               *********************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (382 nodes)
Target sequences:                          1  (412 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: 00:00:00.04
# Mc/sec: 3.45
//
[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