Alignments for a candidate for metB in Klebsiella michiganensis M5al

GapMind for Amino acid biosynthesis

Alignments for a candidate for metB in Klebsiella michiganensis M5al

Align Cystathionine gamma-synthase; CGS; O-succinylhomoserine (thiol)-lyase; EC 2.5.1.48 (characterized)
to candidate BWI76_RS00785 BWI76_RS00785 cystathionine gamma-synthase

Query= SwissProt::P00935
         (386 letters)



>FitnessBrowser__Koxy:BWI76_RS00785
          Length = 386

 Score =  729 bits (1881), Expect = 0.0
 Identities = 371/385 (96%), Positives = 374/385 (97%)

Query: 1   MTRKQATIAVRSGLNDDEQYGCVVPPIHLSSTYNFTGFNEPRAHDYSRRGNPTRDVVQRA 60
           MTRKQATIAVRSGLNDDEQYGCVVPPIHLSSTYNFTGFNEPRAHDYSRRGNPTRDVVQRA
Sbjct: 1   MTRKQATIAVRSGLNDDEQYGCVVPPIHLSSTYNFTGFNEPRAHDYSRRGNPTRDVVQRA 60

Query: 61  LAELEGGAGAVLTNTGMSAIHLVTTVFLKPGDLLVAPHDCYGGSYRLFDSLAKRGCYRVL 120
           LAELEGGAGAVLTNTGMSAI LVTTVFLKPGDLLVAPHDCYGGSYRLFDSLAKRGCYRVL
Sbjct: 61  LAELEGGAGAVLTNTGMSAILLVTTVFLKPGDLLVAPHDCYGGSYRLFDSLAKRGCYRVL 120

Query: 121 FVDQGDEQALRAALAEKPKLVLVESPSNPLLRVVDIAKICHLAREVGAVSVVDNTFLSPA 180
           FVDQ DEQAL AALAEKPKLVLVESPSNPLLRVVDIAKIC LARE GAVSVVDNTFLSPA
Sbjct: 121 FVDQNDEQALSAALAEKPKLVLVESPSNPLLRVVDIAKICGLAREAGAVSVVDNTFLSPA 180

Query: 181 LQNPLALGADLVLHSCTKYLNGHSDVVAGVVIAKDPDVVTELAWWANNIGVTGGAFDSYL 240
           LQNPLALGADLVLHSCTKYLNGHSDVVAGVVIAKDP  VTELAWWANNIGVTGGAFDSYL
Sbjct: 181 LQNPLALGADLVLHSCTKYLNGHSDVVAGVVIAKDPATVTELAWWANNIGVTGGAFDSYL 240

Query: 241 LLRGLRTLVPRMELAQRNAQAIVKYLQTQPLVKKLYHPSLPENQGHEIAARQQKGFGAML 300
           LLRGLRTL PRME+AQRNA AIV YL+TQPLVKKLYHPSLPENQGHEIAARQQKGFGAML
Sbjct: 241 LLRGLRTLSPRMEVAQRNALAIVDYLKTQPLVKKLYHPSLPENQGHEIAARQQKGFGAML 300

Query: 301 SFELDGDEQTLRRFLGGLSLFTLAESLGGVESLISHAATMTHAGMAPEARAAAGISETLL 360
           SFELDGDEQTLRRFL GLSLFTLAESLGGVESLISHAATMTHAGMAPEARAAAGISETLL
Sbjct: 301 SFELDGDEQTLRRFLSGLSLFTLAESLGGVESLISHAATMTHAGMAPEARAAAGISETLL 360

Query: 361 RISTGIEDGEDLIADLENGFRAANK 385
           RISTGIEDGEDLIADLENGFRAAN+
Sbjct: 361 RISTGIEDGEDLIADLENGFRAANE 385


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: 609
Number of extensions: 16
Number of successful extensions: 1
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: 386
Length adjustment: 30
Effective length of query: 356
Effective length of database: 356
Effective search space:   126736
Effective search space used:   126736
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 BWI76_RS00785 BWI76_RS00785 (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.17546.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-213  694.8   0.0   1.4e-213  694.6   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS00785  BWI76_RS00785 cystathionine gamm


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS00785  BWI76_RS00785 cystathionine gamma-synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  694.6   0.0  1.4e-213  1.4e-213       2     381 ..       3     382 ..       2     383 .. 1.00

  Alignments for each domain:
  == domain 1  score: 694.6 bits;  conditional E-value: 1.4e-213
                               TIGR02080   2 rkkatiavrsGlesdkqygavvpPiylsttyefagfnepraydysrsgnPtrdllekalaelekGadavvt 72 
                                             rk+atiavrsGl++d+qyg+vvpPi+ls+ty+f+gfnepra+dysr+gnPtrd++++alaele+Ga+av+t
  lcl|FitnessBrowser__Koxy:BWI76_RS00785   3 RKQATIAVRSGLNDDEQYGCVVPPIHLSSTYNFTGFNEPRAHDYSRRGNPTRDVVQRALAELEGGAGAVLT 73 
                                             89********************************************************************* PP

                               TIGR02080  73 ssGmsaiellviallkpddllvaPhdcyGGtyrllkalakkgklkvqlvdqsdeealekalaekpklvlie 143
                                             ++Gmsai l+++++lkp+dllvaPhdcyGG+yrl+++lak+g+++v++vdq+de+al++alaekpklvl+e
  lcl|FitnessBrowser__Koxy:BWI76_RS00785  74 NTGMSAILLVTTVFLKPGDLLVAPHDCYGGSYRLFDSLAKRGCYRVLFVDQNDEQALSAALAEKPKLVLVE 144
                                             *********************************************************************** PP

                               TIGR02080 144 tPsnPllrvvdiaklcklakaagavvvvdntflsPilqkPlalGadlvlhsatkylnGhsdviaGaviakd 214
                                             +PsnPllrvvdiak+c la++agav+vvdntflsP+lq+PlalGadlvlhs+tkylnGhsdv+aG+viakd
  lcl|FitnessBrowser__Koxy:BWI76_RS00785 145 SPSNPLLRVVDIAKICGLAREAGAVSVVDNTFLSPALQNPLALGADLVLHSCTKYLNGHSDVVAGVVIAKD 215
                                             *********************************************************************** PP

                               TIGR02080 215 kqlaeelawwanalGvtgaafdsylllrGlrtlaarvreqernakkiveylqkqplvkkvyypglpdhagh 285
                                             + +++elawwan++Gvtg+afdsylllrGlrtl+ r+++++rna +iv+yl++qplvkk+y+p+lp+++gh
  lcl|FitnessBrowser__Koxy:BWI76_RS00785 216 PATVTELAWWANNIGVTGGAFDSYLLLRGLRTLSPRMEVAQRNALAIVDYLKTQPLVKKLYHPSLPENQGH 286
                                             *********************************************************************** PP

                               TIGR02080 286 eiaakqqkGfGallsfelkGgeeevkkflkklklftlaeslGGvesliahpatmthaamekeareeaGikd 356
                                             eiaa+qqkGfGa+lsfel+G+e+++++fl+ l+lftlaeslGGvesli+h+atmtha+m++ear++aGi++
  lcl|FitnessBrowser__Koxy:BWI76_RS00785 287 EIAARQQKGFGAMLSFELDGDEQTLRRFLSGLSLFTLAESLGGVESLISHAATMTHAGMAPEARAAAGISE 357
                                             *********************************************************************** PP

                               TIGR02080 357 ellrlsvGledaddliadleqalaa 381
                                             +llr+s+G+ed++dliadle++++a
  lcl|FitnessBrowser__Koxy:BWI76_RS00785 358 TLLRISTGIEDGEDLIADLENGFRA 382
                                             ***********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (382 nodes)
Target sequences:                          1  (386 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: 9.74
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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