Alignments for a candidate for astE in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for astE in Shewanella oneidensis MR-1

Align Succinylglutamate desuccinylase; EC 3.5.1.96 (uncharacterized)
to candidate 201482 SO2338 succinylglutamate desuccinylase (NCBI ptt file)

Query= curated2:A4Y6M4
         (344 letters)



>FitnessBrowser__MR1:201482
          Length = 344

 Score =  623 bits (1607), Expect = 0.0
 Identities = 305/344 (88%), Positives = 322/344 (93%)

Query: 1   MLQALLDSKDFLALTLAHPEQFDGEFSFNLGDHTQVEVWDTGVIVFEPIQNEGKDIVLSC 60
           MLQALLDSKDFLALTLA+P+    EFSF LG+HT+V VWDTGVIVFEP Q +GKD++LSC
Sbjct: 1   MLQALLDSKDFLALTLANPQTLGDEFSFTLGEHTRVNVWDTGVIVFEPAQPQGKDVILSC 60

Query: 61  GVHGNETAPIELCNSLIKQLLQQKIIAKQRTLFLIGNPLAINNGTRIIDENMNRLFSGEH 120
           GVHGNETAPIELCN+LIKQLLQQKIIAKQRTLFLIGNPLAINNGTRIIDENMNRLFSGEH
Sbjct: 61  GVHGNETAPIELCNTLIKQLLQQKIIAKQRTLFLIGNPLAINNGTRIIDENMNRLFSGEH 120

Query: 121 SNPPGLVNPERVRAKKLEAYVDRFFTAAADGRQRIHYDLHTAMRASKHEKFAIYPYRPGR 180
           SNPPGLVNPER+RAKKLE YVDRFF AAA GRQRIHYDLHTAMRASKHEKFAIYPYRPGR
Sbjct: 121 SNPPGLVNPERLRAKKLETYVDRFFKAAAAGRQRIHYDLHTAMRASKHEKFAIYPYRPGR 180

Query: 181 AFSGEQIMFLAASGVDTVLFHHEPTTTFSYFSSERYGADAFTIELGKVYPMGQNDMTRFI 240
           A+S EQIMFLAASGVDTVLFHHEPTTTFSYFSSE+YGADAFTIELGKVYPMGQNDMTRFI
Sbjct: 181 AYSAEQIMFLAASGVDTVLFHHEPTTTFSYFSSEQYGADAFTIELGKVYPMGQNDMTRFI 240

Query: 241 ATHEMFMRLITAKPLELDAFDADKVNLYQVCRVINKHFDDFEFTFATDVENFRSFPKGFV 300
           A  EMF RLIT KPL+L++F  DKVNLYQVCRVINKHFDDFEFTFATDVENFR+FPKGFV
Sbjct: 241 AAQEMFTRLITDKPLQLESFSTDKVNLYQVCRVINKHFDDFEFTFATDVENFRAFPKGFV 300

Query: 301 LAREGGQEIKVEHEFESVVFPNAKVPIGNRTVICLIPAVNADVR 344
           LAREGGQEIKVE E ES+VFPNAKVPIGNRTVICLIP+V  DVR
Sbjct: 301 LAREGGQEIKVEQEVESIVFPNAKVPIGNRTVICLIPSVAPDVR 344


Lambda     K      H
   0.323    0.139    0.412 

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: 513
Number of extensions: 11
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: 344
Length of database: 344
Length adjustment: 29
Effective length of query: 315
Effective length of database: 315
Effective search space:    99225
Effective search space used:    99225
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 49 (23.5 bits)

Align candidate 201482 SO2338 (succinylglutamate desuccinylase (NCBI ptt file))
to HMM TIGR03242 (astE: succinylglutamate desuccinylase (EC 3.5.1.96))

# 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.carbon/TIGR03242.hmm
# target sequence database:        /tmp/gapView.27827.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03242  [M=319]
Accession:   TIGR03242
Description: arg_catab_astE: succinylglutamate desuccinylase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   2.3e-109  351.5   0.1   2.6e-109  351.3   0.1    1.0  1  lcl|FitnessBrowser__MR1:201482  SO2338 succinylglutamate desucci


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:201482  SO2338 succinylglutamate desuccinylase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  351.3   0.1  2.6e-109  2.6e-109       1     318 [.      10     335 ..      10     336 .. 0.94

  Alignments for each domain:
  == domain 1  score: 351.3 bits;  conditional E-value: 2.6e-109
                       TIGR03242   1 dflaltlekkepevtqge...aknvklrwldeGvlelePeaeaekslvisaGihGnetaPielleqllsdiaagklqlk 76 
                                     dflaltl++ ++   +      +  +++  d+Gv+  eP++ + k++++s G+hGnetaPiel ++l+++++++k+  k
  lcl|FitnessBrowser__MR1:201482  10 DFLALTLANPQTLGDEFSftlGEHTRVNVWDTGVIVFEPAQPQGKDVILSCGVHGNETAPIELCNTLIKQLLQQKIIAK 88 
                                     799999998877333333323566778899************************************************* PP

                       TIGR03242  77 vrlLlilGnpaalrkgkRyleedlnRlfgGryqele..eskeklRaeeLeqvveaffeagkasearyhyDlhtaiRask 153
                                     +r+L+++Gnp a+++g R ++e++nRlf+G++ +       e+lRa++Le +v +ff+a+ a ++r hyDlhta+Rask
  lcl|FitnessBrowser__MR1:201482  89 QRTLFLIGNPLAINNGTRIIDENMNRLFSGEHSNPPglVNPERLRAKKLETYVDRFFKAAAAGRQRIHYDLHTAMRASK 167
                                     ********************************9876224579************************************* PP

                       TIGR03242 154 lekfallPyq.ekpfdkellewlaaadldavllhkekggtfshfssekleaeactlelGkarPfGendlsqfqaiteal 231
                                     +ekfa++Py+ ++ +++e++ +laa+++d+vl+h+e+++tfs+fsse+++a+a+t+elGk+ P G+nd+++f a++e  
  lcl|FitnessBrowser__MR1:201482 168 HEKFAIYPYRpGRAYSAEQIMFLAASGVDTVLFHHEPTTTFSYFSSEQYGADAFTIELGKVYPMGQNDMTRFIAAQEMF 246
                                     ******************************************************************************* PP

                       TIGR03242 232 ralisdeaiparkke..elklfevvesilkksdsfelhvaedasnftefakGtllaedkderyrveeeeerilfPnakv 308
                                     ++li+d+ +  ++++  +++l++v + i k+ d+fe+  a d++nf  f+kG++la++  ++ +ve+e e+i+fPnakv
  lcl|FitnessBrowser__MR1:201482 247 TRLITDKPLQLESFStdKVNLYQVCRVINKHFDDFEFTFATDVENFRAFPKGFVLAREGGQEIKVEQEVESIVFPNAKV 325
                                     *******99988876669************************************************************* PP

                       TIGR03242 309 anGlRaglll 318
                                       G R ++ l
  lcl|FitnessBrowser__MR1:201482 326 PIGNRTVICL 335
                                     *****99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (319 nodes)
Target sequences:                          1  (344 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: 9.30
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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

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 catabolism of small carbon sources