Alignments for a candidate for astE in Shewanella sp. ANA-3

GapMind for catabolism of small carbon sources

Alignments for a candidate for astE in Shewanella sp. ANA-3

Align Succinylglutamate desuccinylase; EC 3.5.1.96 (uncharacterized)
to candidate 7024961 Shewana3_2132 succinylglutamate desuccinylase (RefSeq)

Query= curated2:A4Y6M4
         (344 letters)



>FitnessBrowser__ANA3:7024961
          Length = 344

 Score =  628 bits (1620), Expect = 0.0
 Identities = 309/344 (89%), Positives = 323/344 (93%)

Query: 1   MLQALLDSKDFLALTLAHPEQFDGEFSFNLGDHTQVEVWDTGVIVFEPIQNEGKDIVLSC 60
           MLQALLDSKDFLALTLA+PE    EFSF LG+HT+VEVW+TGVIVFEP Q +GKD++LSC
Sbjct: 1   MLQALLDSKDFLALTLANPETLGDEFSFTLGEHTRVEVWNTGVIVFEPAQAQGKDVILSC 60

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

Query: 121 SNPPGLVNPERVRAKKLEAYVDRFFTAAADGRQRIHYDLHTAMRASKHEKFAIYPYRPGR 180
           SNPPGLVNPERVRAKKLEAYVDRFF  AA GRQRIHYDLHTAMRASKHEKFAIYPYRPGR
Sbjct: 121 SNPPGLVNPERVRAKKLEAYVDRFFKGAAAGRQRIHYDLHTAMRASKHEKFAIYPYRPGR 180

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

Query: 241 ATHEMFMRLITAKPLELDAFDADKVNLYQVCRVINKHFDDFEFTFATDVENFRSFPKGFV 300
           A  EMFMRLIT KPL L+ F ADKVNLYQVCRVINKHFDDFEFTFA DVENFRSFPKGFV
Sbjct: 241 AAQEMFMRLITDKPLALEPFSADKVNLYQVCRVINKHFDDFEFTFAADVENFRSFPKGFV 300

Query: 301 LAREGGQEIKVEHEFESVVFPNAKVPIGNRTVICLIPAVNADVR 344
           LAREGGQEIKVE EFE++VFPNAKVPIGNRTVICLIP+V  DVR
Sbjct: 301 LAREGGQEIKVEQEFEAIVFPNAKVPIGNRTVICLIPSVAPDVR 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 7024961 Shewana3_2132 (succinylglutamate desuccinylase (RefSeq))
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.25255.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   4.4e-108  347.3   0.1     5e-108  347.1   0.1    1.0  1  lcl|FitnessBrowser__ANA3:7024961  Shewana3_2132 succinylglutamate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7024961  Shewana3_2132 succinylglutamate desuccinylase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  347.1   0.1    5e-108    5e-108       1     318 [.      10     335 ..      10     336 .. 0.94

  Alignments for each domain:
  == domain 1  score: 347.1 bits;  conditional E-value: 5e-108
                         TIGR03242   1 dflaltlekkepevtqge...aknvklrwldeGvlelePeaeaekslvisaGihGnetaPielleqllsdiaagklq 74 
                                       dflaltl++ e+   +      +  ++   ++Gv+  eP++ + k++++s G+hGnetaPiel ++l+++++++k+ 
  lcl|FitnessBrowser__ANA3:7024961  10 DFLALTLANPETLGDEFSftlGEHTRVEVWNTGVIVFEPAQAQGKDVILSCGVHGNETAPIELCNTLIKQLLQQKII 86 
                                       789999988776333322222566777899*********************************************** PP

                         TIGR03242  75 lkvrlLlilGnpaalrkgkRyleedlnRlfgGryqele..eskeklRaeeLeqvveaffeagkasearyhyDlhtai 149
                                        k+r+L+++Gnp a+++g R ++e++nRlf+G++ +       e+ Ra++Le++v +ff+ + a ++r hyDlhta+
  lcl|FitnessBrowser__ANA3:7024961  87 AKQRTLFLIGNPLAINNGTRIIDENMNRLFSGEHSNPPglVNPERVRAKKLEAYVDRFFKGAAAGRQRIHYDLHTAM 163
                                       **********************************9876224579********************************* PP

                         TIGR03242 150 RasklekfallPyq.ekpfdkellewlaaadldavllhkekggtfshfssekleaeactlelGkarPfGendlsqfq 225
                                       Rask+ekfa++Py+ ++ +++e++ +laa+++d+vl+h+e+++tfs+fsse+++a+a+t+elGk+ P G+nd+++f 
  lcl|FitnessBrowser__ANA3:7024961 164 RASKHEKFAIYPYRpGRAYSAEQIMFLAASGVDTVLFHHEPTTTFSYFSSEQYGADAFTIELGKVYPMGQNDMTRFI 240
                                       ***************************************************************************** PP

                         TIGR03242 226 aitealralisdeaiparkke..elklfevvesilkksdsfelhvaedasnftefakGtllaedkderyrveeeeer 300
                                       a++e  ++li+d+ ++ + ++  +++l++v + i k+ d+fe+  a+d++nf +f+kG++la++  ++ +ve+e e 
  lcl|FitnessBrowser__ANA3:7024961 241 AAQEMFMRLITDKPLALEPFSadKVNLYQVCRVINKHFDDFEFTFAADVENFRSFPKGFVLAREGGQEIKVEQEFEA 317
                                       *************99998776669***************************************************** PP

                         TIGR03242 301 ilfPnakvanGlRaglll 318
                                       i+fPnakv  G R ++ l
  lcl|FitnessBrowser__ANA3:7024961 318 IVFPNAKVPIGNRTVICL 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: 8.06
//
[ok]

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

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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

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