Alignments for a candidate for astE in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Alignments for a candidate for astE in Pseudomonas fluorescens FW300-N2E2

Align Succinylglutamate desuccinylase (EC 3.5.1.96) (characterized)
to candidate Pf6N2E2_5671 Succinylglutamate desuccinylase (EC 3.5.1.96)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1977
         (336 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5671
          Length = 335

 Score =  602 bits (1552), Expect = e-177
 Identities = 305/336 (90%), Positives = 320/336 (95%), Gaps = 1/336 (0%)

Query: 1   MLALGKLLELTLAGREPAEKTQLTVEGVRMRWLSEGALEVRPPEARDNGLDLLLSAGIHG 60
           MLALGKLLELTLAGREPAEKTQLTVEGVRMRWLSEGALEV+PPEARDNGLDLLLSAGIHG
Sbjct: 1   MLALGKLLELTLAGREPAEKTQLTVEGVRMRWLSEGALEVKPPEARDNGLDLLLSAGIHG 60

Query: 61  NETAPIELLDRLLHDIARGDLKPRARILFLFGNPEAIRKGERFVEQDVNRLFNGRHEQSS 120
           NETAPIELLDRLLHDIARG LKPRARILFLFGNPEAIR+GERFVEQDVNRLFNGRHE S 
Sbjct: 61  NETAPIELLDRLLHDIARGHLKPRARILFLFGNPEAIRRGERFVEQDVNRLFNGRHELSG 120

Query: 121 GCEALRACELERLAASFFSLPDRQRLHYDLHTAIRGSKIEQFALYPWKEDRQHSRQELAR 180
           G EALRACELERLAASFFS P+R RLHYDLHTAIRGSKIEQFALYPWKE RQHSR+ELAR
Sbjct: 121 GPEALRACELERLAASFFSRPERSRLHYDLHTAIRGSKIEQFALYPWKEGRQHSRRELAR 180

Query: 181 LRAAGMEAVLLQNKPSIVFSSYTYDKLGAEAFTLELGKARPFGQNDGVNVSLLEKRLKQI 240
           LRA GMEAVLLQNKPSIVFS+YTYD+LGAE+FTLELGKARPFGQNDGVNVSLLE RL+QI
Sbjct: 181 LRAGGMEAVLLQNKPSIVFSAYTYDQLGAESFTLELGKARPFGQNDGVNVSLLETRLQQI 240

Query: 241 IEGTEPELTEDALDGLQLYSVAREIIKHSDSFRLNLPADIENFSELEVGYLLAEDIANTR 300
           IEG EPEL ++ LDGLQL+SVAREIIKHSDSFRLNLPADIENFSEL  GY+LAEDIA TR
Sbjct: 241 IEGNEPEL-DEGLDGLQLFSVAREIIKHSDSFRLNLPADIENFSELGKGYVLAEDIAQTR 299

Query: 301 WIIEEEGARIIFPNPRVKNGLRAGILVVPTTDENLA 336
           W+IEEEGARIIFPNP+VKNGLRAGIL+VP TDENLA
Sbjct: 300 WVIEEEGARIIFPNPKVKNGLRAGILIVPATDENLA 335


Lambda     K      H
   0.319    0.138    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: 507
Number of extensions: 19
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: 336
Length of database: 335
Length adjustment: 28
Effective length of query: 308
Effective length of database: 307
Effective search space:    94556
Effective search space used:    94556
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: 49 (23.5 bits)

Align candidate Pf6N2E2_5671 (Succinylglutamate desuccinylase (EC 3.5.1.96))
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.28113.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   1.2e-121  391.9   0.0   1.3e-121  391.7   0.0    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5671  Succinylglutamate desuccinylase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5671  Succinylglutamate desuccinylase (EC 3.5.1.96)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  391.7   0.0  1.3e-121  1.3e-121       1     319 []       6     327 ..       6     327 .. 0.96

  Alignments for each domain:
  == domain 1  score: 391.7 bits;  conditional E-value: 1.3e-121
                                      TIGR03242   1 dflaltlekkep.evtqgeaknvklrwldeGvlelePe..aeaekslvisaGihGnetaPiell 61 
                                                    ++l+ltl+ +ep e+tq + ++v++rwl eG+le++P   ++   +l++saGihGnetaPiell
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5671   6 KLLELTLAGREPaEKTQLTVEGVRMRWLSEGALEVKPPeaRDNGLDLLLSAGIHGNETAPIELL 69 
                                                    589******9997889999*****************9855677889****************** PP

                                      TIGR03242  62 eqllsdiaagklqlkvrlLlilGnpaalrkgkRyleedlnRlfgGryqeleeskeklRaeeLeq 125
                                                    ++ll+dia+g+l+ ++r+L+++Gnp a+r+g+R++e+d+nRlf+Gr+ el+ + e+lRa eLe 
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5671  70 DRLLHDIARGHLKPRARILFLFGNPEAIRRGERFVEQDVNRLFNGRH-ELSGGPEALRACELER 132
                                                    ***********************************************.9*************** PP

                                      TIGR03242 126 vveaffeagkasearyhyDlhtaiRasklekfallPyq.ekpfdkellewlaaadldavllhke 188
                                                     ++ ff+++++s  r+hyDlhtaiR+sk+e+fal+P + ++++++++l++l+a +++avll+++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5671 133 LAASFFSRPERS--RLHYDLHTAIRGSKIEQFALYPWKeGRQHSRRELARLRAGGMEAVLLQNK 194
                                                    ***********9..8**********************999************************ PP

                                      TIGR03242 189 kggtfshfssekleaeactlelGkarPfGendlsqfqaitealralisdeaiparkke.elklf 251
                                                    +++ fs++++++l+ae++tlelGkarPfG+nd ++++ ++++l+++i +++   ++    l+lf
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5671 195 PSIVFSAYTYDQLGAESFTLELGKARPFGQNDGVNVSLLETRLQQIIEGNEPELDEGLdGLQLF 258
                                                    ***********************************************8877766665449**** PP

                                      TIGR03242 252 evvesilkksdsfelhvaedasnftefakGtllaedkde.ryrveeeeerilfPnakvanGlRa 314
                                                    +v ++i+k+sdsf+l++++d++nf+e+ kG++laed ++ r+++eee++ri+fPn+kv+nGlRa
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5671 259 SVAREIIKHSDSFRLNLPADIENFSELGKGYVLAEDIAQtRWVIEEEGARIIFPNPKVKNGLRA 322
                                                    ************************************9988************************ PP

                                      TIGR03242 315 glllv 319
                                                    g+l+v
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5671 323 GILIV 327
                                                    **996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (319 nodes)
Target sequences:                          1  (335 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: 6.80
//
[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