Alignments for a candidate for astE in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for astE in Pseudomonas fluorescens GW456-L13

Align Succinylglutamate desuccinylase (EC 3.5.1.96) (characterized)
to candidate PfGW456L13_1977 Succinylglutamate desuccinylase (EC 3.5.1.96)

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1977
          Length = 336

 Score =  662 bits (1707), Expect = 0.0
 Identities = 336/336 (100%), Positives = 336/336 (100%)

Query: 1   MLALGKLLELTLAGREPAEKTQLTVEGVRMRWLSEGALEVRPPEARDNGLDLLLSAGIHG 60
           MLALGKLLELTLAGREPAEKTQLTVEGVRMRWLSEGALEVRPPEARDNGLDLLLSAGIHG
Sbjct: 1   MLALGKLLELTLAGREPAEKTQLTVEGVRMRWLSEGALEVRPPEARDNGLDLLLSAGIHG 60

Query: 61  NETAPIELLDRLLHDIARGDLKPRARILFLFGNPEAIRKGERFVEQDVNRLFNGRHEQSS 120
           NETAPIELLDRLLHDIARGDLKPRARILFLFGNPEAIRKGERFVEQDVNRLFNGRHEQSS
Sbjct: 61  NETAPIELLDRLLHDIARGDLKPRARILFLFGNPEAIRKGERFVEQDVNRLFNGRHEQSS 120

Query: 121 GCEALRACELERLAASFFSLPDRQRLHYDLHTAIRGSKIEQFALYPWKEDRQHSRQELAR 180
           GCEALRACELERLAASFFSLPDRQRLHYDLHTAIRGSKIEQFALYPWKEDRQHSRQELAR
Sbjct: 121 GCEALRACELERLAASFFSLPDRQRLHYDLHTAIRGSKIEQFALYPWKEDRQHSRQELAR 180

Query: 181 LRAAGMEAVLLQNKPSIVFSSYTYDKLGAEAFTLELGKARPFGQNDGVNVSLLEKRLKQI 240
           LRAAGMEAVLLQNKPSIVFSSYTYDKLGAEAFTLELGKARPFGQNDGVNVSLLEKRLKQI
Sbjct: 181 LRAAGMEAVLLQNKPSIVFSSYTYDKLGAEAFTLELGKARPFGQNDGVNVSLLEKRLKQI 240

Query: 241 IEGTEPELTEDALDGLQLYSVAREIIKHSDSFRLNLPADIENFSELEVGYLLAEDIANTR 300
           IEGTEPELTEDALDGLQLYSVAREIIKHSDSFRLNLPADIENFSELEVGYLLAEDIANTR
Sbjct: 241 IEGTEPELTEDALDGLQLYSVAREIIKHSDSFRLNLPADIENFSELEVGYLLAEDIANTR 300

Query: 301 WIIEEEGARIIFPNPRVKNGLRAGILVVPTTDENLA 336
           WIIEEEGARIIFPNPRVKNGLRAGILVVPTTDENLA
Sbjct: 301 WIIEEEGARIIFPNPRVKNGLRAGILVVPTTDENLA 336


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: 521
Number of extensions: 13
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: 336
Length of database: 336
Length adjustment: 28
Effective length of query: 308
Effective length of database: 308
Effective search space:    94864
Effective search space used:    94864
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 PfGW456L13_1977 (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.14164.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   5.4e-122  393.0   0.0   6.2e-122  392.8   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1977  Succinylglutamate desuccinylase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1977  Succinylglutamate desuccinylase (EC 3.5.1.96)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  392.8   0.0  6.2e-122  6.2e-122       1     319 []       6     328 ..       6     328 .. 0.95

  Alignments for each domain:
  == domain 1  score: 392.8 bits;  conditional E-value: 6.2e-122
                                               TIGR03242   1 dflaltlekkep.evtqgeaknvklrwldeGvlelePe..aeaekslvisaGihG 52 
                                                             ++l+ltl+ +ep e+tq + ++v++rwl eG+le++P   ++   +l++saGihG
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1977   6 KLLELTLAGREPaEKTQLTVEGVRMRWLSEGALEVRPPeaRDNGLDLLLSAGIHG 60 
                                                             589******9997889999*****************9855677889********* PP

                                               TIGR03242  53 netaPielleqllsdiaagklqlkvrlLlilGnpaalrkgkRyleedlnRlfgGr 107
                                                             netaPiell++ll+dia+g+l+ ++r+L+++Gnp a+rkg+R++e+d+nRlf+Gr
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1977  61 NETAPIELLDRLLHDIARGDLKPRARILFLFGNPEAIRKGERFVEQDVNRLFNGR 115
                                                             ******************************************************* PP

                                               TIGR03242 108 yqeleeskeklRaeeLeqvveaffeagkasearyhyDlhtaiRasklekfallPy 162
                                                             + e +++ e+lRa eLe  ++ ff+ + ++  r+hyDlhtaiR+sk+e+fal+P 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1977 116 H-EQSSGCEALRACELERLAASFFSLPDRQ--RLHYDLHTAIRGSKIEQFALYPW 167
                                                             *.567888*******************998..8********************** PP

                                               TIGR03242 163 q.ekpfdkellewlaaadldavllhkekggtfshfssekleaeactlelGkarPf 216
                                                             + ++++++++l++l+aa+++avll++++++ fs ++++kl+aea+tlelGkarPf
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1977 168 KeDRQHSRQELARLRAAGMEAVLLQNKPSIVFSSYTYDKLGAEAFTLELGKARPF 222
                                                             999**************************************************** PP

                                               TIGR03242 217 Gendlsqfqaitealralisde..aiparkkeelklfevvesilkksdsfelhva 269
                                                             G+nd ++++ ++++l+++i ++  +++++  + l+l++v ++i+k+sdsf+l+++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1977 223 GQNDGVNVSLLEKRLKQIIEGTepELTEDALDGLQLYSVAREIIKHSDSFRLNLP 277
                                                             *******************7651145566667*********************** PP

                                               TIGR03242 270 edasnftefakGtllaedkde.ryrveeeeerilfPnakvanGlRaglllv 319
                                                             +d++nf+e+++G+llaed ++ r+++eee++ri+fPn++v+nGlRag+l+v
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1977 278 ADIENFSELEVGYLLAEDIANtRWIIEEEGARIIFPNPRVKNGLRAGILVV 328
                                                             ******************8665***************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (319 nodes)
Target sequences:                          1  (336 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: 00:00:00.01
# Mc/sec: 8.36
//
[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