Alignments for a candidate for astE in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for astE in Pseudomonas simiae WCS417

Align Succinylglutamate desuccinylase (EC 3.5.1.96) (characterized)
to candidate GFF4232 PS417_21680 succinylglutamate desuccinylase

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



>FitnessBrowser__WCS417:GFF4232
          Length = 334

 Score =  539 bits (1388), Expect = e-158
 Identities = 266/336 (79%), Positives = 306/336 (91%), Gaps = 2/336 (0%)

Query: 1   MLALGKLLELTLAGREPAEKTQLTVEGVRMRWLSEGALEVRPPEARDNGLDLLLSAGIHG 60
           MLALGKLLELTLAGREPA+K QLTV+GV+MRWLSEGALEVRPPEA+DNG DLLLS+GIHG
Sbjct: 1   MLALGKLLELTLAGREPAQKIQLTVDGVQMRWLSEGALEVRPPEAKDNGSDLLLSSGIHG 60

Query: 61  NETAPIELLDRLLHDIARGDLKPRARILFLFGNPEAIRKGERFVEQDVNRLFNGRHEQSS 120
           NETAPIELLDRLLH IARG++KPR RILFLFGNPEA+R+GER++E DVNRLFNGRHE++ 
Sbjct: 61  NETAPIELLDRLLHGIARGEIKPRTRILFLFGNPEAMRRGERYLELDVNRLFNGRHEKNI 120

Query: 121 GCEALRACELERLAASFFSLPDRQRLHYDLHTAIRGSKIEQFALYPWKEDRQHSRQELAR 180
           G EA+RA ELE+LA SFFSLP R RLHYDLHTAIRGSKIEQFALYPWK+ RQHSR +LAR
Sbjct: 121 GPEAMRAAELEQLARSFFSLPGRSRLHYDLHTAIRGSKIEQFALYPWKDGRQHSRHQLAR 180

Query: 181 LRAAGMEAVLLQNKPSIVFSSYTYDKLGAEAFTLELGKARPFGQNDGVNVSLLEKRLKQI 240
           L AAGM+AVLLQNK SI F+++TY++L AEAFTLELGKARPFGQN GV+VS LE RLKQ+
Sbjct: 181 LNAAGMQAVLLQNKTSITFTAFTYEQLDAEAFTLELGKARPFGQNQGVDVSRLETRLKQL 240

Query: 241 IEGTEPELTEDALDGLQLYSVAREIIKHSDSFRLNLPADIENFSELEVGYLLAEDIANTR 300
           IEGTEPE   ++LDGLQL++V+RE+IKHSD+F ++LPAD+ENFS L  GYLLAED+A TR
Sbjct: 241 IEGTEPE--TESLDGLQLFAVSREVIKHSDAFLMHLPADVENFSPLAQGYLLAEDVAKTR 298

Query: 301 WIIEEEGARIIFPNPRVKNGLRAGILVVPTTDENLA 336
           W+IEEEGARIIFPNP+VKNGLRAGIL+VPTT+  LA
Sbjct: 299 WVIEEEGARIIFPNPKVKNGLRAGILIVPTTEAGLA 334


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: 431
Number of extensions: 15
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: 334
Length adjustment: 28
Effective length of query: 308
Effective length of database: 306
Effective search space:    94248
Effective search space used:    94248
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 GFF4232 PS417_21680 (succinylglutamate desuccinylase)
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.27496.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.5e-122  394.8   0.0   1.7e-122  394.7   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF4232  PS417_21680 succinylglutamate de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF4232  PS417_21680 succinylglutamate desuccinylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  394.7   0.0  1.7e-122  1.7e-122       1     319 []       6     326 ..       6     326 .. 0.97

  Alignments for each domain:
  == domain 1  score: 394.7 bits;  conditional E-value: 1.7e-122
                           TIGR03242   1 dflaltlekkep.evtqgeaknvklrwldeGvlelePe..aeaekslvisaGihGnetaPielleqllsdiaagk 72 
                                         ++l+ltl+ +ep ++ q +  +v++rwl eG+le++P   ++   +l++s+GihGnetaPiell++ll+ ia+g+
  lcl|FitnessBrowser__WCS417:GFF4232   6 KLLELTLAGREPaQKIQLTVDGVQMRWLSEGALEVRPPeaKDNGSDLLLSSGIHGNETAPIELLDRLLHGIARGE 80 
                                         589******9997889999*****************9866778899***************************** PP

                           TIGR03242  73 lqlkvrlLlilGnpaalrkgkRyleedlnRlfgGryqeleeskeklRaeeLeqvveaffeagkasearyhyDlht 147
                                         ++ ++r+L+++Gnp a+r+g+Ryle d+nRlf+Gr+ e + + e++Ra+eLeq ++ ff+ +++s  r+hyDlht
  lcl|FitnessBrowser__WCS417:GFF4232  81 IKPRTRILFLFGNPEAMRRGERYLELDVNRLFNGRH-EKNIGPEAMRAAELEQLARSFFSLPGRS--RLHYDLHT 152
                                         ************************************.7799***********************9..8******* PP

                           TIGR03242 148 aiRasklekfallPyq.ekpfdkellewlaaadldavllhkekggtfshfssekleaeactlelGkarPfGendl 221
                                         aiR+sk+e+fal+P + ++++++++l++l+aa+++avll++++++tf++f++e+l+aea+tlelGkarPfG+n+ 
  lcl|FitnessBrowser__WCS417:GFF4232 153 AIRGSKIEQFALYPWKdGRQHSRHQLARLNAAGMQAVLLQNKTSITFTAFTYEQLDAEAFTLELGKARPFGQNQG 227
                                         ****************99********************************************************* PP

                           TIGR03242 222 sqfqaitealralisdeaiparkkeelklfevvesilkksdsfelhvaedasnftefakGtllaedkde.ryrve 295
                                         + ++ ++++l++li +++  +++ + l+lf v ++++k+sd+f +h+++d++nf+++a+G+llaed ++ r+++e
  lcl|FitnessBrowser__WCS417:GFF4232 228 VDVSRLETRLKQLIEGTEPETESLDGLQLFAVSREVIKHSDAFLMHLPADVENFSPLAQGYLLAEDVAKtRWVIE 302
                                         **************88777778888*****************************************9887***** PP

                           TIGR03242 296 eeeerilfPnakvanGlRaglllv 319
                                         ee++ri+fPn+kv+nGlRag+l+v
  lcl|FitnessBrowser__WCS417:GFF4232 303 EEGARIIFPNPKVKNGLRAGILIV 326
                                         *********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (319 nodes)
Target sequences:                          1  (334 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 11.83
//
[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