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.21395.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.29
//
[ok]

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

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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:

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:

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:

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:

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