GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Sinorhizobium meliloti 1021

Align phosphate acetyltransferase (EC 2.3.1.8) (characterized)
to candidate SM_b21532 SM_b21532 phosphate acetyltransferase

Query= BRENDA::Q5LMK3
         (337 letters)



>FitnessBrowser__Smeli:SM_b21532
          Length = 330

 Score =  328 bits (842), Expect = 9e-95
 Identities = 184/327 (56%), Positives = 215/327 (65%)

Query: 6   PIDLLLSDPPARRATVALSEGSDPRVVAGALAAHSAGIADVILVGQAAEIRAALKAQGAP 65
           P+D ++         V L EG DPR+VAGA+ A   G+A + LVG    I   L A  A 
Sbjct: 3   PLDRIIDAARKAPRHVVLPEGEDPRIVAGAVQARREGLAAITLVGNREVITQRLAALDAI 62

Query: 66  ADSLTIHDPDSSPLTAEFAAAYYGLRRHKGVSEAAALAAVRTPLVYAAMLVRGDHAVGTV 125
                I DP  SPLT +FA AY   RR KGV  AAA AAV +PL +AAM+VR   A GTV
Sbjct: 63  PQEFRIEDPACSPLTDDFATAYLERRRSKGVDAAAARAAVLSPLTFAAMMVREGIADGTV 122

Query: 126 GGAVATTSDVVRTAIQVIGAAPGAAMVSSFFLMYPPEAATAHARAMLYSDSGLVIDPSVA 185
           GGAVATT+D VR A+QVIG APG  +VSSFFLM   E   A   A +++D GLV+DP  A
Sbjct: 123 GGAVATTADTVRAALQVIGRAPGVGLVSSFFLMMLCEPHHARKGAFVFADCGLVVDPDAA 182

Query: 186 ELAAIAAASAASCRALLRAEPKIAMLSFSTKGSARHPHVSKVTDALARLRADHPDLDADG 245
            LA IA  SA S   L     K+AMLSFST GSA H  VSKV +A    R   PDL  DG
Sbjct: 183 GLADIARMSAKSYEMLAGERAKVAMLSFSTGGSAAHERVSKVVEATGMARRAEPDLIIDG 242

Query: 246 ELQFDAAFVPSVGASKAPGSDVAGQANVMIFPNLDAGNIGYKITQRLGGYTAIGPVLQGL 305
           ELQFD+AFV +V  +KAP S + G+ANV +FPNLDA NIGYKI QR+GG TAIGP+LQGL
Sbjct: 243 ELQFDSAFVEAVCLTKAPHSALRGEANVFVFPNLDAANIGYKIAQRIGGATAIGPILQGL 302

Query: 306 AKPANDLSRGCVAGDVTQMIAVTVLQA 332
           ++PANDLSRGC A DV  MIAVTV+QA
Sbjct: 303 SRPANDLSRGCTAADVFHMIAVTVVQA 329


Lambda     K      H
   0.317    0.130    0.362 

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: 285
Number of extensions: 5
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: 337
Length of database: 330
Length adjustment: 28
Effective length of query: 309
Effective length of database: 302
Effective search space:    93318
Effective search space used:    93318
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate SM_b21532 SM_b21532 (phosphate acetyltransferase)
to HMM TIGR00651 (pta: phosphate acetyltransferase (EC 2.3.1.8))

# 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/TIGR00651.hmm
# target sequence database:        /tmp/gapView.25521.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00651  [M=304]
Accession:   TIGR00651
Description: pta: phosphate acetyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   9.3e-110  352.8   0.0   1.1e-109  352.6   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SM_b21532  SM_b21532 phosphate acetyltransf


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SM_b21532  SM_b21532 phosphate acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  352.6   0.0  1.1e-109  1.1e-109       1     304 []      18     326 ..      18     326 .. 0.98

  Alignments for each domain:
  == domain 1  score: 352.6 bits;  conditional E-value: 1.1e-109
                            TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverlyekrkh 74 
                                          +vlPEg+++r++  a +  ++++a+ +l++n e +++ + + ++   ++ ++edp  s+ +++++ ++ e+r+ 
  lcl|FitnessBrowser__Smeli:SM_b21532  18 VVLPEGEDPRIVAGAVQARREGLAAITLVGNREVITQ-RLAALDAIPQEFRIEDPACSPLTDDFATAYLERRRS 90 
                                          79********************999888887777666.999********************************* PP

                            TIGR00651  75 kGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekee..... 143
                                          kGv+ ++ar ++  ++++aa++v+ g adg+v Gav tta+t+r+alq+i++++gv lvss+f+m + e     
  lcl|FitnessBrowser__Smeli:SM_b21532  91 KGVDAAAARAAVLSPLTFAAMMVREGIADGTVGGAVATTADTVRAALQVIGRAPGVGLVSSFFLMMLCEphhar 164
                                          *****************************************************************999999999 PP

                            TIGR00651 144 .evlvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdl 216
                                           + +vfaDC ++vdP+a  LA+iA  saks ++l +e  kva+ls+st+gs++ e v kv+eA+ +++  epdl
  lcl|FitnessBrowser__Smeli:SM_b21532 165 kGAFVFADCGLVVDPDAAGLADIARMSAKSYEMLAGERAKVAMLSFSTGGSAAHERVSKVVEATGMARRAEPDL 238
                                          99************************************************************************ PP

                            TIGR00651 217 lldGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRG 290
                                           +dGelqfD+A+ve v   kap+s+++g+anvfvFP+Lda nigYki+qR+++a+aiGPilqGl++P nDLsRG
  lcl|FitnessBrowser__Smeli:SM_b21532 239 IIDGELQFDSAFVEAVCLTKAPHSALRGEANVFVFPNLDAANIGYKIAQRIGGATAIGPILQGLSRPANDLSRG 312
                                          ************************************************************************** PP

                            TIGR00651 291 asvedivnvviita 304
                                          +++ d+++++++t+
  lcl|FitnessBrowser__Smeli:SM_b21532 313 CTAADVFHMIAVTV 326
                                          ***********995 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (330 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: 7.82
//
[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:

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