Alignments for a candidate for pta in Sinorhizobium meliloti 1021

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.29912.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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 8.00
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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