GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Bacteroides thetaiotaomicron VPI-5482

Align phosphotransacetylase (EC 2.3.1.8) (characterized)
to candidate 353218 BT3692 phosphate acetyltransferase (NCBI ptt file)

Query= metacyc::PTACLOS-MONOMER
         (333 letters)



>FitnessBrowser__Btheta:353218
          Length = 339

 Score =  329 bits (843), Expect = 7e-95
 Identities = 175/331 (52%), Positives = 235/331 (70%), Gaps = 2/331 (0%)

Query: 1   MDLIESIWECAKQDKKRIILAEGEEKRNLIAADKIIKEGLAELVLVGDENKIKEKASELN 60
           ++LI  I   AK D++RI+L EG E+R L AA++I+ + +A+L+L+G   +I E A +  
Sbjct: 2   LNLINQIVARAKADRQRIVLPEGTEERTLKAANQILTDEVADLILLGKPAEINELAVKWG 61

Query: 61  L-DISKAEIMDPETSLKTETYARDFYELRKHKGMTIEKSEKMVRDPLYFATMALKDGYVD 119
           L +ISKA I+DPETS K E YA+   ELRK KGMTIE++ ++  DPL++  + +K G  D
Sbjct: 62  LGNISKATIIDPETSPKHEEYAQLLCELRKKKGMTIEEARQLTNDPLFYGCLMIKSGDAD 121

Query: 120 GMVSGAVHTTGDLLRPGLQIIKTAPGVKIVSGFFVMIIPDCDYGEEGLLLFADCAVNPNP 179
           G ++GA +TTG++LRP LQIIKTAPG+  VSG  +++    +YG+ G+L+  D AV P P
Sbjct: 122 GQLAGARNTTGNVLRPALQIIKTAPGITCVSGAMLLLTHAPEYGKNGILVMGDVAVTPVP 181

Query: 180 TSDELADIAITTAETARKLCNVE-PKVAMLSFSTMGSAKGEMVDKVKNAVEITKKFRPDL 238
             ++LA IA+ TA+TA+ +  +E PKVAMLSFST GSAK E+VDKV  A +I K+  P L
Sbjct: 182 DPNQLAQIAVCTAQTAKAVAGIENPKVAMLSFSTKGSAKHEVVDKVVEATKIAKEMAPTL 241

Query: 239 AIDGELQLDAAIDSEVAALKAPSSNVAGNANVLVFPDLQTGNIGYKLVQRFAKAKAIGPI 298
            +DGE+Q DAA+  EV A KAP S VAG ANVL+ P L+ GNI YKLVQR   A AIGPI
Sbjct: 242 DLDGEMQADAALVPEVGASKAPGSPVAGEANVLIVPSLEVGNISYKLVQRLGHADAIGPI 301

Query: 299 CQGFAKPINDLSRGCSSEDIVNVVAITVVQA 329
            QG A+P+NDLSRGCS ED+  ++AIT  QA
Sbjct: 302 LQGIARPVNDLSRGCSIEDVYRMIAITANQA 332


Lambda     K      H
   0.316    0.134    0.374 

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: 308
Number of extensions: 8
Number of successful extensions: 3
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: 333
Length of database: 339
Length adjustment: 28
Effective length of query: 305
Effective length of database: 311
Effective search space:    94855
Effective search space used:    94855
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 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate 353218 BT3692 (phosphate acetyltransferase (NCBI ptt file))
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.13910.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
     1e-111  359.2   0.1   1.2e-111  359.1   0.1    1.0  1  lcl|FitnessBrowser__Btheta:353218  BT3692 phosphate acetyltransfera


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:353218  BT3692 phosphate acetyltransferase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  359.1   0.1  1.2e-111  1.2e-111       1     304 []      19     329 ..      19     329 .. 0.98

  Alignments for each domain:
  == domain 1  score: 359.1 bits;  conditional E-value: 1.2e-111
                          TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverlyekrkhkG 76 
                                        ivlPEg+eer+lkAa+++++ ++a+ +ll++ +e+++ ++k    +++k +++dp++s++ e+y++ l e+rk+kG
  lcl|FitnessBrowser__Btheta:353218  19 IVLPEGTEERTLKAANQILTDEVADLILLGKPAEINELAVKWGLGNISKATIIDPETSPKHEEYAQLLCELRKKKG 94 
                                        8***********************************9777766678999*************************** PP

                          TIGR00651  77 vtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekee......evl 146
                                        +t +ear+  +D++ ++ l+++ g adg  +Ga +tt ++lrpalqiikt++g+ +vs+ +++ ++       ++l
  lcl|FitnessBrowser__Btheta:353218  95 MTIEEARQLTNDPLFYGCLMIKSGDADGQLAGARNTTGNVLRPALQIIKTAPGITCVSGAMLLLTHApeygknGIL 170
                                        ***************************************************************9998889999*** PP

                          TIGR00651 147 vfaDCavavdPnaeeLAeiAlqsaksakslgeee.pkvallsystkgsgkgeevekvkeAvkilkekepdllldGe 221
                                        v +D av++ P++++LA+iA+ +a++ak++ ++e pkva+ls+stkgs+k e v+kv+eA+ki+ke +p l ldGe
  lcl|FitnessBrowser__Btheta:353218 171 VMGDVAVTPVPDPNQLAQIAVCTAQTAKAVAGIEnPKVAMLSFSTKGSAKHEVVDKVVEATKIAKEMAPTLDLDGE 246
                                        ******************************987549**************************************** PP

                          TIGR00651 222 lqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGasvediv 297
                                        +q DaAlv++v ++kap s+vag+anv++ P+L+ Gni+Yk+vqRl++a+aiGPilqG+a+PvnDLsRG+s+ed++
  lcl|FitnessBrowser__Btheta:353218 247 MQADAALVPEVGASKAPGSPVAGEANVLIVPSLEVGNISYKLVQRLGHADAIGPILQGIARPVNDLSRGCSIEDVY 322
                                        **************************************************************************** PP

                          TIGR00651 298 nvviita 304
                                         +++ita
  lcl|FitnessBrowser__Btheta:353218 323 RMIAITA 329
                                        *****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (339 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 10.87
//
[ok]

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

Links

Downloads

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:

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