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

GapMind for catabolism of small carbon sources

Aligments 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.5337.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.13
//
[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, or view the source code.

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