GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Bacteroides clarus YIT 12056

Align phosphotransacetylase (EC 2.3.1.8) (characterized)
to candidate WP_009121834.1 BUB52_RS13605 phosphate acetyltransferase

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



>NCBI__GCF_900129655.1:WP_009121834.1
          Length = 338

 Score =  344 bits (882), Expect = 2e-99
 Identities = 177/328 (53%), Positives = 239/328 (72%), Gaps = 1/328 (0%)

Query: 3   LIESIWECAKQDKKRIILAEGEEKRNLIAADKIIKEGLAELVLVGDENKIKEKASELNL- 61
           LI  I E AK D++RI+L EG E+R L AA++I+ +G+A+L+L+G+  +I   A+E  L 
Sbjct: 4   LINEILERAKADRQRIVLPEGTEERTLKAANQILTDGIADLILLGNPAEINACATEWGLG 63

Query: 62  DISKAEIMDPETSLKTETYARDFYELRKHKGMTIEKSEKMVRDPLYFATMALKDGYVDGM 121
           +ISKA I+DPE + + E YA+  +ELRK KGMTIE++ K+  +PLY   + +K+G  DG 
Sbjct: 64  NISKATIIDPENNPRLEEYAQLLFELRKKKGMTIEEARKLATNPLYLGCLIIKNGDADGQ 123

Query: 122 VSGAVHTTGDLLRPGLQIIKTAPGVKIVSGFFVMIIPDCDYGEEGLLLFADCAVNPNPTS 181
           ++GA +TTGD+LRP LQIIKTAPG+  VSG  +++    +YG+ G+L+  D AV P P +
Sbjct: 124 LAGARNTTGDVLRPALQIIKTAPGITCVSGAMLLLTHAPEYGKNGILVMGDVAVTPVPDA 183

Query: 182 DELADIAITTAETARKLCNVEPKVAMLSFSTMGSAKGEMVDKVKNAVEITKKFRPDLAID 241
            +LA IA+ TA TA+ +  ++PKVA+LSFST GSAK E+VDKV  A++I K+  PD+AID
Sbjct: 184 SQLAQIAVCTARTAKAVAGLDPKVALLSFSTKGSAKHEVVDKVVEALKIAKEMAPDIAID 243

Query: 242 GELQLDAAIDSEVAALKAPSSNVAGNANVLVFPDLQTGNIGYKLVQRFAKAKAIGPICQG 301
           GELQ DAA+  EV A KAP S +AGNANVLV P L+ GNI YKLVQR   A A+GPI QG
Sbjct: 244 GELQADAALVPEVGASKAPGSAIAGNANVLVVPSLEVGNISYKLVQRLGHADAVGPILQG 303

Query: 302 FAKPINDLSRGCSSEDIVNVVAITVVQA 329
            A+P+NDLSRGCS ED+  ++AIT  QA
Sbjct: 304 IARPVNDLSRGCSIEDVYRMIAITANQA 331


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: 332
Number of extensions: 7
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: 333
Length of database: 338
Length adjustment: 28
Effective length of query: 305
Effective length of database: 310
Effective search space:    94550
Effective search space used:    94550
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 WP_009121834.1 BUB52_RS13605 (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.4049441.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.1e-113  362.8   0.1   9.2e-113  362.7   0.1    1.0  1  NCBI__GCF_900129655.1:WP_009121834.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900129655.1:WP_009121834.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  362.7   0.1  9.2e-113  9.2e-113       1     304 []      19     328 ..      19     328 .. 0.98

  Alignments for each domain:
  == domain 1  score: 362.7 bits;  conditional E-value: 9.2e-113
                             TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverlyekrk 73 
                                           ivlPEg+eer+lkAa+++++ +ia+ +ll+n +e+++ +++    +++k +++dp+  + +e+y++ l+e+rk
  NCBI__GCF_900129655.1:WP_009121834.1  19 IVLPEGTEERTLKAANQILTDGIADLILLGNPAEINACATEWGLGNISKATIIDPENNPRLEEYAQLLFELRK 91 
                                           8***********************************975555555799999********************** PP

                             TIGR00651  74 hkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekee... 143
                                           +kG+t +ear+  +++++l+ l+++ g adg  +Ga +tt ++lrpalqiikt++g+ +vs+ +++ ++    
  NCBI__GCF_900129655.1:WP_009121834.1  92 KKGMTIEEARKLATNPLYLGCLIIKNGDADGQLAGARNTTGDVLRPALQIIKTAPGITCVSGAMLLLTHApey 164
                                           ******************************************************************9998889 PP

                             TIGR00651 144 ...evlvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkeke 213
                                              ++lv +D av++ P+a +LA+iA+ +a +ak++ + +pkvalls+stkgs+k e v+kv+eA+ki+ke +
  NCBI__GCF_900129655.1:WP_009121834.1 165 gknGILVMGDVAVTPVPDASQLAQIAVCTARTAKAVAGLDPKVALLSFSTKGSAKHEVVDKVVEALKIAKEMA 237
                                           999********************************************************************** PP

                             TIGR00651 214 pdllldGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnD 286
                                           pd+++dGelq DaAlv++v ++kap s++ag+anv+v P+L+ Gni+Yk+vqRl++a+a+GPilqG+a+PvnD
  NCBI__GCF_900129655.1:WP_009121834.1 238 PDIAIDGELQADAALVPEVGASKAPGSAIAGNANVLVVPSLEVGNISYKLVQRLGHADAVGPILQGIARPVND 310
                                           ************************************************************************* PP

                             TIGR00651 287 LsRGasvedivnvviita 304
                                           LsRG+s+ed++ +++ita
  NCBI__GCF_900129655.1:WP_009121834.1 311 LSRGCSIEDVYRMIAITA 328
                                           ****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (338 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: 00:00:00.00
# Mc/sec: 15.46
//
[ok]

This GapMind analysis is from Sep 24 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