GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Lentibacillus jeotgali Grbi

Align phosphotransacetylase (EC 2.3.1.8) (characterized)
to candidate WP_010531539.1 ON01_RS13225 phosphate acetyltransferase

Query= metacyc::MONOMER-13062
         (328 letters)



>NCBI__GCF_000224785.1:WP_010531539.1
          Length = 322

 Score =  381 bits (978), Expect = e-110
 Identities = 187/322 (58%), Positives = 247/322 (76%), Gaps = 2/322 (0%)

Query: 2   DLFESLKSKIKDRKIKLVFPEGEDERIISAASRLANDDLAIPVLLGNEAEIKKTADALNV 61
           +LFE +K ++ +   K+VFPEG DERI++AAS+L    +  P+LLG++ EIK+ A++  V
Sbjct: 3   NLFEEIKDQLANADKKIVFPEGRDERILTAASQLGASGIVTPILLGDKGEIKQQAESAGV 62

Query: 62  SLDGIEIVDIENVPGEVRQQMVQAIVERRKGKTTADQAAQWLKDPNYFGTTMVYMDDVDG 121
           ++   E++D  + P     +M+   V+RRKGK TAD+A Q L D NYFGT +VYMD  DG
Sbjct: 63  NVSACELIDPHDFPEF--DEMIDVFVKRRKGKVTADEARQTLLDENYFGTMLVYMDKADG 120

Query: 122 MVSGAAHPTGDTVRPALQIIKTKPGVNLISGSFVMQKGDQRYLFADCAININPNETQLAE 181
           +VSGAAH T DTVRPALQIIKTK GV   SG F+M + D++Y+FADCAIN+NP+   LAE
Sbjct: 121 LVSGAAHSTADTVRPALQIIKTKEGVKKTSGVFIMVRNDEKYVFADCAINVNPDSQDLAE 180

Query: 182 IAVESGKTARLFDIDPRVALLSFSTNGSAKSPEVEKVHNATKLAQEMDPAMPIDGEMQFD 241
           IA ES  TA+LF +DPR+A+LSFST GSA+S E EKV NA +LA+E + ++ IDGE QFD
Sbjct: 181 IAAESANTAKLFRVDPRIAMLSFSTKGSAQSEETEKVVNALELAKEKNASLVIDGEFQFD 240

Query: 242 AAFVPAVAKAKYSDSKVAGHATVFVFPELQSGNIGYKIAQRMGGFEAIGPILQGLNKPVS 301
           AAFVP+VA  K  ++ + G A+VF+FP L++GNIGYKIAQR+G FEA+GPILQGLNKPV+
Sbjct: 241 AAFVPSVAAKKAPNAVIKGDASVFIFPSLEAGNIGYKIAQRLGEFEAVGPILQGLNKPVN 300

Query: 302 DLSRGCNAEDVYKVSIITATQA 323
           DLSRGC++EDVY +++ITA QA
Sbjct: 301 DLSRGCSSEDVYNLALITAAQA 322


Lambda     K      H
   0.315    0.133    0.369 

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: 326
Number of extensions: 11
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: 328
Length of database: 322
Length adjustment: 28
Effective length of query: 300
Effective length of database: 294
Effective search space:    88200
Effective search space used:    88200
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: 48 (23.1 bits)

Align candidate WP_010531539.1 ON01_RS13225 (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.2211681.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.5e-129  416.6   0.4     4e-129  416.4   0.4    1.0  1  NCBI__GCF_000224785.1:WP_010531539.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000224785.1:WP_010531539.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  416.4   0.4    4e-129    4e-129       1     304 []      19     319 ..      19     319 .. 0.99

  Alignments for each domain:
  == domain 1  score: 416.4 bits;  conditional E-value: 4e-129
                             TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverlyekrk 73 
                                           iv+PEg +er+l Aa++l  ++i++++ll++k e+++ +a++   +++ ++++dp+ +++ ++ ++ ++++rk
  NCBI__GCF_000224785.1:WP_010531539.1  19 IVFPEGRDERILTAASQLGASGIVTPILLGDKGEIKQ-QAESAGVNVSACELIDPHDFPEFDEMIDVFVKRRK 90 
                                           8******************************999999.8899999999************************* PP

                             TIGR00651  74 hkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeevl 146
                                            k vt  ear++l De++++++lv++++adglvsGa+++ta+t+rpalqiikt+egvk +s+vfim +++e +
  NCBI__GCF_000224785.1:WP_010531539.1  91 GK-VTADEARQTLLDENYFGTMLVYMDKADGLVSGAAHSTADTVRPALQIIKTKEGVKKTSGVFIMVRNDEKY 162
                                           **.********************************************************************** PP

                             TIGR00651 147 vfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdllld 219
                                           vfaDCa++v+P++++LAeiA +sa++ak +   +p++a+ls+stkgs+++ee+ekv++A++++kek++ l++d
  NCBI__GCF_000224785.1:WP_010531539.1 163 VFADCAINVNPDSQDLAEIAAESANTAKLFR-VDPRIAMLSFSTKGSAQSEETEKVVNALELAKEKNASLVID 234
                                           *******************************.***************************************** PP

                             TIGR00651 220 GelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGas 292
                                           Ge+qfDaA+v++va+kkap+  ++g+a vf+FP+L+aGnigYki+qRl+++ea+GPilqGl+kPvnDLsRG+s
  NCBI__GCF_000224785.1:WP_010531539.1 235 GEFQFDAAFVPSVAAKKAPNAVIKGDASVFIFPSLEAGNIGYKIAQRLGEFEAVGPILQGLNKPVNDLSRGCS 307
                                           ************************************************************************* PP

                             TIGR00651 293 vedivnvviita 304
                                            ed++n+++ita
  NCBI__GCF_000224785.1:WP_010531539.1 308 SEDVYNLALITA 319
                                           **********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (322 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 13.68
//
[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