Alignments for a candidate for pta in Coprobacter fastidiosus NSB1

GapMind for catabolism of small carbon sources

Alignments for a candidate for pta in Coprobacter fastidiosus NSB1

Align phosphate acetyltransferase (EC 2.3.1.8) (characterized)
to candidate WP_022603079.1 NSB1T_RS28250 phosphate acetyltransferase

Query= BRENDA::O52593
         (332 letters)



>NCBI__GCF_000473955.1:WP_022603079.1
          Length = 335

 Score =  347 bits (889), Expect = e-100
 Identities = 178/330 (53%), Positives = 233/330 (70%), Gaps = 3/330 (0%)

Query: 1   MSFLEQIIERAKSDVKTIVLPESTDLRVIKAASMIMKKGIAKVVLIGNEKEIKSLAGDID 60
           M  + QII RAK+D++ IVLPE T+ R +KAA  ++   +A + LIGN  EI +LA    
Sbjct: 1   MELMNQIIARAKADMQRIVLPEGTEERTLKAADKLIADKVAHITLIGNPAEIMALAEKHG 60

Query: 61  LEGV---MIEDSLNSEKLEDYANTLYELRKSKGMTIEAARETIKDPLYYGVMMVKKGEAD 117
           L+ +   +I D  N E+ E+YAN L+ELRK KGMT E A + ++DPL+   +M+K G AD
Sbjct: 61  LQNIGNAIIVDPKNHERKEEYANLLFELRKKKGMTEEQAAKQVEDPLFLAALMIKSGHAD 120

Query: 118 GMVAGAVNSTANTLRPALQILKTAPGTKLVSSFFVMVVPNCEYGHNGTFVYADCGLVENP 177
           G VAGA N+T N LR A QI+KTAPG  +VS  F+M +PN  YG NG  V+ADC ++ NP
Sbjct: 121 GEVAGAQNTTGNVLRAAFQIVKTAPGVSVVSGAFLMFLPNKNYGENGIMVFADCAVLPNP 180

Query: 178 DADQLSEIAISASKSFEMLVGAKPQVAMLSYSSYGSAKSELTEKVIKATQLAKEKAPHLA 237
           +A++L++IA+S   +   L G +P++AMLS+S+ GSAK E+ +KV++AT++AKE    L 
Sbjct: 181 NAEELAQIAVSTGHTTRTLAGFEPRIAMLSFSTKGSAKHEMVDKVVEATRIAKEMDSSLK 240

Query: 238 IDGELQVDAAIVPEVAKSKAKGSSVAGKANVLIFPDLDAGNIAYKLTQRLAKAEAYGPIT 297
           IDGELQ DAAIVP V  SKA  S +AG ANVL+FP L+ GNI YKL QRLA AEA GPI 
Sbjct: 241 IDGELQADAAIVPAVGMSKAPDSEIAGNANVLVFPSLETGNITYKLVQRLAGAEAVGPIL 300

Query: 298 QGLARPVNDLSRGCSAEDIVGVAAITAVQA 327
           QG+A P+NDLSRGCS EDI  + AITA QA
Sbjct: 301 QGIAAPINDLSRGCSVEDIYKMVAITANQA 330


Lambda     K      H
   0.313    0.129    0.346 

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: 298
Number of extensions: 8
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: 332
Length of database: 335
Length adjustment: 28
Effective length of query: 304
Effective length of database: 307
Effective search space:    93328
Effective search space used:    93328
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 49 (23.5 bits)

Align candidate WP_022603079.1 NSB1T_RS28250 (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.2984553.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     9e-124  398.8   1.0     1e-123  398.6   1.0    1.0  1  NCBI__GCF_000473955.1:WP_022603079.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000473955.1:WP_022603079.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  398.6   1.0    1e-123    1e-123       1     304 []      18     327 ..      18     327 .. 0.98

  Alignments for each domain:
  == domain 1  score: 398.6 bits;  conditional E-value: 1e-123
                             TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverlyekrk 73 
                                           ivlPEg+eer+lkAa +l+  k+a+ +l++n +e+++ + k+  +++g+ +++dp+ ++ +e+y++ l+e+rk
  NCBI__GCF_000473955.1:WP_022603079.1  18 IVLPEGTEERTLKAADKLIADKVAHITLIGNPAEIMALAEKHGLQNIGNAIIVDPKNHERKEEYANLLFELRK 90 
                                           8************************************8777778899************************** PP

                             TIGR00651  74 hkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekee... 143
                                           +kG+te++a++q++D++ laal+++ g+adg+v+Ga++tt ++lr+a+qi+kt++gv++vs+ f+m +++   
  NCBI__GCF_000473955.1:WP_022603079.1  91 KKGMTEEQAAKQVEDPLFLAALMIKSGHADGEVAGAQNTTGNVLRAAFQIVKTAPGVSVVSGAFLMFLPNkny 163
                                           ******************************************************************9999899 PP

                             TIGR00651 144 ...evlvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkeke 213
                                              +++vfaDCav ++PnaeeLA+iA+++ +++++l + ep++a+ls+stkgs+k e+v+kv+eA++i+ke  
  NCBI__GCF_000473955.1:WP_022603079.1 164 genGIMVFADCAVLPNPNAEELAQIAVSTGHTTRTLAGFEPRIAMLSFSTKGSAKHEMVDKVVEATRIAKEMD 236
                                           9999********************************************************************* PP

                             TIGR00651 214 pdllldGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnD 286
                                           + l++dGelq DaA+v+ v  +kap+se+ag+anv+vFP+L++Gni+Yk+vqRla+aea+GPilqG+a P+nD
  NCBI__GCF_000473955.1:WP_022603079.1 237 SSLKIDGELQADAAIVPAVGMSKAPDSEIAGNANVLVFPSLETGNITYKLVQRLAGAEAVGPILQGIAAPIND 309
                                           ************************************************************************* PP

                             TIGR00651 287 LsRGasvedivnvviita 304
                                           LsRG+svedi+++v+ita
  NCBI__GCF_000473955.1:WP_022603079.1 310 LSRGCSVEDIYKMVAITA 327
                                           ****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (335 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: 25.20
//
[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:

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