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.2109331.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: 23.95
//
[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