Aligments for a candidate for pta in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Aligments for a candidate for pta in Klebsiella michiganensis M5al

Align phosphate acetyltransferase (EC 2.3.1.8) (characterized)
to candidate BWI76_RS20805 BWI76_RS20805 phosphate acetyltransferase

Query= BRENDA::P41790
         (338 letters)



>FitnessBrowser__Koxy:BWI76_RS20805
          Length = 338

 Score =  573 bits (1477), Expect = e-168
 Identities = 290/337 (86%), Positives = 313/337 (92%)

Query: 1   MIIERARELAVRAPARVVFPDALDERVLKAAHYLQQYGLARPVLVASPFALRQFALSHRM 60
           MIIERAR+LA+R+PARVVF DALD RVLKAAHYLQQ  LA+P+L+ASPFALRQFAL+HR+
Sbjct: 1   MIIERARQLALRSPARVVFADALDIRVLKAAHYLQQQRLAKPILIASPFALRQFALNHRL 60

Query: 61  AMDGIQVIDPHSNLSMRQRFAQRWLARAGEKTPPDAVEKLSDPLMFAAAMVSAGEADVCI 120
            MDG+Q++DP SN  +R  FA+RWL RAGEKTPPDA EKL+DPLMFAAAMV AG+ADVCI
Sbjct: 61  PMDGMQIVDPLSNRQIRAAFARRWLDRAGEKTPPDAEEKLNDPLMFAAAMVGAGQADVCI 120

Query: 121 AGNLSSTANVLRAGLRVIGLQPGCKTLSSIFLMLPQYAGPALGFADCSVVPQPTAAQLAD 180
           AGNLSSTANVLRAGLR+IGLQPGCKTLSSIFLMLPQYAGPALGFADCSVVPQPTAAQLAD
Sbjct: 121 AGNLSSTANVLRAGLRIIGLQPGCKTLSSIFLMLPQYAGPALGFADCSVVPQPTAAQLAD 180

Query: 181 IALASADTWRAITGEEPRVAMLSFSSNGSARHPNVANVQQATELVRERAPQLLVDGELQF 240
           IA+ASA+TW+AITGEEPRVAMLSFSSNGSARHPNVANVQQAT +VR+RAPQL+VDGELQF
Sbjct: 181 IAIASAETWQAITGEEPRVAMLSFSSNGSARHPNVANVQQATGIVRQRAPQLMVDGELQF 240

Query: 241 DAAFVPEVAAQKAPDSPLQGRANVMIFPSLEAGNIGYKITQRLGGYRAVGPLIQGLAAPL 300
           DAAFVPEVAAQKAP SPLQGRANVM+FPSLEAGNIGYKI QRLGGYRAVGPLIQGLAAPL
Sbjct: 241 DAAFVPEVAAQKAPASPLQGRANVMVFPSLEAGNIGYKIAQRLGGYRAVGPLIQGLAAPL 300

Query: 301 HDLSRGCSVQEIIELALVAAVPRQADVSRERSLHTLV 337
           HDLSRGCSVQEIIELALVAAVPRQ D SR     T V
Sbjct: 301 HDLSRGCSVQEIIELALVAAVPRQTDASRVNRSQTRV 337


Lambda     K      H
   0.321    0.134    0.384 

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: 467
Number of extensions: 7
Number of successful extensions: 1
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: 338
Length of database: 338
Length adjustment: 28
Effective length of query: 310
Effective length of database: 310
Effective search space:    96100
Effective search space used:    96100
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 49 (23.5 bits)

Align candidate BWI76_RS20805 BWI76_RS20805 (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.31893.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   1.8e-100  322.3   0.0     2e-100  322.1   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS20805  BWI76_RS20805 phosphate acetyltr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS20805  BWI76_RS20805 phosphate acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  322.1   0.0    2e-100    2e-100       1     303 [.      17     319 ..      17     320 .. 0.95

  Alignments for each domain:
  == domain 1  score: 322.1 bits;  conditional E-value: 2e-100
                               TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvskd.iekyverlye 70 
                                             +v+ ++ + rvlkAa+ l+++++a+++l+++  +  +  a +  l +  ++++dp + ++ +  ++ r+ +
  lcl|FitnessBrowser__Koxy:BWI76_RS20805  17 VVFADALDIRVLKAAHYLQQQRLAKPILIASPFALRQ-FALNHRLPMDGMQIVDPLSNRQiRAAFARRWLD 86 
                                             6999***************************999998.556667777788887776665516789999999 PP

                               TIGR00651  71 krkhkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimek 141
                                             +  +k  t   a+e+l+D++++aa +v +g+ad +++G+ s+ta++lr++l+ii+ ++g k+ ss+f+m  
  lcl|FitnessBrowser__Koxy:BWI76_RS20805  87 RAGEK--TPPDAEEKLNDPLMFAAAMVGAGQADVCIAGNLSSTANVLRAGLRIIGLQPGCKTLSSIFLMLP 155
                                             99999..999***********************************************************88 PP

                               TIGR00651 142 ee..evlvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilk 210
                                             +     l faDC+v+++P+a +LA+iA+ sa++ +++++eep+va+ls+s++gs++  +v  v++A+ i++
  lcl|FitnessBrowser__Koxy:BWI76_RS20805 156 QYagPALGFADCSVVPQPTAAQLADIAIASAETWQAITGEEPRVAMLSFSSNGSARHPNVANVQQATGIVR 226
                                             765579***************************************************************** PP

                               TIGR00651 211 ekepdllldGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGla 281
                                             +++p+l++dGelqfDaA+v++va++kap s+++g+anv+vFP+L+aGnigYki+qRl++++a+GP++qGla
  lcl|FitnessBrowser__Koxy:BWI76_RS20805 227 QRAPQLMVDGELQFDAAFVPEVAAQKAPASPLQGRANVMVFPSLEAGNIGYKIAQRLGGYRAVGPLIQGLA 297
                                             *********************************************************************** PP

                               TIGR00651 282 kPvnDLsRGasvedivnvviit 303
                                              P+ DLsRG+sv++i+ ++++ 
  lcl|FitnessBrowser__Koxy:BWI76_RS20805 298 APLHDLSRGCSVQEIIELALVA 319
                                             ****************998876 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: 12.69
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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