Alignments for a candidate for pta in Klebsiella variicola At-22

GapMind for catabolism of small carbon sources

Alignments for a candidate for pta in Klebsiella variicola At-22

Align phosphate acetyltransferase (EC 2.3.1.8) (characterized)
to candidate WP_012967509.1 KVAR_RS06905 phosphate acetyltransferase

Query= BRENDA::P0A9M8
         (714 letters)



>NCBI__GCF_000025465.1:WP_012967509.1
          Length = 715

 Score = 1330 bits (3443), Expect = 0.0
 Identities = 686/714 (96%), Positives = 702/714 (98%)

Query: 1   MSRIIMLIPTGTSVGLTSVSLGVIRAMERKGVRLSVFKPIAQPRTGGDAPDQTTTIVRAN 60
           MSR IMLIPTGTSVGLTSVSLGVIRAMERKGVRLSVFKPIAQPR+GGDAPDQTTTIVRA+
Sbjct: 1   MSRTIMLIPTGTSVGLTSVSLGVIRAMERKGVRLSVFKPIAQPRSGGDAPDQTTTIVRAS 60

Query: 61  SSTTTAAEPLKMSYVEGLLSSNQKDVLMEEIVANYHANTKDAEVVLVEGLVPTRKHQFAQ 120
           SSTTTAAEPLKM++VE LLSSNQKDVLMEEI+ANYHANT+DAEVVLVEGLVPTRKHQFAQ
Sbjct: 61  SSTTTAAEPLKMNHVESLLSSNQKDVLMEEIIANYHANTQDAEVVLVEGLVPTRKHQFAQ 120

Query: 121 SLNYEIAKTLNAEIVFVMSQGTDTPEQLKERIELTRNSFGGAKNTNITGVIVNKLNAPVD 180
           +LN+EIAKTLNAEIVFVMSQGTDTPEQL ERIELTRNSFGGAKNT+ITGVIVNKLNAPVD
Sbjct: 121 ALNFEIAKTLNAEIVFVMSQGTDTPEQLNERIELTRNSFGGAKNTSITGVIVNKLNAPVD 180

Query: 181 EQGRTRPDLSEIFDDSSKAKVNNVDPAKLQESSPLPVLGAVPWSFDLIATRAIDMARHLN 240
           EQGRTRPDLSEIFDDSSKAKV  +DPA+LQ+ S LPVLGAVPWSFDLIATRAIDMA HLN
Sbjct: 181 EQGRTRPDLSEIFDDSSKAKVVKIDPAQLQKGSSLPVLGAVPWSFDLIATRAIDMAHHLN 240

Query: 241 ATIINEGDINTRRVKSVTFCARSIPHMLEHFRAGSLLVTSADRPDVLVAACLAAMNGVEI 300
           ATIINEGDINTRRVKSVTFCARSIPHMLEHFRAGSLLVTSADRPDVLVAACLAAMNGVEI
Sbjct: 241 ATIINEGDINTRRVKSVTFCARSIPHMLEHFRAGSLLVTSADRPDVLVAACLAAMNGVEI 300

Query: 301 GALLLTGGYEMDARISKLCERAFATGLPVFMVNTNTWQTSLSLQSFNLEVPVDDHERIEK 360
           GA+LLTGGYEMDARISKLCERAFATGLPVFMVNTNTWQTSLSLQSFNLEVPVDDHERIEK
Sbjct: 301 GAILLTGGYEMDARISKLCERAFATGLPVFMVNTNTWQTSLSLQSFNLEVPVDDHERIEK 360

Query: 361 VQEYVANYINADWIESLTATSERSRRLSPPAFRYQLTELARKAGKRIVLPEGDEPRTVKA 420
           VQEYVANYINADWIESLTATSERSRRLSPPAFRYQLTELARKAGKR+VLPEGDEPRTVKA
Sbjct: 361 VQEYVANYINADWIESLTATSERSRRLSPPAFRYQLTELARKAGKRVVLPEGDEPRTVKA 420

Query: 421 AAICAERGIATCVLLGNPAEINRVAASQGVELGAGIEIVDPEVVRESYVGRLVELRKNKG 480
           AAICAERGIATCVLLGNP EINRVAA+QGVELGAGIEIVDPEVVRESYV RLVELRK+KG
Sbjct: 421 AAICAERGIATCVLLGNPDEINRVAAAQGVELGAGIEIVDPEVVRESYVARLVELRKSKG 480

Query: 481 MTETVAREQLEDNVVLGTLMLEQDEVDGLVSGAVHTTANTIRPPLQLIKTAPGSSLVSSV 540
           MTE VAREQLEDNVVLGTLMLEQDEVDGLVSGAVHTTANTIRPPLQLIKTAPGSSLVSSV
Sbjct: 481 MTEAVAREQLEDNVVLGTLMLEQDEVDGLVSGAVHTTANTIRPPLQLIKTAPGSSLVSSV 540

Query: 541 FFMLLPEQVYVYGDCAINPDPTAEQLAEIAIQSADSAAAFGIEPRVAMLSYSTGTSGAGS 600
           FFMLLPEQVYVYGDCAINPDPTAEQLAEIAIQSADSA AFGIEPRVAMLSYSTGTSGAGS
Sbjct: 541 FFMLLPEQVYVYGDCAINPDPTAEQLAEIAIQSADSAIAFGIEPRVAMLSYSTGTSGAGS 600

Query: 601 DVEKVREATRLAQEKRPDLMIDGPLQYDAAVMADVAKSKAPNSPVAGRATVFIFPDLNTG 660
           DVEKVREATRLAQEKRPDLMIDGPLQYDAAVMADVAKSKAPNSPVAGRATVFIFPDLNTG
Sbjct: 601 DVEKVREATRLAQEKRPDLMIDGPLQYDAAVMADVAKSKAPNSPVAGRATVFIFPDLNTG 660

Query: 661 NTTYKAVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQSAQQQ 714
           NTTYKAVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQSAQQQ
Sbjct: 661 NTTYKAVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQSAQQQ 714


Lambda     K      H
   0.316    0.131    0.363 

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: 1546
Number of extensions: 35
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: 714
Length of database: 715
Length adjustment: 39
Effective length of query: 675
Effective length of database: 676
Effective search space:   456300
Effective search space used:   456300
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: 55 (25.8 bits)

Align candidate WP_012967509.1 KVAR_RS06905 (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.971008.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     7e-142  458.3   0.1   1.2e-141  457.6   0.1    1.4  1  NCBI__GCF_000025465.1:WP_012967509.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000025465.1:WP_012967509.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  457.6   0.1  1.2e-141  1.2e-141       1     304 []     407     707 ..     407     707 .. 0.98

  Alignments for each domain:
  == domain 1  score: 457.6 bits;  conditional E-value: 1.2e-141
                             TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevkn.kakevnlklgkvvvedpdvskdiekyverlyekr 72 
                                           +vlPEg+e+r++kAaa++ae++ia++vll+n +e++++ +a++v+l +g  +v++ +v   +e+yv rl+e+r
  NCBI__GCF_000025465.1:WP_012967509.1 407 VVLPEGDEPRTVKAAAICAERGIATCVLLGNPDEINRVaAAQGVELGAGIEIVDP-EVV--RESYVARLVELR 476
                                           69************************************78999999998766655.555..5*********** PP

                             TIGR00651  73 khkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeev 145
                                           k kG+te+ areql+D+v+l++l++e++e+dglvsGav+tta+t+rp+lq+ikt++g++lvssvf+m ++e+v
  NCBI__GCF_000025465.1:WP_012967509.1 477 KSKGMTEAVAREQLEDNVVLGTLMLEQDEVDGLVSGAVHTTANTIRPPLQLIKTAPGSSLVSSVFFMLLPEQV 549
                                           ************************************************************************* PP

                             TIGR00651 146 lvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdlll 218
                                           +v++DCa+++dP+ae+LAeiA+qsa+sa ++g +ep+va+lsyst++sg+g++vekv+eA+++++ek+pdl++
  NCBI__GCF_000025465.1:WP_012967509.1 550 YVYGDCAINPDPTAEQLAEIAIQSADSAIAFG-IEPRVAMLSYSTGTSGAGSDVEKVREATRLAQEKRPDLMI 621
                                           ********************************.**************************************** PP

                             TIGR00651 219 dGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGa 291
                                           dG+lq+DaA++++va++kap+s+vag+a+vf+FPdL++Gn++Yk+vqR+ad+ +iGP+lqG++kPvnDLsRGa
  NCBI__GCF_000025465.1:WP_012967509.1 622 DGPLQYDAAVMADVAKSKAPNSPVAGRATVFIFPDLNTGNTTYKAVQRSADLISIGPMLQGMRKPVNDLSRGA 694
                                           ************************************************************************* PP

                             TIGR00651 292 svedivnvviita 304
                                           +v+div+++++ta
  NCBI__GCF_000025465.1:WP_012967509.1 695 LVDDIVYTIALTA 707
                                           ***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (715 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 37.92
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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