GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Hafnia paralvei ATCC 29927

Align phosphate acetyltransferase (EC 2.3.1.8) (characterized)
to candidate WP_020303665.1 M988_RS06645 phosphate acetyltransferase

Query= BRENDA::Q8ZND6
         (714 letters)



>NCBI__GCF_001655005.1:WP_020303665.1
          Length = 718

 Score = 1219 bits (3154), Expect = 0.0
 Identities = 618/711 (86%), Positives = 669/711 (94%)

Query: 1   MSRIIMLIPTGTSVGLTSVSLGVIRAMERKGVRLSVFKPIAQPRAGGDAPDQTTTIVRAN 60
           MSR IMLIPT TSVGLTSVSLGVIR+ME+KGVRLSVFKPIAQPR GGD+ DQTTTI+RAN
Sbjct: 1   MSRTIMLIPTSTSVGLTSVSLGVIRSMEQKGVRLSVFKPIAQPRTGGDSLDQTTTIIRAN 60

Query: 61  STLPAAEPLKMSHVESLLSSNQKDVLMEEIIANYHANTKDAEVVLVEGLVPTRKHQFAQS 120
           S++PAAEPL+MSHVE+LLSSNQ+DVLMEEI+A YH NTKDAEVVLVEGLVPTRKHQFA +
Sbjct: 61  SSIPAAEPLRMSHVETLLSSNQQDVLMEEIVARYHENTKDAEVVLVEGLVPTRKHQFANA 120

Query: 121 LNYEIAKTLNAEIVFVMSQGTDTPEQLNERIELTRSSFGGAKNTNITGVIINKLNAPVDE 180
           LNYEIAKTLNAEIVFVM+ G DT  Q+ ERIEL RSSFGG+KN NITGVIINKLNAPVD+
Sbjct: 121 LNYEIAKTLNAEIVFVMALGNDTASQVKERIELARSSFGGSKNKNITGVIINKLNAPVDD 180

Query: 181 QGRTRPDLSEIFDDSSKAQVIKIDPAKLQESSPLPVLGAVPWSFDLIATRAIDMARHLNA 240
           QGRTRPDLSEIFDDS+KA V  +D A+L  +SPLPVLG VPWSF+LIATRAIDMA HL A
Sbjct: 181 QGRTRPDLSEIFDDSNKASVANLDTAQLVANSPLPVLGCVPWSFELIATRAIDMANHLKA 240

Query: 241 TIINEGDIKTRRVKSVTFCARSIPHMLEHFRAGSLLVTSADRPDVLVAACLAAMNGVEIG 300
            I+NEGDIKTRR+KSVTFCARSIPHMLEHFR GSLLVTSADRPDVLVAACLAAMNGVEIG
Sbjct: 241 RIVNEGDIKTRRIKSVTFCARSIPHMLEHFRPGSLLVTSADRPDVLVAACLAAMNGVEIG 300

Query: 301 ALLLTGGYEMDARISKLCERAFATGLPVFMVNTNTWQTSLSLQSFNLEVPVDDHERIEKV 360
           A+LLTGGY+MD RI+KLCERAF TGLPVFMV+TNTWQTSLSLQSFNLEVP DDH+R+EK+
Sbjct: 301 AILLTGGYDMDERIAKLCERAFQTGLPVFMVDTNTWQTSLSLQSFNLEVPADDHQRVEKL 360

Query: 361 QEYVANYVNAEWIESLTATSERSRRLSPPAFRYQLTELARKAGKRVVLPEGDEPRTVKAA 420
           Q YVA++++++WI+SLTA SERSRRLSPPAFRY+LTELARKA KRVVLPEGDEPRTVKAA
Sbjct: 361 QNYVASHIDSKWIDSLTAASERSRRLSPPAFRYELTELARKACKRVVLPEGDEPRTVKAA 420

Query: 421 AICAERGIATCVLLGNPDEINRVAASQGVELGAGIEIVDPEVVRESYVARLVELRKSKGM 480
           AICAERGIA CVLLGNP+EI RVAA+QGV LG GIEIVDP VVRE YV RLVELRK+KGM
Sbjct: 421 AICAERGIAECVLLGNPEEIQRVAAAQGVVLGKGIEIVDPNVVREQYVPRLVELRKNKGM 480

Query: 481 TEPVAREQLEDNVVLGTLMLEQDEVDGLVSGAVHTTANTIRPPLQLIKTAPGSSLVSSVF 540
           TE VAREQLEDNVVLGTLMLEQ++VDGLVSGAVHTTANTIRPPLQLIKTAPGSSLVSSVF
Sbjct: 481 TEVVAREQLEDNVVLGTLMLEQNQVDGLVSGAVHTTANTIRPPLQLIKTAPGSSLVSSVF 540

Query: 541 FMLLPEQVYVYGDCAINPDPTAEQLAEIAIQSADSAIAFGIEPRVAMLSYSTGTSGAGSD 600
           FMLLP+QV VYGDCAINPDPTAEQL+EIAIQSADSA AFGIEPRVAM+SYSTG SGAGSD
Sbjct: 541 FMLLPDQVLVYGDCAINPDPTAEQLSEIAIQSADSAAAFGIEPRVAMISYSTGNSGAGSD 600

Query: 601 VEKVREATRLAQEKRPDLMIDGPLQYDAAVMADVAKSKAPNSPVAGRATVFIFPDLNTGN 660
           VEKVREATRLAQEKRPDL+IDGPLQYDAA+MADVAKSKAPNSPVAG+ATVFIFPDLNTGN
Sbjct: 601 VEKVREATRLAQEKRPDLIIDGPLQYDAAIMADVAKSKAPNSPVAGKATVFIFPDLNTGN 660

Query: 661 TTYKAVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQASQ 711
           TTYKAVQRSADL+SIGPMLQGMRKPVNDLSRGALVDDIVYT+ALTAIQA+Q
Sbjct: 661 TTYKAVQRSADLVSIGPMLQGMRKPVNDLSRGALVDDIVYTVALTAIQAAQ 711


Lambda     K      H
   0.316    0.131    0.364 

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: 1446
Number of extensions: 44
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: 718
Length adjustment: 40
Effective length of query: 674
Effective length of database: 678
Effective search space:   456972
Effective search space used:   456972
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_020303665.1 M988_RS06645 (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.3088462.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.6e-140  451.4   0.1   1.3e-139  450.8   0.1    1.3  1  NCBI__GCF_001655005.1:WP_020303665.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001655005.1:WP_020303665.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  450.8   0.1  1.3e-139  1.3e-139       1     304 []     406     706 ..     406     706 .. 0.97

  Alignments for each domain:
  == domain 1  score: 450.8 bits;  conditional E-value: 1.3e-139
                             TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevkn.kakevnlklgkvvvedpdvskdiekyverlyekr 72 
                                           +vlPEg+e+r++kAaa++ae++iae+vll+n ee++++ +a++v l  g ++++dp+v   +e+yv rl+e+r
  NCBI__GCF_001655005.1:WP_020303665.1 406 VVLPEGDEPRTVKAAAICAERGIAECVLLGNPEEIQRVaAAQGVVLGKG-IEIVDPNVV--REQYVPRLVELR 475
                                           69***********************************966777777665.667777777..7*********** PP

                             TIGR00651  73 khkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeev 145
                                           k+kG+te  areql+D+v+l++l++e++++dglvsGav+tta+t+rp+lq+ikt++g++lvssvf+m ++++v
  NCBI__GCF_001655005.1:WP_020303665.1 476 KNKGMTEVVAREQLEDNVVLGTLMLEQNQVDGLVSGAVHTTANTIRPPLQLIKTAPGSSLVSSVFFMLLPDQV 548
                                           ************************************************************************* PP

                             TIGR00651 146 lvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdlll 218
                                           lv++DCa+++dP+ae+L eiA+qsa+sa ++g +ep+va++syst+ sg+g++vekv+eA+++++ek+pdl +
  NCBI__GCF_001655005.1:WP_020303665.1 549 LVYGDCAINPDPTAEQLSEIAIQSADSAAAFG-IEPRVAMISYSTGNSGAGSDVEKVREATRLAQEKRPDLII 620
                                           ********************************.**************************************** PP

                             TIGR00651 219 dGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGa 291
                                           dG+lq+DaA++++va++kap+s+vagka+vf+FPdL++Gn++Yk+vqR+ad+ +iGP+lqG++kPvnDLsRGa
  NCBI__GCF_001655005.1:WP_020303665.1 621 DGPLQYDAAIMADVAKSKAPNSPVAGKATVFIFPDLNTGNTTYKAVQRSADLVSIGPMLQGMRKPVNDLSRGA 693
                                           ************************************************************************* PP

                             TIGR00651 292 svedivnvviita 304
                                           +v+div++v++ta
  NCBI__GCF_001655005.1:WP_020303665.1 694 LVDDIVYTVALTA 706
                                           ***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (718 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 29.37
//
[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