GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Frischella perrara PEB0191

Align phosphate acetyltransferase (EC 2.3.1.8) (characterized)
to candidate WP_039104752.1 FPB0191_RS06180 phosphate acetyltransferase

Query= BRENDA::Q8ZND6
         (714 letters)



>NCBI__GCF_000807275.1:WP_039104752.1
          Length = 712

 Score = 1042 bits (2694), Expect = 0.0
 Identities = 519/713 (72%), Positives = 615/713 (86%), Gaps = 2/713 (0%)

Query: 1   MSRIIMLIPTGTSVGLTSVSLGVIRAMERKGVRLSVFKPIAQPRAGGDAPDQTTTIVRAN 60
           M+R IMLIPT ++VGLT VSLGVIR+MER+GV++S+FKP+AQP  GGD PDQTTT++++N
Sbjct: 1   MARTIMLIPTSSNVGLTGVSLGVIRSMERQGVKISLFKPVAQPALGGDRPDQTTTLIQSN 60

Query: 61  STLPAAEPLKMSHVESLLSSNQKDVLMEEIIANYHANTKDAEVVLVEGLVPTRKHQFAQS 120
           +++P+ +PLKMSHVE L+  NQ+DVLMEEIIA +  N K +EVVLVEG+VPT  + FA  
Sbjct: 61  TSIPSNKPLKMSHVEKLIGLNQQDVLMEEIIALFAENNKQSEVVLVEGIVPTNNYPFASE 120

Query: 121 LNYEIAKTLNAEIVFVMSQGTDTPEQLNERIELTRSSFGGAKNTNITGVIINKLNAPVDE 180
           LNY IAKTL AEI+FVMS G+DTPEQL ER+E+ RS+FGG KN  ITGVIINK+NAP+D 
Sbjct: 121 LNYNIAKTLGAEIIFVMSMGSDTPEQLKERVEIARSNFGGVKNEKITGVIINKVNAPIDA 180

Query: 181 QGRTRPDLSEIFDDSSKAQVIKIDPAKLQESSPLPVLGAVPWSFDLIATRAIDMARHLNA 240
           Q   RPD+S+I+  + K     I    L++ SPLPVLG +PW+ DL A RAIDMA HL+A
Sbjct: 181 QTLARPDVSDIYH-TPKFDGKTITIEDLRQHSPLPVLGCIPWNIDLTACRAIDMANHLSA 239

Query: 241 TIINEGDIKTRRVKSVTFCARSIPHMLEHFRAGSLLVTSADRPDVLVAACLAAMNGVEIG 300
            IINEG IK RR+K V+FC+RS+P+++ H R  +LLVTSADR D++    LA MNG EIG
Sbjct: 240 KIINEGGIKQRRIKHVSFCSRSVPNIISHLRPNALLVTSADRADIITTISLAVMNGTEIG 299

Query: 301 ALLLTGGYEMDARISKLCERAFATGLPVFMVNTNTWQTSLSLQSFNLEVPVDDHERIEKV 360
            +LLTGGYE+DA ++KLC+ AF TGLPVF V+TNT+QTS++LQ FNLE+PVDD ER++  
Sbjct: 300 GVLLTGGYELDANVAKLCKPAFETGLPVFSVDTNTFQTSINLQRFNLEIPVDDKERLDNT 359

Query: 361 QEYVANYVNAEWIESLTATSERS-RRLSPPAFRYQLTELARKAGKRVVLPEGDEPRTVKA 419
           Q +VA+++++EWI++L   S     R+SPPAFRYQLTE ARKAGK +VLPEGDEPRT+KA
Sbjct: 360 QNFVADHIDSEWIKALKNESTSGIARMSPPAFRYQLTEFARKAGKTIVLPEGDEPRTIKA 419

Query: 420 AAICAERGIATCVLLGNPDEINRVAASQGVELGAGIEIVDPEVVRESYVARLVELRKSKG 479
           A ICAERGIA CVLLGNPDEI RVAA+QGV LGAGIEI+DPE +RE+YV RLVELRK+KG
Sbjct: 420 AVICAERGIAKCVLLGNPDEIKRVAATQGVTLGAGIEIMDPEAIRENYVPRLVELRKNKG 479

Query: 480 MTEPVAREQLEDNVVLGTLMLEQDEVDGLVSGAVHTTANTIRPPLQLIKTAPGSSLVSSV 539
           MTE +AREQL DNVVLGT+MLE+DEVDGLVSGAVHTTANTIRPPLQLIKTAPGSSLVSSV
Sbjct: 480 MTEILAREQLADNVVLGTMMLERDEVDGLVSGAVHTTANTIRPPLQLIKTAPGSSLVSSV 539

Query: 540 FFMLLPEQVYVYGDCAINPDPTAEQLAEIAIQSADSAIAFGIEPRVAMLSYSTGTSGAGS 599
           FFML+PEQVY+YGDCAINPDP A++LAEIAIQSAD+AIAFGIEP+VAM+SYSTG SG G+
Sbjct: 540 FFMLMPEQVYIYGDCAINPDPNAQELAEIAIQSADTAIAFGIEPKVAMISYSTGNSGQGA 599

Query: 600 DVEKVREATRLAQEKRPDLMIDGPLQYDAAVMADVAKSKAPNSPVAGRATVFIFPDLNTG 659
           DVEKV+EATR+A+EKRPDL+IDGPLQYDAAVM DVAKSKAPNS VAG+ATVFIFPDLNTG
Sbjct: 600 DVEKVKEATRIAKEKRPDLLIDGPLQYDAAVMPDVAKSKAPNSQVAGQATVFIFPDLNTG 659

Query: 660 NTTYKAVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQASQQ 712
           NTTYKAVQRSADL+SIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQA+QQ
Sbjct: 660 NTTYKAVQRSADLVSIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQATQQ 712


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: 1355
Number of extensions: 41
Number of successful extensions: 3
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: 712
Length adjustment: 39
Effective length of query: 675
Effective length of database: 673
Effective search space:   454275
Effective search space used:   454275
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_039104752.1 FPB0191_RS06180 (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.2188355.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.7e-140  451.3   0.1   1.3e-139  450.9   0.1    1.1  1  NCBI__GCF_000807275.1:WP_039104752.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000807275.1:WP_039104752.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  450.9   0.1  1.3e-139  1.3e-139       1     304 []     406     706 ..     406     706 .. 0.97

  Alignments for each domain:
  == domain 1  score: 450.9 bits;  conditional E-value: 1.3e-139
                             TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevkn.kakevnlklgkvvvedpdvskdiekyverlyekr 72 
                                           ivlPEg+e+r++kAa ++ae++ia++vll+n +e++++ ++++v l +g  +++dp+    +e+yv rl+e+r
  NCBI__GCF_000807275.1:WP_039104752.1 406 IVLPEGDEPRTIKAAVICAERGIAKCVLLGNPDEIKRVaATQGVTLGAGI-EIMDPEAI--RENYVPRLVELR 475
                                           8************************************9667888887775.56666666..6*********** PP

                             TIGR00651  73 khkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeev 145
                                           k+kG+te  areql D+v+l+++++e +e+dglvsGav+tta+t+rp+lq+ikt++g++lvssvf+m  +e+v
  NCBI__GCF_000807275.1:WP_039104752.1 476 KNKGMTEILAREQLADNVVLGTMMLERDEVDGLVSGAVHTTANTIRPPLQLIKTAPGSSLVSSVFFMLMPEQV 548
                                           ************************************************************************* PP

                             TIGR00651 146 lvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdlll 218
                                           ++++DCa+++dPna+eLAeiA+qsa++a ++g +epkva++syst+ sg+g++vekvkeA++i+kek+pdll+
  NCBI__GCF_000807275.1:WP_039104752.1 549 YIYGDCAINPDPNAQELAEIAIQSADTAIAFG-IEPKVAMISYSTGNSGQGADVEKVKEATRIAKEKRPDLLI 620
                                           ********************************.**************************************** PP

                             TIGR00651 219 dGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGa 291
                                           dG+lq+DaA++++va++kap+s+vag+a+vf+FPdL++Gn++Yk+vqR+ad+ +iGP+lqG++kPvnDLsRGa
  NCBI__GCF_000807275.1:WP_039104752.1 621 DGPLQYDAAVMPDVAKSKAPNSQVAGQATVFIFPDLNTGNTTYKAVQRSADLVSIGPMLQGMRKPVNDLSRGA 693
                                           ************************************************************************* PP

                             TIGR00651 292 svedivnvviita 304
                                           +v+div+++++ta
  NCBI__GCF_000807275.1:WP_039104752.1 694 LVDDIVYTIALTA 706
                                           ***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (712 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: 26.03
//
[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