GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Psychromonas ossibalaenae JAMM 0738

Align phosphate acetyltransferase (EC 2.3.1.8) (characterized)
to candidate WP_033298495.1 G327_RS0116360 phosphate acetyltransferase

Query= BRENDA::P0A9M8
         (714 letters)



>NCBI__GCF_000381745.1:WP_033298495.1
          Length = 715

 Score =  956 bits (2472), Expect = 0.0
 Identities = 473/709 (66%), Positives = 582/709 (82%), Gaps = 1/709 (0%)

Query: 6   MLIPTGTSVGLTSVSLGVIRAMERKGVRLSVFKPIAQPRTGGDAPDQTTTIVRANSSTTT 65
           MLIP G+ VG+TSVSLG++RAMER+GV ++ FKPIAQPR G   P+++TT +R N S+ T
Sbjct: 1   MLIPIGSGVGVTSVSLGMVRAMERQGVAVNFFKPIAQPRPGDTGPERSTTTLR-NGSSLT 59

Query: 66  AAEPLKMSYVEGLLSSNQKDVLMEEIVANYHANTKDAEVVLVEGLVPTRKHQFAQSLNYE 125
             EP  M Y E L+SS +   L+E IV  +   TK+++V++VEGLVPT KHQFA  +NY 
Sbjct: 60  PPEPFSMKYAENLISSGRTSDLLENIVERFREGTKESDVIIVEGLVPTDKHQFANEINYS 119

Query: 126 IAKTLNAEIVFVMSQGTDTPEQLKERIELTRNSFGGAKNTNITGVIVNKLNAPVDEQGRT 185
           IAK L+AE+VFV     D+ +QLKER+E+  +SFGG KN  I G I+NK+ APVDE  ++
Sbjct: 120 IAKALSAEMVFVTHPSNDSSQQLKERMEIAVSSFGGKKNKRIAGCIINKVGAPVDENDKS 179

Query: 186 RPDLSEIFDDSSKAKVNNVDPAKLQESSPLPVLGAVPWSFDLIATRAIDMARHLNATIIN 245
           RPDL+E+FD       NN++  ++   SPLP+LG +PWS +LIA R  D+A HL A ++N
Sbjct: 180 RPDLTEMFDIPDGVVNNNLEVLQMFSKSPLPILGCIPWSAELIAPRVKDLATHLEAQVLN 239

Query: 246 EGDINTRRVKSVTFCARSIPHMLEHFRAGSLLVTSADRPDVLVAACLAAMNGVEIGALLL 305
            GD++ RR+ SVTFCARSIP+M+EHF+AGS+LVTS DR DV++AACLA MNG++IG LLL
Sbjct: 240 VGDLDNRRLHSVTFCARSIPNMVEHFKAGSMLVTSGDRSDVIIAACLAVMNGMKIGCLLL 299

Query: 306 TGGYEMDARISKLCERAFATGLPVFMVNTNTWQTSLSLQSFNLEVPVDDHERIEKVQEYV 365
           TG Y  +  + KLC RA  +GLP+ ++ +NTWQT+  LQ FN+E+PVDD ERIEKVQEY+
Sbjct: 300 TGDYPPEEEVMKLCSRAMESGLPILLIKSNTWQTAQRLQHFNMEIPVDDIERIEKVQEYI 359

Query: 366 ANYINADWIESLTATSERSRRLSPPAFRYQLTELARKAGKRIVLPEGDEPRTVKAAAICA 425
           A++I+  W+ +LT  S  +RRLSPPAFRY LTELARK  +RIVLPEG+EPRT++AA ICA
Sbjct: 360 ASHIDKHWLNTLTEDSSLTRRLSPPAFRYHLTELARKTSQRIVLPEGEEPRTIQAALICA 419

Query: 426 ERGIATCVLLGNPAEINRVAASQGVELGAGIEIVDPEVVRESYVGRLVELRKNKGMTETV 485
           +RGIA  VLLGNP EI+R+A  QG+EL   +EI++P  V E+YV  +VELRK KG+TE V
Sbjct: 420 QRGIAKPVLLGNPEEIHRIATQQGIELTDDVEIINPFDVLENYVAPMVELRKAKGLTEVV 479

Query: 486 AREQLEDNVVLGTLMLEQDEVDGLVSGAVHTTANTIRPPLQLIKTAPGSSLVSSVFFMLL 545
           AREQL+D VVLGT+ML ++EV GLVSGAVHTTANTIRPPLQL+KTAP +SLVSS+FFMLL
Sbjct: 480 AREQLQDTVVLGTMMLAENEVAGLVSGAVHTTANTIRPPLQLVKTAPDASLVSSIFFMLL 539

Query: 546 PEQVYVYGDCAINPDPTAEQLAEIAIQSADSAAAFGIEPRVAMLSYSTGTSGAGSDVEKV 605
           P+QV VYGDCAINPDPTAEQLA+IAIQSADSA AFGI+P+VAM+SYSTGTSGAGSDVEKV
Sbjct: 540 PDQVLVYGDCAINPDPTAEQLADIAIQSADSAIAFGIDPKVAMISYSTGTSGAGSDVEKV 599

Query: 606 REATRLAQEKRPDLMIDGPLQYDAAVMADVAKSKAPNSPVAGRATVFIFPDLNTGNTTYK 665
           REAT++AQ++RPDL+IDGPLQYDAAVM +VA+SKAPNSPVAG+ATVFIFPDLNTGNTTYK
Sbjct: 600 REATKIAQDRRPDLLIDGPLQYDAAVMENVAQSKAPNSPVAGKATVFIFPDLNTGNTTYK 659

Query: 666 AVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQSAQQQ 714
           AVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQ+ Q +
Sbjct: 660 AVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQATQAE 708


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: 1303
Number of extensions: 44
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: 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_033298495.1 G327_RS0116360 (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.2227328.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.5e-134  433.5   0.6   4.2e-134  432.7   0.1    1.6  2  NCBI__GCF_000381745.1:WP_033298495.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000381745.1:WP_033298495.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.16      0.16      26      72 ..     322     366 ..     306     376 .. 0.64
   2 !  432.7   0.1  4.2e-134  4.2e-134       1     304 []     401     701 ..     401     701 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.16
                             TIGR00651  26 kvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverlyekr 72 
                                           ++ll+++++ ++  a+++++   ++ v+d +  +++++y+   ++k+
  NCBI__GCF_000381745.1:WP_033298495.1 322 PILLIKSNTWQT--AQRLQHFNMEIPVDDIERIEKVQEYIASHIDKH 366
                                           456666665555..566666666677777777777788887777665 PP

  == domain 2  score: 432.7 bits;  conditional E-value: 4.2e-134
                             TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevkn.kakevnlklgkvvvedpdvskdiekyverlyekr 72 
                                           ivlPEg+e+r+++Aa ++a+++ia++vll+n ee+++  + ++++l+    ++++ dv    e+yv  ++e+r
  NCBI__GCF_000381745.1:WP_033298495.1 401 IVLPEGEEPRTIQAALICAQRGIAKPVLLGNPEEIHRIaTQQGIELTDDVEIINPFDVL---ENYVAPMVELR 470
                                           8************************************9778899998888888888888...*********** PP

                             TIGR00651  73 khkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeev 145
                                           k+kG+te  areql+D+v+l++++++ +e+ glvsGav+tta+t+rp+lq++kt++  +lvss+f+m ++++v
  NCBI__GCF_000381745.1:WP_033298495.1 471 KAKGLTEVVAREQLQDTVVLGTMMLAENEVAGLVSGAVHTTANTIRPPLQLVKTAPDASLVSSIFFMLLPDQV 543
                                           ************************************************************************* PP

                             TIGR00651 146 lvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdlll 218
                                           lv++DCa+++dP+ae+LA+iA+qsa+sa ++g ++pkva++syst++sg+g++vekv+eA+ki+++++pdll+
  NCBI__GCF_000381745.1:WP_033298495.1 544 LVYGDCAINPDPTAEQLADIAIQSADSAIAFG-IDPKVAMISYSTGTSGAGSDVEKVREATKIAQDRRPDLLI 615
                                           ********************************.**************************************** PP

                             TIGR00651 219 dGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGa 291
                                           dG+lq+DaA++e+va++kap+s+vagka+vf+FPdL++Gn++Yk+vqR+ad+ +iGP+lqG++kPvnDLsRGa
  NCBI__GCF_000381745.1:WP_033298495.1 616 DGPLQYDAAVMENVAQSKAPNSPVAGKATVFIFPDLNTGNTTYKAVQRSADLISIGPMLQGMRKPVNDLSRGA 688
                                           ************************************************************************* PP

                             TIGR00651 292 svedivnvviita 304
                                           +v+div+++++ta
  NCBI__GCF_000381745.1:WP_033298495.1 689 LVDDIVYTIALTA 701
                                           ***********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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 36.78
//
[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