GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Shewanella oneidensis MR-1

Align phosphate acetyltransferase (EC 2.3.1.8) (characterized)
to candidate 202040 SO2916 phosphate acetyltransferase (NCBI ptt file)

Query= BRENDA::Q8ZND6
         (714 letters)



>FitnessBrowser__MR1:202040
          Length = 717

 Score =  956 bits (2470), Expect = 0.0
 Identities = 479/711 (67%), Positives = 584/711 (82%)

Query: 1   MSRIIMLIPTGTSVGLTSVSLGVIRAMERKGVRLSVFKPIAQPRAGGDAPDQTTTIVRAN 60
           MSR IMLIP GT VGLTS+SLG++RA+ER GV++  FKPI+Q R   + P+++TTI+  +
Sbjct: 1   MSRNIMLIPIGTGVGLTSLSLGMVRALERHGVKVQFFKPISQLRPNDNGPERSTTILSKS 60

Query: 61  STLPAAEPLKMSHVESLLSSNQKDVLMEEIIANYHANTKDAEVVLVEGLVPTRKHQFAQS 120
            T+   EP  M+H E+L+ ++Q DVLME+IIA       + E ++VEGLVPTR H FA  
Sbjct: 61  PTVNPLEPFDMAHAEALIRADQTDVLMEQIIARAAECASNTETLIVEGLVPTRNHPFADD 120

Query: 121 LNYEIAKTLNAEIVFVMSQGTDTPEQLNERIELTRSSFGGAKNTNITGVIINKLNAPVDE 180
           +NY IAK ++A+++F+ + G+DTP  L  R+E+  +S+GG  N  + G +INK+ APVD+
Sbjct: 121 VNYAIAKAMDADVIFIATPGSDTPTGLMNRLEIAYNSWGGKNNKRLIGAVINKIGAPVDD 180

Query: 181 QGRTRPDLSEIFDDSSKAQVIKIDPAKLQESSPLPVLGAVPWSFDLIATRAIDMARHLNA 240
           +GR RPDLSE+FD     +       +L   SPL +LG+VP++ DL+A RA D+A+HL A
Sbjct: 181 EGRARPDLSEVFDHQGVQRSDASIMFQLPGKSPLRILGSVPYNLDLVAPRASDLAKHLRA 240

Query: 241 TIINEGDIKTRRVKSVTFCARSIPHMLEHFRAGSLLVTSADRPDVLVAACLAAMNGVEIG 300
            I+N G++  RR++ VTFCARS+P+M+ H +  SLLVTS DR DV+V+ACLAAMNGV+IG
Sbjct: 241 RILNAGEMNIRRLRKVTFCARSLPNMVNHIKTDSLLVTSGDRSDVIVSACLAAMNGVKIG 300

Query: 301 ALLLTGGYEMDARISKLCERAFATGLPVFMVNTNTWQTSLSLQSFNLEVPVDDHERIEKV 360
           ALLLTG YE +  I KLCE+AF TGLPVF+++TNTWQTSL++Q F+ EVPVDD  RI+ V
Sbjct: 301 ALLLTGSYEPEPEILKLCEQAFETGLPVFLIDTNTWQTSLNIQRFDHEVPVDDAVRIDLV 360

Query: 361 QEYVANYVNAEWIESLTATSERSRRLSPPAFRYQLTELARKAGKRVVLPEGDEPRTVKAA 420
           QEYVA++++  WIES+T  S R  RLSPPAFRY+LTELAR A K VVLPEGDEPRT+KAA
Sbjct: 361 QEYVASHIDQTWIESVTKNSPREHRLSPPAFRYKLTELARAAHKTVVLPEGDEPRTIKAA 420

Query: 421 AICAERGIATCVLLGNPDEINRVAASQGVELGAGIEIVDPEVVRESYVARLVELRKSKGM 480
           AICAERGIA CVLLG  DEI R+AA Q V LG G+ IVDP+ VR  YV  ++ELR+SKG+
Sbjct: 421 AICAERGIARCVLLGKKDEILRIAAQQDVVLGEGVVIVDPDEVRARYVEPMLELRRSKGL 480

Query: 481 TEPVAREQLEDNVVLGTLMLEQDEVDGLVSGAVHTTANTIRPPLQLIKTAPGSSLVSSVF 540
           TE VA+EQLEDN+VLGT+ML QDEVDG+VSGAV+TTANTIRPPLQLIKTAPGSSLVSS+F
Sbjct: 481 TEVVAKEQLEDNMVLGTMMLAQDEVDGIVSGAVNTTANTIRPPLQLIKTAPGSSLVSSIF 540

Query: 541 FMLLPEQVYVYGDCAINPDPTAEQLAEIAIQSADSAIAFGIEPRVAMLSYSTGTSGAGSD 600
           FML+P+QV VYGDCAINPDP AEQLA+IAIQSA+SA AFGIEPRVAM+SYSTG SG GSD
Sbjct: 541 FMLMPDQVLVYGDCAINPDPNAEQLADIAIQSAESAKAFGIEPRVAMISYSTGNSGTGSD 600

Query: 601 VEKVREATRLAQEKRPDLMIDGPLQYDAAVMADVAKSKAPNSPVAGRATVFIFPDLNTGN 660
           V+KVREATR+A+EKRPDL+IDGPLQYDAAVM +VA+SKAPNSPVAG+ATVF+FPDLNTGN
Sbjct: 601 VDKVREATRIAKEKRPDLVIDGPLQYDAAVMPNVARSKAPNSPVAGQATVFVFPDLNTGN 660

Query: 661 TTYKAVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQASQ 711
           TTYKAVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQASQ
Sbjct: 661 TTYKAVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQASQ 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: 1393
Number of extensions: 48
Number of successful extensions: 2
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: 717
Length adjustment: 39
Effective length of query: 675
Effective length of database: 678
Effective search space:   457650
Effective search space used:   457650
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 202040 SO2916 (phosphate acetyltransferase (NCBI ptt file))
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.12951.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.3e-136  441.0   0.2   1.8e-136  440.5   0.2    1.2  1  lcl|FitnessBrowser__MR1:202040  SO2916 phosphate acetyltransfera


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:202040  SO2916 phosphate acetyltransferase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  440.5   0.2  1.8e-136  1.8e-136       1     304 []     406     706 ..     406     706 .. 0.96

  Alignments for each domain:
  == domain 1  score: 440.5 bits;  conditional E-value: 1.8e-136
                       TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevkn.kakevnlklgkvvvedpdvskdiekyverlyekrkhkGvt 78 
                                     +vlPEg+e+r++kAaa++ae++ia++vll++k+e+ +  + ++v l  g vv++dpd    + +yve + e+r+ kG+t
  lcl|FitnessBrowser__MR1:202040 406 VVLPEGDEPRTIKAAAICAERGIARCVLLGKKDEILRIaAQQDVVLGEG-VVIVDPDEV--RARYVEPMLELRRSKGLT 481
                                     69*********************************99734445555544.555566655..59**************** PP

                       TIGR00651  79 ekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeevlvfaDCavavdP 157
                                     e  a+eql+D+++l++++++++e+dg+vsGav+tta+t+rp+lq+ikt++g++lvss+f+m  +++vlv++DCa+++dP
  lcl|FitnessBrowser__MR1:202040 482 EVVAKEQLEDNMVLGTMMLAQDEVDGIVSGAVNTTANTIRPPLQLIKTAPGSSLVSSIFFMLMPDQVLVYGDCAINPDP 560
                                     ******************************************************************************* PP

                       TIGR00651 158 naeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdllldGelqfDaAlvekvaekk 236
                                     nae+LA+iA+qsa+sak++g +ep+va++syst+ sg g++v+kv+eA++i+kek+pdl++dG+lq+DaA++++va++k
  lcl|FitnessBrowser__MR1:202040 561 NAEQLADIAIQSAESAKAFG-IEPRVAMISYSTGNSGTGSDVDKVREATRIAKEKRPDLVIDGPLQYDAAVMPNVARSK 638
                                     ********************.********************************************************** PP

                       TIGR00651 237 apesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGasvedivnvviita 304
                                     ap+s+vag+a+vfvFPdL++Gn++Yk+vqR+ad+ +iGP+lqG++kPvnDLsRGa+v+div+++++ta
  lcl|FitnessBrowser__MR1:202040 639 APNSPVAGQATVFVFPDLNTGNTTYKAVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTA 706
                                     ******************************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (717 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: 00:00:00.01
# Mc/sec: 16.20
//
[ok]

This GapMind analysis is from Sep 17 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