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

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.30203.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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 21.95
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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 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