Alignments for a candidate for pta in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for pta in Shewanella loihica PV-4

Align phosphate acetyltransferase (EC 2.3.1.8) (characterized)
to candidate 5209946 Shew_2394 phosphate acetyltransferase (RefSeq)

Query= BRENDA::P0A9M8
         (714 letters)



>FitnessBrowser__PV4:5209946
          Length = 712

 Score =  966 bits (2496), Expect = 0.0
 Identities = 479/712 (67%), Positives = 590/712 (82%), Gaps = 1/712 (0%)

Query: 1   MSRIIMLIPTGTSVGLTSVSLGVIRAMERKGVRLSVFKPIAQPRTGGDAPDQTTTIVRAN 60
           MSR IMLIP GT VGLTS+SLG++RA+ER GV++  FKPIAQ R     P+++TTI+ + 
Sbjct: 1   MSRNIMLIPNGTGVGLTSISLGMVRALERHGVKVRFFKPIAQQRPTDKGPERSTTIL-SK 59

Query: 61  SSTTTAAEPLKMSYVEGLLSSNQKDVLMEEIVANYHANTKDAEVVLVEGLVPTRKHQFAQ 120
           S T    EP  M++ E L+ ++Q DVLME+I+A        +E ++VEGLV TR H F+ 
Sbjct: 60  SPTVNPLEPFDMAHAEHLIRTDQTDVLMEQIIARATECADPSETLIVEGLVQTRNHPFSD 119

Query: 121 SLNYEIAKTLNAEIVFVMSQGTDTPEQLKERIELTRNSFGGAKNTNITGVIVNKLNAPVD 180
            +NYEIAK L+A+I+FV + G +TP  L  R+E+  N++GG+KN  + G I+NK+ APVD
Sbjct: 120 DINYEIAKALDADIIFVAAPGNETPTALMNRLEIAHNAWGGSKNKRLIGAIINKIGAPVD 179

Query: 181 EQGRTRPDLSEIFDDSSKAKVNNVDPAKLQESSPLPVLGAVPWSFDLIATRAIDMARHLN 240
           ++GR RPDLSE+FD     + +     +L   S L +LG+VP++ +L+A RA D+A+HL+
Sbjct: 180 DEGRARPDLSEVFDHQDVQRPDAASMFQLPGKSKLRILGSVPYNLNLVAPRASDLAKHLS 239

Query: 241 ATIINEGDINTRRVKSVTFCARSIPHMLEHFRAGSLLVTSADRPDVLVAACLAAMNGVEI 300
           A IIN G++NTRR++ VTFCARSIP+M+ H +  SLLVTS DR DV+V+ACLAAMNGV++
Sbjct: 240 ARIINAGEMNTRRLRKVTFCARSIPNMVTHIKTDSLLVTSGDRSDVIVSACLAAMNGVKV 299

Query: 301 GALLLTGGYEMDARISKLCERAFATGLPVFMVNTNTWQTSLSLQSFNLEVPVDDHERIEK 360
           GALLLTG YE +  I  LCE+AF TGLPVF+++TNTWQTSL++Q F+ EVPVDD  RIE+
Sbjct: 300 GALLLTGSYEPEPEIMALCEQAFETGLPVFLIDTNTWQTSLNIQRFDHEVPVDDAVRIEE 359

Query: 361 VQEYVANYINADWIESLTATSERSRRLSPPAFRYQLTELARKAGKRIVLPEGDEPRTVKA 420
           VQEYVA++I+  W+ES+T  S R  RLSPPAFRY+LTELAR A K +VLPEGDEPRT++A
Sbjct: 360 VQEYVASHIDQSWVESVTMNSPREHRLSPPAFRYKLTELARAAAKTVVLPEGDEPRTIEA 419

Query: 421 AAICAERGIATCVLLGNPAEINRVAASQGVELGAGIEIVDPEVVRESYVGRLVELRKNKG 480
           AAICAERGIA CVL+GNP EI R+A+ QGV LG G+EI++PE  RE YV  +VELR++KG
Sbjct: 420 AAICAERGIARCVLIGNPEEIQRIASQQGVTLGEGVEIIEPETARERYVAPMVELRRHKG 479

Query: 481 MTETVAREQLEDNVVLGTLMLEQDEVDGLVSGAVHTTANTIRPPLQLIKTAPGSSLVSSV 540
           MTE VAREQLEDN+VLGT+ML Q EVDG+VSGAV+TTANTIRPPLQLIKTAPGSSLVSS+
Sbjct: 480 MTEVVAREQLEDNMVLGTMMLAQGEVDGIVSGAVNTTANTIRPPLQLIKTAPGSSLVSSI 539

Query: 541 FFMLLPEQVYVYGDCAINPDPTAEQLAEIAIQSADSAAAFGIEPRVAMLSYSTGTSGAGS 600
           FFML+P+QV VYGDCAINPDP AEQLA+IAIQSADSAAAFGIEP+VAM+SYSTG+SG GS
Sbjct: 540 FFMLMPDQVLVYGDCAINPDPNAEQLADIAIQSADSAAAFGIEPKVAMISYSTGSSGTGS 599

Query: 601 DVEKVREATRLAQEKRPDLMIDGPLQYDAAVMADVAKSKAPNSPVAGRATVFIFPDLNTG 660
           DV+KVREATR+A+EKRP+L+IDGPLQYDAAVM +VA+SKAPNSPVAG+ATVF+FPDLNTG
Sbjct: 600 DVDKVREATRIAKEKRPELVIDGPLQYDAAVMPNVAQSKAPNSPVAGQATVFVFPDLNTG 659

Query: 661 NTTYKAVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQSAQ 712
           NTTYKAVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQ++Q
Sbjct: 660 NTTYKAVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQASQ 711


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: 1362
Number of extensions: 41
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: 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 5209946 Shew_2394 (phosphate acetyltransferase (RefSeq))
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.15467.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   5.4e-139  448.8   0.1   8.8e-139  448.1   0.1    1.3  1  lcl|FitnessBrowser__PV4:5209946  Shew_2394 phosphate acetyltransf


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5209946  Shew_2394 phosphate acetyltransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  448.1   0.1  8.8e-139  8.8e-139       1     304 []     406     706 ..     406     706 .. 0.97

  Alignments for each domain:
  == domain 1  score: 448.1 bits;  conditional E-value: 8.8e-139
                        TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevkn.kakevnlklgkvvvedpdvskdiekyverlyekrkhkGv 77 
                                      +vlPEg+e+r+++Aaa++ae++ia++vl++n ee+++  + ++v l  + v++++p++   +e+yv  ++e+r+hkG+
  lcl|FitnessBrowser__PV4:5209946 406 VVLPEGDEPRTIEAAAICAERGIARCVLIGNPEEIQRIaSQQGVTLG-EGVEIIEPETA--RERYVAPMVELRRHKGM 480
                                      69***********************************7334444444.45778888888..8**************** PP

                        TIGR00651  78 tekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeevlvfaDCavav 155
                                      te  areql+D+++l+++++++ge+dg+vsGav+tta+t+rp+lq+ikt++g++lvss+f+m  +++vlv++DCa+++
  lcl|FitnessBrowser__PV4:5209946 481 TEVVAREQLEDNMVLGTMMLAQGEVDGIVSGAVNTTANTIRPPLQLIKTAPGSSLVSSIFFMLMPDQVLVYGDCAINP 558
                                      ****************************************************************************** PP

                        TIGR00651 156 dPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdllldGelqfDaAlvekva 233
                                      dPnae+LA+iA+qsa+sa ++g +epkva++syst++sg g++v+kv+eA++i+kek+p+l++dG+lq+DaA++++va
  lcl|FitnessBrowser__PV4:5209946 559 DPNAEQLADIAIQSADSAAAFG-IEPKVAMISYSTGSSGTGSDVDKVREATRIAKEKRPELVIDGPLQYDAAVMPNVA 635
                                      **********************.******************************************************* PP

                        TIGR00651 234 ekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGasvedivnvviita 304
                                      ++kap+s+vag+a+vfvFPdL++Gn++Yk+vqR+ad+ +iGP+lqG++kPvnDLsRGa+v+div+++++ta
  lcl|FitnessBrowser__PV4:5209946 636 QSKAPNSPVAGQATVFVFPDLNTGNTTYKAVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTA 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: 00:00:00.01
# Mc/sec: 19.83
//
[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