GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Pseudomonas fluorescens FW300-N2E3

Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate AO353_05065 AO353_05065 phosphate acetyltransferase

Query= SwissProt::Q9I5A5
         (704 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_05065
          Length = 699

 Score = 1072 bits (2773), Expect = 0.0
 Identities = 552/699 (78%), Positives = 614/699 (87%), Gaps = 8/699 (1%)

Query: 1   MHTFFIAPTGFGVGLTSISLGLLRALERAGLKVGFFKPIAQLHPGDLGPERSSELVARTH 60
           M TFFIAPT FGVGLTSISLGL+R LERAGLKVGFFKPIAQ HPGD GPERS+ELVARTH
Sbjct: 1   MQTFFIAPTDFGVGLTSISLGLVRTLERAGLKVGFFKPIAQPHPGDTGPERSTELVARTH 60

Query: 61  GLDTPKPLPLAQVERMLGDGQLDELLEEIISLYQRAAADKDVVIVEGMVPTRHASYAARV 120
           GL  P+PL LA VERMLGDGQLDELLEEII+LYQ+AA  KDV++VEGMVPTR ASYAARV
Sbjct: 61  GLKPPQPLGLAHVERMLGDGQLDELLEEIITLYQQAAIGKDVLVVEGMVPTRSASYAARV 120

Query: 121 NFHLAKSLDAEVILVSAPENETLTELTDRIEIQAQLFGGPRDPKVLGVILNKVRGEADAA 180
           N HLAKSLDAEVILVSAPENE LTEL+ R+E+QAQLFGGP+DPKVLGVILNKV+      
Sbjct: 121 NLHLAKSLDAEVILVSAPENEVLTELSGRVELQAQLFGGPKDPKVLGVILNKVK------ 174

Query: 181 NAEDGVADFARRLTEHSPLLRD-DFRLIGCIPWQDELNAARTRDIADLLSARVINAGDYE 239
             ++ +  FA RL EHSPLLR  DFRL+GCIP+Q ELNA RTRD+ADL+ A+V+NAGDYE
Sbjct: 175 -TDESMEAFAARLKEHSPLLRSGDFRLLGCIPFQPELNAPRTRDVADLMGAQVLNAGDYE 233

Query: 240 QRRVQKIVLCARAVPNTVQLLKPGVLVVTPGDRDDIILAASLAAMNGVPLAGLLLCSDFP 299
            RR+ KI++CAR + NTV+LLKPGVLVVTPGDRDDIILA SLAA+NGVPLAGLLL S   
Sbjct: 234 TRRMSKIIICARTMRNTVELLKPGVLVVTPGDRDDIILAVSLAAINGVPLAGLLLTSGTL 293

Query: 300 PDPRIMELCRGALQGGLPVLSVATGSYDTATNLNRMNKEIPVDDRERAERVTEFVAGHID 359
           PDPRIM+LCRGALQ GLPVLSV+TGSY+TA  LN +NKEIP+DDRERAE +T+FVA H+D
Sbjct: 294 PDPRIMDLCRGALQAGLPVLSVSTGSYETANQLNGLNKEIPIDDRERAEIITDFVASHLD 353

Query: 360 FEWLKQRCGTPRELRLSPPAFRYQVVQRAQKAGKRIVLPEGSEPRTVQAAAICQARGIAR 419
             WL QRCGTPRE+RLSP  FRYQ++QRAQ A KRIVLPEGSEP TVQAAAICQARGIAR
Sbjct: 354 ANWLHQRCGTPREMRLSPAVFRYQLIQRAQAANKRIVLPEGSEPLTVQAAAICQARGIAR 413

Query: 420 CVLLAKPEEVQAVAQAQGIVLPEGLEIIDPDLVRQRYVEPMVELRKGKGLNAPMAEQQLE 479
           CVLLAKPE+VQAVA+AQGI LPEGLEI+DPDL+RQRYVEPMV LRK K LNAPMAEQQLE
Sbjct: 414 CVLLAKPEDVQAVARAQGIELPEGLEILDPDLIRQRYVEPMVALRKTKSLNAPMAEQQLE 473

Query: 480 DSVVLATMMLALDEVDGLVSGAIHTTASTIRPALQLIKTAPGYNLVSSVFFMLLPDQVLV 539
           D+VV+ TMMLALDEVDGLVSG IH+TA+TIRPALQLIKTAPG  LVSSVFFML P++VLV
Sbjct: 474 DTVVIGTMMLALDEVDGLVSGVIHSTANTIRPALQLIKTAPGCTLVSSVFFMLFPEEVLV 533

Query: 540 YGDCAVNPDPSASDLAEIAVQSAASAQAFGIPARVAMISYSTGDSGSGVDVDKVREATRL 599
           YGDC +NP PSAS+LAEIA+QSA SA AFGI  RVAM+SYS+G+S SG +V+KVREAT L
Sbjct: 534 YGDCIMNPHPSASELAEIALQSADSAAAFGITPRVAMLSYSSGESASGEEVEKVREATLL 593

Query: 600 AREQRPDLLIDGPLQYDAAAIASVGRQKAPNSPVAGQATVFIFPDLNTGNTTYKAVQRSA 659
           A E +  LLIDGPLQYDAAA  +V RQ APNS VAG+ATVFIFPDLNTGNTT+KAVQRSA
Sbjct: 594 AHEAQNALLIDGPLQYDAAANENVARQLAPNSQVAGRATVFIFPDLNTGNTTHKAVQRSA 653

Query: 660 DCVSVGPMLQGLRKPVNDLSRGALVEDIVYTIALTAIQA 698
           DCVS+GPMLQGLRKPVNDL RGA V+DIVYTIALTAIQA
Sbjct: 654 DCVSLGPMLQGLRKPVNDLPRGAQVDDIVYTIALTAIQA 692


Lambda     K      H
   0.319    0.136    0.388 

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: 1394
Number of extensions: 52
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: 704
Length of database: 699
Length adjustment: 39
Effective length of query: 665
Effective length of database: 660
Effective search space:   438900
Effective search space used:   438900
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)

Align candidate AO353_05065 AO353_05065 (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.21289.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   1.9e-117  378.0   0.0   2.6e-117  377.6   0.0    1.2  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05065  AO353_05065 phosphate acetyltran


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_05065  AO353_05065 phosphate acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  377.6   0.0  2.6e-117  2.6e-117       1     304 []     389     689 ..     389     689 .. 0.98

  Alignments for each domain:
  == domain 1  score: 377.6 bits;  conditional E-value: 2.6e-117
                                     TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevkn.kakevnlklgkvvvedpdvskdieky 64 
                                                   ivlPEgse+ +++Aaa+++ ++ia++vll++ e+++++ +a++++l  g +++ dpd+   +++y
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05065 389 IVLPEGSEPLTVQAAAICQARGIARCVLLAKPEDVQAVaRAQGIELPEG-LEILDPDLI--RQRY 450
                                                   8************************************978999998765.788899999..89** PP

                                     TIGR00651  65 verlyekrkhkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktleg 129
                                                   ve ++ +rk+k ++  +a++ql+D+v++++++++l+e+dglvsG  ++ta+t+rpalq+ikt++g
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05065 451 VEPMVALRKTKSLNAPMAEQQLEDTVVIGTMMLALDEVDGLVSGVIHSTANTIRPALQLIKTAPG 515
                                                   ***************************************************************** PP

                                     TIGR00651 130 vklvssvfimekeeevlvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsg 194
                                                     lvssvf+m  +eevlv++DC ++++P+a eLAeiAlqsa+sa ++g + p+va+lsys++ s+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05065 516 CTLVSSVFFMLFPEEVLVYGDCIMNPHPSASELAEIALQSADSAAAFG-ITPRVAMLSYSSGESA 579
                                                   ************************************************.**************** PP

                                     TIGR00651 195 kgeevekvkeAvkilkekepdllldGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGni 259
                                                   +geevekv+eA+ +++e +  ll+dG+lq+DaA  e+va++ ap+s+vag+a+vf+FPdL++Gn+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05065 580 SGEEVEKVREATLLAHEAQNALLIDGPLQYDAAANENVARQLAPNSQVAGRATVFIFPDLNTGNT 644
                                                   ***************************************************************** PP

                                     TIGR00651 260 gYkivqRladaeaiGPilqGlakPvnDLsRGasvedivnvviita 304
                                                   + k+vqR+ad  ++GP+lqGl+kPvnDL RGa+v+div+++++ta
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05065 645 THKAVQRSADCVSLGPMLQGLRKPVNDLPRGAQVDDIVYTIALTA 689
                                                   *******************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (699 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 12.44
//
[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