GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Pseudomonas fluorescens FW300-N2C3

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate AO356_09015 AO356_09015 transcriptional regulator

Query= reanno::pseudo3_N2E3:AO353_12810
         (1317 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_09015
          Length = 1317

 Score = 2458 bits (6370), Expect = 0.0
 Identities = 1248/1317 (94%), Positives = 1278/1317 (97%)

Query: 1    MATTTLGVKLDDPTRERLKAAATSIDRTPHWLIKQAIFNYLEKLEGGATLTELSGLTRSE 60
            MATTTLGVKLDDPTRERLKAAATSIDRTPHWLIKQAIFNYLEKLEGGATLTEL+G  R++
Sbjct: 1    MATTTLGVKLDDPTRERLKAAATSIDRTPHWLIKQAIFNYLEKLEGGATLTELNGSPRAD 60

Query: 61   ADEGAEVHVDHAHQCFLEFAESILPQSVLRASITAAYRRPEPEVVPMLIEQARLPAPMAE 120
            +D+  +V VDHAHQCFLEFAESILPQSVLRASITAAYRRPEPEVVPMLIEQARLP  MAE
Sbjct: 61   SDDAGDVQVDHAHQCFLEFAESILPQSVLRASITAAYRRPEPEVVPMLIEQARLPLEMAE 120

Query: 121  ATNKLAASIAEKLRNQKSAGGRAGIVQGLLQEFSLSSQEGVALMCLAEALLRIPDKGTRD 180
            ATNKLAASIAEKLRNQKSAGGRAGIVQGLLQEFSLSSQEGVALMCLAEALLRIPDKGTRD
Sbjct: 121  ATNKLAASIAEKLRNQKSAGGRAGIVQGLLQEFSLSSQEGVALMCLAEALLRIPDKGTRD 180

Query: 181  ALIRDKISTGNWQPHLGNSPSLFVNAATWGLLLTGKLVATHNEAGLTSSLSRIIGKSGEP 240
            ALIRDKISTGNWQPHLGNSPSLFVNAATWGLLLTGKLVATHNE GLTSSLSRIIGKSGEP
Sbjct: 181  ALIRDKISTGNWQPHLGNSPSLFVNAATWGLLLTGKLVATHNETGLTSSLSRIIGKSGEP 240

Query: 241  MIRKGVDMAMRLMGEQFVTGETIAEALANASKFEAKGFRYSYDMLGEAALTEHDAQKYLA 300
            MIRKGVDMAMRLMGEQFVTGETIAEALANASKFEAKGFRYSYDMLGEAALTEHDAQKYLA
Sbjct: 241  MIRKGVDMAMRLMGEQFVTGETIAEALANASKFEAKGFRYSYDMLGEAALTEHDAQKYLA 300

Query: 301  SYEQAIHSIGKASHGRGIYEGPGISIKLSALHPRYSRAQYERVMDELYPRLLSLTLLAKQ 360
            SYEQAIHSIGKASHGRGIYEGPGISIKLSALHPRYSRAQYERVMDELYPRLLSLTLLAKQ
Sbjct: 301  SYEQAIHSIGKASHGRGIYEGPGISIKLSALHPRYSRAQYERVMDELYPRLLSLTLLAKQ 360

Query: 361  YDIGLNIDAEEADRLELSLDLLERLCFEPQLTGWNGIGFVIQAYQKRCPYVIDYVIDLAR 420
            YDIGLNIDAEEADRLELSLDLLERLCFEPQLTGWNGIGFVIQAYQKRCPYVIDYVIDLAR
Sbjct: 361  YDIGLNIDAEEADRLELSLDLLERLCFEPQLTGWNGIGFVIQAYQKRCPYVIDYVIDLAR 420

Query: 421  RSRHRLMIRLVKGAYWDSEIKRAQVEGLEGYPVYTRKVYTDVSYIACARKLLSVPEVIYP 480
            RSRHRLMIRLVKGAYWDSEIKRAQVEGLEGYPVYTRKVYTDVSYIACARKLLSVPEVIYP
Sbjct: 421  RSRHRLMIRLVKGAYWDSEIKRAQVEGLEGYPVYTRKVYTDVSYIACARKLLSVPEVIYP 480

Query: 481  QFATHNAHTLSAIYHIAGQNYYPGQYEFQCLHGMGEPLYEQVVGKVSEGKLNRPCRVYAP 540
            QFATHNAHTLSAIYHIAGQNYYPGQYEFQCLHGMGEPLYEQVVGKVSEGKLNRPCRVYAP
Sbjct: 481  QFATHNAHTLSAIYHIAGQNYYPGQYEFQCLHGMGEPLYEQVVGKVSEGKLNRPCRVYAP 540

Query: 541  VGTHETLLAYLVRRLLENGANTSFVNRIADQSISIQELVADPVSSIEQMATLEGGFGLPH 600
            VGTHETLLAYLVRRLLENGANTSFVNRIADQSISIQELVADPV+SIEQMATLEGGFGLPH
Sbjct: 541  VGTHETLLAYLVRRLLENGANTSFVNRIADQSISIQELVADPVASIEQMATLEGGFGLPH 600

Query: 601  PRIPLPRDLYGSERANSSGIDLANEHRLASLSCALLATAHNNWKAAPMLGCAASAETPVP 660
            PRIPLPRDLYGS+RANSSGIDLANEHRLASLSCALLATAHN+WKAAPMLGCAAS ETP  
Sbjct: 601  PRIPLPRDLYGSDRANSSGIDLANEHRLASLSCALLATAHNDWKAAPMLGCAASEETPAA 660

Query: 661  VLNPSDLRDVVGHVQEATVTDADNAIQCALNAAPIWQATPPAERAAILERAADLMESEIQ 720
            VLNPSD RDVVGHVQEATV D DNAIQCALNAAPIWQATPPAERAAILERAADLME EIQ
Sbjct: 661  VLNPSDHRDVVGHVQEATVADVDNAIQCALNAAPIWQATPPAERAAILERAADLMEGEIQ 720

Query: 721  PLMGLLAREAGKTFANAIAEVREAVDFLRYYAVQARNDFTNDAHRPLGPVVCISPWNFPL 780
            PLMGLLAREAGKTFANAIAEVREAVDFLRYYAVQARNDFTNDAHRPLGPVVCISPWNFPL
Sbjct: 721  PLMGLLAREAGKTFANAIAEVREAVDFLRYYAVQARNDFTNDAHRPLGPVVCISPWNFPL 780

Query: 781  AIFSGQVAAALAAGNPVLAKPAEQTPLVAAQAVRILLEAGIPEGVLQLLPGRGETVGARL 840
            AIFSGQVAAALAAGNPVLAKPAEQTPLVAAQAVR++LEAGIPEGVLQLLPGRGETVGARL
Sbjct: 781  AIFSGQVAAALAAGNPVLAKPAEQTPLVAAQAVRLMLEAGIPEGVLQLLPGRGETVGARL 840

Query: 841  VGDDRVKGVMFTGSTEVARLLQRNVAGRLDAQGRPIPLIAETGGQNAMIVDSSALTEQVV 900
            VGDDRVKGVMFTGSTEVARLLQRN+AGRLD QGRPIPLIAETGGQNAMIVDSSALTEQVV
Sbjct: 841  VGDDRVKGVMFTGSTEVARLLQRNIAGRLDNQGRPIPLIAETGGQNAMIVDSSALTEQVV 900

Query: 901  IDVVSSAFDSAGQRCSALRVLCLQEDSADRVIEMLKGAMAECRLGNPERLSVDIGPVIDA 960
            IDVVSSAFDSAGQRCSALRVLCLQEDSADRVIEMLKGAMAE RLGNPERLSVDIGPVIDA
Sbjct: 901  IDVVSSAFDSAGQRCSALRVLCLQEDSADRVIEMLKGAMAEARLGNPERLSVDIGPVIDA 960

Query: 961  EAKAGIEKHIQAMRDKGRNVYQVAIADMEECKRGTFVMPTLIELESFDELQREIFGPVLH 1020
            EAKAGIEKHIQAMRDKGR+VYQ+AIAD +ECKRGTFVMPTLIELESFDELQREIFGPVLH
Sbjct: 961  EAKAGIEKHIQAMRDKGRSVYQMAIADSDECKRGTFVMPTLIELESFDELQREIFGPVLH 1020

Query: 1021 VVRYKRKDIDQLIGQINASGYGLTLGVHTRIDETIAKVIDNVNAGNVYVNRNIVGAVVGV 1080
            VVRYKRK++ QLI QINASGYGLTLGVHTRIDETIAKVIDNV+AGNVYVNRNIVGAVVGV
Sbjct: 1021 VVRYKRKELGQLIDQINASGYGLTLGVHTRIDETIAKVIDNVHAGNVYVNRNIVGAVVGV 1080

Query: 1081 QPFGGEGLSGTGPKAGGPLYLYRLLSTRPTDAIEQSFARGDTLSAPDVRLRDAMSKPLTA 1140
            QPFGGEGLSGTGPKAGGPLYLYRLLSTRPTDAI+QSF RGD L APD+RLRDAMSKPLTA
Sbjct: 1081 QPFGGEGLSGTGPKAGGPLYLYRLLSTRPTDAIQQSFVRGDALVAPDLRLRDAMSKPLTA 1140

Query: 1141 LKTWADSHKLTELSALCAQFATQSQSGITRTLNGPTGERNSYAILPREHVLCLAEVESDL 1200
            L+ WADS KL ELSALC QFA QSQSGITR L GPTGERNSYAILPREHVLCLA+VE DL
Sbjct: 1141 LQAWADSQKLAELSALCVQFAAQSQSGITRQLTGPTGERNSYAILPREHVLCLADVEGDL 1200

Query: 1201 LSQLAAVLAVGGSAVWPEGELSKALLARLPKDVQARIKLVADWNKDEVVFDAVLHHGHSD 1260
            L+QLAAVLAVGGSAVWPE + SKAL ARLPK++QARI+ VADW KD+V+FDAVLHHG SD
Sbjct: 1201 LTQLAAVLAVGGSAVWPETDTSKALFARLPKEIQARIQRVADWTKDDVLFDAVLHHGDSD 1260

Query: 1261 QLRAVCQQVAKRAGAIIGVQGLSQGETNIALERLVIERALSVNTAAAGGNASLMTIG 1317
            QLR VCQQVAKRAGAI+GV GLSQGETNIALERLVIERALSVNTAAAGGNASLMTIG
Sbjct: 1261 QLRDVCQQVAKRAGAIVGVHGLSQGETNIALERLVIERALSVNTAAAGGNASLMTIG 1317


Lambda     K      H
   0.318    0.134    0.386 

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: 4491
Number of extensions: 151
Number of successful extensions: 1
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: 1317
Length of database: 1317
Length adjustment: 48
Effective length of query: 1269
Effective length of database: 1269
Effective search space:  1610361
Effective search space used:  1610361
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 (21.7 bits)
S2: 59 (27.3 bits)

Align candidate AO356_09015 AO356_09015 (transcriptional regulator)
to HMM TIGR01238 (delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88))

# 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/TIGR01238.hmm
# target sequence database:        /tmp/gapView.24023.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01238  [M=500]
Accession:   TIGR01238
Description: D1pyr5carbox3: delta-1-pyrroline-5-carboxylate dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
     2e-249  814.1   0.8   2.8e-249  813.6   0.8    1.2  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09015  AO356_09015 transcriptional regu


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09015  AO356_09015 transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  813.6   0.8  2.8e-249  2.8e-249       1     499 [.     608    1108 ..     608    1109 .. 0.99

  Alignments for each domain:
  == domain 1  score: 813.6 bits;  conditional E-value: 2.8e-249
                                       TIGR01238    1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadr 61  
                                                      dlyg+ r ns G+dlane++l+sl+  ll++a+++++aap++g  a +e+    v np d+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09015  608 DLYGSDRANSSGIDLANEHRLASLSCALLATAHNDWKAAPMLGC-AASEETPAAVLNPSDH 667 
                                                      89****************************************55.5555666789****** PP

                                       TIGR01238   62 kdivGqvseadaaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvr 122 
                                                      +d+vG+v+ea  a+v++a+++a++a+++w+at+++eraailer+adl+e ++  l++ll r
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09015  668 RDVVGHVQEATVADVDNAIQCALNAAPIWQATPPAERAAILERAADLMEGEIQPLMGLLAR 728 
                                                      ************************************************************* PP

                                       TIGR01238  123 eaGktlsnaiaevreavdflryyakqvedvldeesakalGavvcispwnfplaiftGqiaa 183 
                                                      eaGkt+ naiaevreavdflryya q+++++ ++++++lG+vvcispwnfplaif Gq+aa
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09015  729 EAGKTFANAIAEVREAVDFLRYYAVQARNDFTNDAHRPLGPVVCISPWNFPLAIFSGQVAA 789 
                                                      ************************************************************* PP

                                       TIGR01238  184 alaaGntviakpaeqtsliaaravellqeaGvpagviqllpGrGedvGaaltsderiaGvi 244 
                                                      alaaGn v+akpaeqt+l+aa+av l++eaG+p gv+qllpGrGe+vGa l  d+r++Gv+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09015  790 ALAAGNPVLAKPAEQTPLVAAQAVRLMLEAGIPEGVLQLLPGRGETVGARLVGDDRVKGVM 850 
                                                      ************************************************************* PP

                                       TIGR01238  245 ftGstevarlinkalakredap...vpliaetGGqnamivdstalaeqvvadvlasafdsa 302 
                                                      ftGstevarl+++++a r d++   +pliaetGGqnamivds+al+eqvv+dv++safdsa
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09015  851 FTGSTEVARLLQRNIAGRLDNQgrpIPLIAETGGQNAMIVDSSALTEQVVIDVVSSAFDSA 911 
                                                      *********************9999************************************ PP

                                       TIGR01238  303 GqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidaeakqnllahiek 363 
                                                      Gqrcsalrvlc+qed adrv++++kGam e ++g+p+rl  d+Gpvidaeak  +++hi++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09015  912 GQRCSALRVLCLQEDSADRVIEMLKGAMAEARLGNPERLSVDIGPVIDAEAKAGIEKHIQA 972 
                                                      ************************************************************* PP

                                       TIGR01238  364 mkakakkvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkvv 424 
                                                      m++k+++v+q+  +d+ e+++gtfv ptl+el+++del++e+fGpvlhvvryk++el +++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09015  973 MRDKGRSVYQMAIADSDECKRGTFVMPTLIELESFDELQREIFGPVLHVVRYKRKELGQLI 1033
                                                      ************************************************************* PP

                                       TIGR01238  425 dkinakGygltlGvhsrieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpk 485 
                                                      d+ina+GygltlGvh+ri+et++++ +++++Gnvyvnrn+vGavvGvqpfGGeGlsGtGpk
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09015 1034 DQINASGYGLTLGVHTRIDETIAKVIDNVHAGNVYVNRNIVGAVVGVQPFGGEGLSGTGPK 1094
                                                      ************************************************************* PP

                                       TIGR01238  486 aGGplylyrltrvr 499 
                                                      aGGplylyrl+++r
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09015 1095 AGGPLYLYRLLSTR 1108
                                                      **********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (500 nodes)
Target sequences:                          1  (1317 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 24.79
//
[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