GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Pseudomonas simiae WCS417

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate GFF427 PS417_02175 transcriptional regulator

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



>FitnessBrowser__WCS417:GFF427
          Length = 1317

 Score = 2471 bits (6404), Expect = 0.0
 Identities = 1253/1317 (95%), Positives = 1284/1317 (97%)

Query: 1    MATTTLGVKLDDPTRERLKAAATSIDRTPHWLIKQAIFNYLEKLEGGATLTELSGLTRSE 60
            MATTTLGVKLDDPTRERLKAAATSIDRTPHWLIKQAIFNYLEKLEGGATLTEL+GL+  +
Sbjct: 1    MATTTLGVKLDDPTRERLKAAATSIDRTPHWLIKQAIFNYLEKLEGGATLTELNGLSSKD 60

Query: 61   ADEGAEVHVDHAHQCFLEFAESILPQSVLRASITAAYRRPEPEVVPMLIEQARLPAPMAE 120
            AD+  EV  DHAHQCFLEFAESILPQSVLRASITAAYRRPEPEVVPMLIEQARLP PMAE
Sbjct: 61   ADDAGEVQTDHAHQCFLEFAESILPQSVLRASITAAYRRPEPEVVPMLIEQARLPTPMAE 120

Query: 121  ATNKLAASIAEKLRNQKSAGGRAGIVQGLLQEFSLSSQEGVALMCLAEALLRIPDKGTRD 180
            ATNKLAASIAEKLRNQKSAGGRAGIVQGLLQEFSLSSQEGVALMCLAEALLRIPDKGTRD
Sbjct: 121  ATNKLAASIAEKLRNQKSAGGRAGIVQGLLQEFSLSSQEGVALMCLAEALLRIPDKGTRD 180

Query: 181  ALIRDKISTGNWQPHLGNSPSLFVNAATWGLLLTGKLVATHNEAGLTSSLSRIIGKSGEP 240
            ALIRDKISTGNWQPHLGNSPSLFVNAATWGLLLTGKLVATHNEAGLTSSLSRIIGKSGEP
Sbjct: 181  ALIRDKISTGNWQPHLGNSPSLFVNAATWGLLLTGKLVATHNEAGLTSSLSRIIGKSGEP 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
            QFATHNAHTLSAIYHIAGQNYYPGQYEFQCLHGMGEPLYEQVVGKVS+GKLNRPCRVYAP
Sbjct: 481  QFATHNAHTLSAIYHIAGQNYYPGQYEFQCLHGMGEPLYEQVVGKVSDGKLNRPCRVYAP 540

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

Query: 601  PRIPLPRDLYGSERANSSGIDLANEHRLASLSCALLATAHNNWKAAPMLGCAASAETPVP 660
            PRIPLPRDLYGS+RANS+GIDLANEHRLASLSCALLATAHNNWKAAPMLGCA+S +   P
Sbjct: 601  PRIPLPRDLYGSDRANSAGIDLANEHRLASLSCALLATAHNNWKAAPMLGCASSEQAAAP 660

Query: 661  VLNPSDLRDVVGHVQEATVTDADNAIQCALNAAPIWQATPPAERAAILERAADLMESEIQ 720
            VLNPSDLRDVVGHVQEATV D DNAIQCA++A PIWQATPPAERAAILERAADLME EIQ
Sbjct: 661  VLNPSDLRDVVGHVQEATVEDVDNAIQCAISAGPIWQATPPAERAAILERAADLMEGEIQ 720

Query: 721  PLMGLLAREAGKTFANAIAEVREAVDFLRYYAVQARNDFTNDAHRPLGPVVCISPWNFPL 780
            PLMGLLAREAGKTFANAIAEVREAVDFLRYYAVQARNDFTNDAHRPLGPVVCISPWNFPL
Sbjct: 721  PLMGLLAREAGKTFANAIAEVREAVDFLRYYAVQARNDFTNDAHRPLGPVVCISPWNFPL 780

Query: 781  AIFSGQVAAALAAGNPVLAKPAEQTPLVAAQAVRILLEAGIPEGVLQLLPGRGETVGARL 840
            AIFSGQVAAALAAGNPVLAKPAEQTPLVAAQAVRILLEAGIPEGVLQLLPG+GETVGARL
Sbjct: 781  AIFSGQVAAALAAGNPVLAKPAEQTPLVAAQAVRILLEAGIPEGVLQLLPGQGETVGARL 840

Query: 841  VGDDRVKGVMFTGSTEVARLLQRNVAGRLDAQGRPIPLIAETGGQNAMIVDSSALTEQVV 900
            VGDDRVKGVMFTGSTEVARLLQRNVAGRLDAQGRPIPLIAETGGQNAMIVDSSALTEQVV
Sbjct: 841  VGDDRVKGVMFTGSTEVARLLQRNVAGRLDAQGRPIPLIAETGGQNAMIVDSSALTEQVV 900

Query: 901  IDVVSSAFDSAGQRCSALRVLCLQEDSADRVIEMLKGAMAECRLGNPERLSVDIGPVIDA 960
            IDVVSSAFDSAGQRCSALRVLCLQEDSADRVIEMLKGAMAECRLGNPERLSVDIGPVIDA
Sbjct: 901  IDVVSSAFDSAGQRCSALRVLCLQEDSADRVIEMLKGAMAECRLGNPERLSVDIGPVIDA 960

Query: 961  EAKAGIEKHIQAMRDKGRNVYQVAIADMEECKRGTFVMPTLIELESFDELQREIFGPVLH 1020
            EAKAGIEKHIQAMRDKGRNVYQVAIAD EE KRGTFVMPTLIEL+SFDELQREIFGPVLH
Sbjct: 961  EAKAGIEKHIQAMRDKGRNVYQVAIADGEEIKRGTFVMPTLIELDSFDELQREIFGPVLH 1020

Query: 1021 VVRYKRKDIDQLIGQINASGYGLTLGVHTRIDETIAKVIDNVNAGNVYVNRNIVGAVVGV 1080
            VVRYKRK+IDQLIGQINASGYGLTLGVHTRIDETIAKVIDNVNAGNVYVNRNIVGAVVGV
Sbjct: 1021 VVRYKRKEIDQLIGQINASGYGLTLGVHTRIDETIAKVIDNVNAGNVYVNRNIVGAVVGV 1080

Query: 1081 QPFGGEGLSGTGPKAGGPLYLYRLLSTRPTDAIEQSFARGDTLSAPDVRLRDAMSKPLTA 1140
            QPFGGEGLSGTGPKAGGPLYLYRLLSTRPTDAIEQSF RGD L+APDVRLRDAMS+PLTA
Sbjct: 1081 QPFGGEGLSGTGPKAGGPLYLYRLLSTRPTDAIEQSFVRGDALAAPDVRLRDAMSQPLTA 1140

Query: 1141 LKTWADSHKLTELSALCAQFATQSQSGITRTLNGPTGERNSYAILPREHVLCLAEVESDL 1200
            LKTWAD +K ++LSALC+QFA QSQSGITR L GPTGERNSYAILPREHVLCLA+VE DL
Sbjct: 1141 LKTWADGNKFSDLSALCSQFAAQSQSGITRQLAGPTGERNSYAILPREHVLCLADVEGDL 1200

Query: 1201 LSQLAAVLAVGGSAVWPEGELSKALLARLPKDVQARIKLVADWNKDEVVFDAVLHHGHSD 1260
            L+QLAAVLAVGGSAVWPE +L+KAL  RLPK++QA+IK VADW KDEVVFDAVLHHG SD
Sbjct: 1201 LTQLAAVLAVGGSAVWPETDLTKALFPRLPKEIQAKIKRVADWTKDEVVFDAVLHHGDSD 1260

Query: 1261 QLRAVCQQVAKRAGAIIGVQGLSQGETNIALERLVIERALSVNTAAAGGNASLMTIG 1317
            QLRAVCQQVA+R GAI+GVQGLSQGET +ALERLVIERALSVNTAAAGGNASLMTIG
Sbjct: 1261 QLRAVCQQVAQRGGAIVGVQGLSQGETAVALERLVIERALSVNTAAAGGNASLMTIG 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: 4529
Number of extensions: 147
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 GFF427 PS417_02175 (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.17166.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   7.9e-248  808.8   1.4   1.2e-247  808.2   1.4    1.3  1  lcl|FitnessBrowser__WCS417:GFF427  PS417_02175 transcriptional regu


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF427  PS417_02175 transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  808.2   1.4  1.2e-247  1.2e-247       1     499 [.     608    1108 ..     608    1109 .. 0.99

  Alignments for each domain:
  == domain 1  score: 808.2 bits;  conditional E-value: 1.2e-247
                          TIGR01238    1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvseadaa 74  
                                         dlyg+ r ns+G+dlane++l+sl+  ll++a+++++aap++ + a +e+ a pv np d +d+vG+v+ea  +
  lcl|FitnessBrowser__WCS417:GFF427  608 DLYGSDRANSAGIDLANEHRLASLSCALLATAHNNWKAAPML-GCASSEQAAAPVLNPSDLRDVVGHVQEATVE 680 
                                         89****************************************.77889999*********************** PP

                          TIGR01238   75 evqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdflryyakq 148 
                                         +v++a+++a++a ++w+at+++eraailer+adl+e ++  l++ll reaGkt+ naiaevreavdflryya q
  lcl|FitnessBrowser__WCS417:GFF427  681 DVDNAIQCAISAGPIWQATPPAERAAILERAADLMEGEIQPLMGLLAREAGKTFANAIAEVREAVDFLRYYAVQ 754 
                                         ************************************************************************** PP

                          TIGR01238  149 vedvldeesakalGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaaravellqeaGvpagviql 222 
                                         +++++ ++++++lG+vvcispwnfplaif Gq+aaalaaGn v+akpaeqt+l+aa+av +l+eaG+p gv+ql
  lcl|FitnessBrowser__WCS417:GFF427  755 ARNDFTNDAHRPLGPVVCISPWNFPLAIFSGQVAAALAAGNPVLAKPAEQTPLVAAQAVRILLEAGIPEGVLQL 828 
                                         ************************************************************************** PP

                          TIGR01238  223 lpGrGedvGaaltsderiaGviftGstevarlinkalakredap...vpliaetGGqnamivdstalaeqvvad 293 
                                         lpG+Ge+vGa l  d+r++Gv+ftGstevarl+++++a r da+   +pliaetGGqnamivds+al+eqvv+d
  lcl|FitnessBrowser__WCS417:GFF427  829 LPGQGETVGARLVGDDRVKGVMFTGSTEVARLLQRNVAGRLDAQgrpIPLIAETGGQNAMIVDSSALTEQVVID 902 
                                         ******************************************99988*************************** PP

                          TIGR01238  294 vlasafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidaeakqnllahiekmkak 367 
                                         v++safdsaGqrcsalrvlc+qed adrv++++kGam e+++g+p+rl  d+Gpvidaeak  +++hi++m++k
  lcl|FitnessBrowser__WCS417:GFF427  903 VVSSAFDSAGQRCSALRVLCLQEDSADRVIEMLKGAMAECRLGNPERLSVDIGPVIDAEAKAGIEKHIQAMRDK 976 
                                         ************************************************************************** PP

                          TIGR01238  368 akkvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkvvdkinakGygltlGvhsr 441 
                                         +++v+qv  +d  e+++gtfv ptl+eld++del++e+fGpvlhvvryk++e+d+++ +ina+GygltlGvh+r
  lcl|FitnessBrowser__WCS417:GFF427  977 GRNVYQVAIADGEEIKRGTFVMPTLIELDSFDELQREIFGPVLHVVRYKRKEIDQLIGQINASGYGLTLGVHTR 1050
                                         ************************************************************************** PP

                          TIGR01238  442 ieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrltrvr 499 
                                         i+et++++ +++++Gnvyvnrn+vGavvGvqpfGGeGlsGtGpkaGGplylyrl+++r
  lcl|FitnessBrowser__WCS417:GFF427 1051 IDETIAKVIDNVNAGNVYVNRNIVGAVVGVQPFGGEGLSGTGPKAGGPLYLYRLLSTR 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: 0.03u 0.02s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 14.76
//
[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