GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Pseudomonas fluorescens FW300-N2E2

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate Pf6N2E2_3685 Transcriptional repressor of PutA and PutP / Proline dehydrogenase (EC 1.5.99.8) (Proline oxidase) / Delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.1.12)

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



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3685
          Length = 1317

 Score = 2463 bits (6383), Expect = 0.0
 Identities = 1248/1317 (94%), Positives = 1282/1317 (97%)

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

Query: 61   ADEGAEVHVDHAHQCFLEFAESILPQSVLRASITAAYRRPEPEVVPMLIEQARLPAPMAE 120
            +D+  +V VDHAHQCFLEFAESILPQSVLRASITAAYRRPEPEVVPMLIEQARLPA MAE
Sbjct: 61   SDDAGDVQVDHAHQCFLEFAESILPQSVLRASITAAYRRPEPEVVPMLIEQARLPAQMAE 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
            QFATHNAHTL+AIYHIAGQNYYPGQYEFQCLHGMGEPLYEQVVGKVSEGKLNRPCRVYAP
Sbjct: 481  QFATHNAHTLAAIYHIAGQNYYPGQYEFQCLHGMGEPLYEQVVGKVSEGKLNRPCRVYAP 540

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

Query: 601  PRIPLPRDLYGSERANSSGIDLANEHRLASLSCALLATAHNNWKAAPMLGCAASAETPVP 660
            PRIPLPRDLYGS+RANSSGIDLANEHRLASLSCALLATAHN+WKA PMLGCAAS ETP P
Sbjct: 601  PRIPLPRDLYGSDRANSSGIDLANEHRLASLSCALLATAHNDWKAVPMLGCAASEETPAP 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
            VGD+RVKGVMFTGSTEVARLLQRN+AGRLD QGRPIPLIAETGGQNAMIVDSSALTEQVV
Sbjct: 841  VGDERVKGVMFTGSTEVARLLQRNIAGRLDNQGRPIPLIAETGGQNAMIVDSSALTEQVV 900

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

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

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

Query: 1081 QPFGGEGLSGTGPKAGGPLYLYRLLSTRPTDAIEQSFARGDTLSAPDVRLRDAMSKPLTA 1140
            QPFGGEGLSGTGPKAGGPLYLYRLLSTRPTDAI+QSFARGD L+APD+RLRDAMSKPLTA
Sbjct: 1081 QPFGGEGLSGTGPKAGGPLYLYRLLSTRPTDAIQQSFARGDALTAPDLRLRDAMSKPLTA 1140

Query: 1141 LKTWADSHKLTELSALCAQFATQSQSGITRTLNGPTGERNSYAILPREHVLCLAEVESDL 1200
            L+ WADS KL ELSALC QFA QSQSGITRTL GPTGERNSYAILPREHVLCLA+VE DL
Sbjct: 1141 LQAWADSQKLAELSALCVQFAAQSQSGITRTLTGPTGERNSYAILPREHVLCLADVEGDL 1200

Query: 1201 LSQLAAVLAVGGSAVWPEGELSKALLARLPKDVQARIKLVADWNKDEVVFDAVLHHGHSD 1260
            L+QLAAVLAVGGSAVWPE + SKAL ARLPK++QARI+ VADW+KDEV+FDAVLHHG SD
Sbjct: 1201 LTQLAAVLAVGGSAVWPETDTSKALFARLPKEIQARIQRVADWSKDEVLFDAVLHHGDSD 1260

Query: 1261 QLRAVCQQVAKRAGAIIGVQGLSQGETNIALERLVIERALSVNTAAAGGNASLMTIG 1317
            QLR VCQQVAKR GAI+GV GLSQGET++ALERLVIERALSVNTAAAGGNASLMTIG
Sbjct: 1261 QLRGVCQQVAKRTGAIVGVHGLSQGETSVALERLVIERALSVNTAAAGGNASLMTIG 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: 4495
Number of extensions: 150
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 Pf6N2E2_3685 (Transcriptional repressor of PutA and PutP / Proline dehydrogenase (EC 1.5.99.8) (Proline oxidase) / Delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.1.12))
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.16465.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   1.8e-250  817.6   0.5   2.6e-250  817.0   0.5    1.2  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3685  Transcriptional repressor of Put


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3685  Transcriptional repressor of PutA and PutP / Proline dehydrogenase (EC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  817.0   0.5  2.6e-250  2.6e-250       1     499 [.     608    1108 ..     608    1109 .. 0.99

  Alignments for each domain:
  == domain 1  score: 817.0 bits;  conditional E-value: 2.6e-250
                                      TIGR01238    1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrk 62  
                                                     dlyg+ r ns G+dlane++l+sl+  ll++a+++++a+p++ + a +e+   pv np d++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3685  608 DLYGSDRANSSGIDLANEHRLASLSCALLATAHNDWKAVPML-GCAASEETPAPVLNPSDHR 668 
                                                     89****************************************.5566677788********* PP

                                      TIGR01238   63 divGqvseadaaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvrea 124 
                                                     d+vG+v+ea  a+v++a+++a++a+++w+at+++eraailer+adl+e ++  l++ll rea
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3685  669 DVVGHVQEATVADVDNAIQCALNAAPIWQATPPAERAAILERAADLMEGEIQPLMGLLAREA 730 
                                                     ************************************************************** PP

                                      TIGR01238  125 GktlsnaiaevreavdflryyakqvedvldeesakalGavvcispwnfplaiftGqiaaala 186 
                                                     Gkt+ naiaevreavdflryya q+++++ ++++++lG+vvcispwnfplaif Gq+aaala
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3685  731 GKTFANAIAEVREAVDFLRYYAVQARNDFTNDAHRPLGPVVCISPWNFPLAIFSGQVAAALA 792 
                                                     ************************************************************** PP

                                      TIGR01238  187 aGntviakpaeqtsliaaravellqeaGvpagviqllpGrGedvGaaltsderiaGviftGs 248 
                                                     aGn v+akpaeqt+l+aa+av l++eaG+p gv+qllpGrGe+vGa l  der++Gv+ftGs
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3685  793 AGNPVLAKPAEQTPLVAAQAVRLMLEAGIPEGVLQLLPGRGETVGARLVGDERVKGVMFTGS 854 
                                                     ************************************************************** PP

                                      TIGR01238  249 tevarlinkalakredap...vpliaetGGqnamivdstalaeqvvadvlasafdsaGqrcs 307 
                                                     tevarl+++++a r d++   +pliaetGGqnamivds+al+eqvv+dv++safdsaGqrcs
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3685  855 TEVARLLQRNIAGRLDNQgrpIPLIAETGGQNAMIVDSSALTEQVVIDVVSSAFDSAGQRCS 916 
                                                     *****************9999***************************************** PP

                                      TIGR01238  308 alrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidaeakqnllahiekmkakak 369 
                                                     alrvlc+qed adrv++++kGam e ++g+p+rl  d+Gpvidaeak  +++hi++m++k++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3685  917 ALRVLCLQEDSADRVIEMLKGAMAESRLGNPERLSVDIGPVIDAEAKAGIEKHIQAMRDKGR 978 
                                                     ************************************************************** PP

                                      TIGR01238  370 kvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkvvdkinakG 431 
                                                     +v+q+  +d+ e+++gtfv ptl+el+++del++e+fGpvlhvvryk++el +++d+ina+G
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3685  979 TVYQMAIADSDECKRGTFVMPTLIELESFDELQREIFGPVLHVVRYKRKELGQLIDQINASG 1040
                                                     ************************************************************** PP

                                      TIGR01238  432 ygltlGvhsrieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplyly 493 
                                                     ygltlGvh+ri+et++++ +++++Gnvyvnrn+vGavvGvqpfGGeGlsGtGpkaGGplyly
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3685 1041 YGLTLGVHTRIDETIAKVIDNVHAGNVYVNRNIVGAVVGVQPFGGEGLSGTGPKAGGPLYLY 1102
                                                     ************************************************************** PP

                                      TIGR01238  494 rltrvr 499 
                                                     rl+++r
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3685 1103 RLLSTR 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 0.01s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 14.55
//
[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