GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA in Pseudomonas putida KT2440

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate PP_4947 PP_4947 proline dehydrogenase/1-pyrroline-5-carboxylate dehydrogenase

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



>FitnessBrowser__Putida:PP_4947
          Length = 1317

 Score = 2313 bits (5995), Expect = 0.0
 Identities = 1165/1317 (88%), Positives = 1235/1317 (93%)

Query: 1    MATTTLGVKLDDPTRERLKAAATSIDRTPHWLIKQAIFNYLEKLEGGATLTELSGLTRSE 60
            MATTTLGVKLDDPTRERLKAAA SIDRTPHWLIKQAIFNYLEKLEGGATLTEL+G   + 
Sbjct: 1    MATTTLGVKLDDPTRERLKAAAQSIDRTPHWLIKQAIFNYLEKLEGGATLTELNGHASNP 60

Query: 61   ADEGAEVHVDHAHQCFLEFAESILPQSVLRASITAAYRRPEPEVVPMLIEQARLPAPMAE 120
            AD+  EV  DH+HQCFLEFAESILPQSVLR++ITAAYRRPE EVVPML+EQARL AP+A+
Sbjct: 61   ADDAGEVQADHSHQCFLEFAESILPQSVLRSAITAAYRRPEQEVVPMLLEQARLSAPLAD 120

Query: 121  ATNKLAASIAEKLRNQKSAGGRAGIVQGLLQEFSLSSQEGVALMCLAEALLRIPDKGTRD 180
            ATNKLAASIAEKLRNQKS GGRAGIVQGLLQEFSLSSQEGVALMCLAEALLRIPDKGTRD
Sbjct: 121  ATNKLAASIAEKLRNQKSVGGRAGIVQGLLQEFSLSSQEGVALMCLAEALLRIPDKGTRD 180

Query: 181  ALIRDKISTGNWQPHLGNSPSLFVNAATWGLLLTGKLVATHNEAGLTSSLSRIIGKSGEP 240
            ALIRDKISTGNWQPHLGNSPSLFVNAATWGLLLTGKLV+THNE GLTSSL+RIIGKSGEP
Sbjct: 181  ALIRDKISTGNWQPHLGNSPSLFVNAATWGLLLTGKLVSTHNETGLTSSLTRIIGKSGEP 240

Query: 241  MIRKGVDMAMRLMGEQFVTGETIAEALANASKFEAKGFRYSYDMLGEAALTEHDAQKYLA 300
            MIRKGVDMAMRLMGEQFVTGETIAEALANAS+FEAKGFRYSYDMLGEAALTEHDAQKYLA
Sbjct: 241  MIRKGVDMAMRLMGEQFVTGETIAEALANASRFEAKGFRYSYDMLGEAALTEHDAQKYLA 300

Query: 301  SYEQAIHSIGKASHGRGIYEGPGISIKLSALHPRYSRAQYERVMDELYPRLLSLTLLAKQ 360
            SYEQAIHSIGKASHGRGIYEGPGISIKLSALHPRYSRAQYERVM+ELYPRLLSLTLLAKQ
Sbjct: 301  SYEQAIHSIGKASHGRGIYEGPGISIKLSALHPRYSRAQYERVMEELYPRLLSLTLLAKQ 360

Query: 361  YDIGLNIDAEEADRLELSLDLLERLCFEPQLTGWNGIGFVIQAYQKRCPYVIDYVIDLAR 420
            YDIGLNIDAEEADRLELSLDLLERLCFEP L GWNGIGFVIQAYQKRCPYVIDYVIDLA+
Sbjct: 361  YDIGLNIDAEEADRLELSLDLLERLCFEPSLAGWNGIGFVIQAYQKRCPYVIDYVIDLAK 420

Query: 421  RSRHRLMIRLVKGAYWDSEIKRAQVEGLEGYPVYTRKVYTDVSYIACARKLLSVPEVIYP 480
            RSRHRLMIRLVKGAYWDSEIKRAQVEGLEGYPVYTRKVYTDVSY+ACARKLL+VPE IYP
Sbjct: 421  RSRHRLMIRLVKGAYWDSEIKRAQVEGLEGYPVYTRKVYTDVSYVACARKLLAVPEAIYP 480

Query: 481  QFATHNAHTLSAIYHIAGQNYYPGQYEFQCLHGMGEPLYEQVVGKVSEGKLNRPCRVYAP 540
            QFATHNAHTLSAIYHIAGQNYYPGQYEFQCLHGMGEPLYEQVVGK+++GKLNRPCRVYAP
Sbjct: 481  QFATHNAHTLSAIYHIAGQNYYPGQYEFQCLHGMGEPLYEQVVGKIADGKLNRPCRVYAP 540

Query: 541  VGTHETLLAYLVRRLLENGANTSFVNRIADQSISIQELVADPVSSIEQMATLEGGFGLPH 600
            VGTHETLLAYLVRRLLENGANTSFVNRIAD SISIQELVADPV+SIE+M T EG  GLPH
Sbjct: 541  VGTHETLLAYLVRRLLENGANTSFVNRIADHSISIQELVADPVASIERMGTQEGSIGLPH 600

Query: 601  PRIPLPRDLYGSERANSSGIDLANEHRLASLSCALLATAHNNWKAAPMLGCAASAETPVP 660
            PRIPLPRDLYG+ERANS+GID+ANEHRLASLSCA+LATAHN+WKAAP+L CAAS     P
Sbjct: 601  PRIPLPRDLYGTERANSAGIDMANEHRLASLSCAMLATAHNDWKAAPLLACAASESAAAP 660

Query: 661  VLNPSDLRDVVGHVQEATVTDADNAIQCALNAAPIWQATPPAERAAILERAADLMESEIQ 720
            VLNP+D RDVVGHVQEATV D DNAIQCALNAAPIWQATPPAERAAILER ADLME+EIQ
Sbjct: 661  VLNPADHRDVVGHVQEATVADVDNAIQCALNAAPIWQATPPAERAAILERTADLMEAEIQ 720

Query: 721  PLMGLLAREAGKTFANAIAEVREAVDFLRYYAVQARNDFTNDAHRPLGPVVCISPWNFPL 780
            PLMGLL REAGKTFANAIAEVREAVDFLRYYAVQARNDF+NDAHRPLGPVVCISPWNFPL
Sbjct: 721  PLMGLLIREAGKTFANAIAEVREAVDFLRYYAVQARNDFSNDAHRPLGPVVCISPWNFPL 780

Query: 781  AIFSGQVAAALAAGNPVLAKPAEQTPLVAAQAVRILLEAGIPEGVLQLLPGRGETVGARL 840
            AIF+GQVAAALAAGNPVLAKPAEQTPL+AAQAVR+LLEAGIPEGVLQLLPGRGETVGA L
Sbjct: 781  AIFTGQVAAALAAGNPVLAKPAEQTPLIAAQAVRLLLEAGIPEGVLQLLPGRGETVGAGL 840

Query: 841  VGDDRVKGVMFTGSTEVARLLQRNVAGRLDAQGRPIPLIAETGGQNAMIVDSSALTEQVV 900
            VGD+RVKGVMFTGSTEVARLLQRNVAGRLD QGRPIPLIAETGGQNAMIVDSSALTEQVV
Sbjct: 841  VGDERVKGVMFTGSTEVARLLQRNVAGRLDNQGRPIPLIAETGGQNAMIVDSSALTEQVV 900

Query: 901  IDVVSSAFDSAGQRCSALRVLCLQEDSADRVIEMLKGAMAECRLGNPERLSVDIGPVIDA 960
            IDVVSSAFDSAGQRCSALRVLCLQEDSADRVIEMLKGAMAE RLG P+RL+VDIGPVIDA
Sbjct: 901  IDVVSSAFDSAGQRCSALRVLCLQEDSADRVIEMLKGAMAESRLGCPDRLAVDIGPVIDA 960

Query: 961  EAKAGIEKHIQAMRDKGRNVYQVAIADMEECKRGTFVMPTLIELESFDELQREIFGPVLH 1020
            EAKAGIEKHIQ MR+KGR VYQVAIAD  E KRGTFVMPTLIEL+SFDEL+REIFGPVLH
Sbjct: 961  EAKAGIEKHIQGMREKGRPVYQVAIADAAEIKRGTFVMPTLIELDSFDELKREIFGPVLH 1020

Query: 1021 VVRYKRKDIDQLIGQINASGYGLTLGVHTRIDETIAKVIDNVNAGNVYVNRNIVGAVVGV 1080
            VVRY R+++DQLI QIN SGYGLTLGVHTRIDETIAKV++  NAGN+YVNRNIVGAVVGV
Sbjct: 1021 VVRYNRRNLDQLIEQINNSGYGLTLGVHTRIDETIAKVVETANAGNMYVNRNIVGAVVGV 1080

Query: 1081 QPFGGEGLSGTGPKAGGPLYLYRLLSTRPTDAIEQSFARGDTLSAPDVRLRDAMSKPLTA 1140
            QPFGGEGLSGTGPKAGGPLYLYRLLSTRP DAI + F + D    PD  L + + KPL  
Sbjct: 1081 QPFGGEGLSGTGPKAGGPLYLYRLLSTRPADAIGRHFQQQDGEGTPDRTLHEQLVKPLHG 1140

Query: 1141 LKTWADSHKLTELSALCAQFATQSQSGITRTLNGPTGERNSYAILPREHVLCLAEVESDL 1200
            LK WA++++L +L+ALC+QFA+QSQSGI R L GPTGERNSY ILPREHVLCLA+ E+DL
Sbjct: 1141 LKAWAENNQLADLAALCSQFASQSQSGIARLLPGPTGERNSYTILPREHVLCLADNETDL 1200

Query: 1201 LSQLAAVLAVGGSAVWPEGELSKALLARLPKDVQARIKLVADWNKDEVVFDAVLHHGHSD 1260
            L+Q AAVLAVG SAVW +GE  KAL ARLP+++QA++KLVADWNKDEV FDAV+HHG SD
Sbjct: 1201 LAQFAAVLAVGSSAVWVDGEPGKALRARLPRELQAKVKLVADWNKDEVAFDAVIHHGDSD 1260

Query: 1261 QLRAVCQQVAKRAGAIIGVQGLSQGETNIALERLVIERALSVNTAAAGGNASLMTIG 1317
            QLR VCQQVAKRAGAI+GV GLS G+  IALERLVIERA+SVNTAAAGGNASLMTIG
Sbjct: 1261 QLRGVCQQVAKRAGAIVGVHGLSSGDHQIALERLVIERAVSVNTAAAGGNASLMTIG 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: 4440
Number of extensions: 155
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 PP_4947 PP_4947 (proline dehydrogenase/1-pyrroline-5-carboxylate dehydrogenase)
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.27793.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   8.3e-250  815.3   1.6   1.2e-249  814.9   1.6    1.2  1  lcl|FitnessBrowser__Putida:PP_4947  PP_4947 proline dehydrogenase/1-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_4947  PP_4947 proline dehydrogenase/1-pyrroline-5-carboxylate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  814.9   1.6  1.2e-249  1.2e-249       1     499 [.     608    1108 ..     608    1109 .. 0.99

  Alignments for each domain:
  == domain 1  score: 814.9 bits;  conditional E-value: 1.2e-249
                           TIGR01238    1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvseada 73  
                                          dlyg  r ns+G+d+ane++l+sl+  +l++a+++++aap++   a +e  a pv npad++d+vG+v+ea  
  lcl|FitnessBrowser__Putida:PP_4947  608 DLYGTERANSAGIDMANEHRLASLSCAMLATAHNDWKAAPLL-ACAASESAAAPVLNPADHRDVVGHVQEATV 679 
                                          89****************************************.677889999********************* PP

                           TIGR01238   74 aevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdflryya 146 
                                          a+v++a+++a++a+++w+at+++eraailer adl+e ++  l++ll+reaGkt+ naiaevreavdflryya
  lcl|FitnessBrowser__Putida:PP_4947  680 ADVDNAIQCALNAAPIWQATPPAERAAILERTADLMEAEIQPLMGLLIREAGKTFANAIAEVREAVDFLRYYA 752 
                                          ************************************************************************* PP

                           TIGR01238  147 kqvedvldeesakalGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaaravellqeaGvpagv 219 
                                           q++++++++++++lG+vvcispwnfplaiftGq+aaalaaGn v+akpaeqt+liaa+av ll+eaG+p gv
  lcl|FitnessBrowser__Putida:PP_4947  753 VQARNDFSNDAHRPLGPVVCISPWNFPLAIFTGQVAAALAAGNPVLAKPAEQTPLIAAQAVRLLLEAGIPEGV 825 
                                          ************************************************************************* PP

                           TIGR01238  220 iqllpGrGedvGaaltsderiaGviftGstevarlinkalakredap...vpliaetGGqnamivdstalaeq 289 
                                          +qllpGrGe+vGa l  der++Gv+ftGstevarl+++++a r d++   +pliaetGGqnamivds+al+eq
  lcl|FitnessBrowser__Putida:PP_4947  826 LQLLPGRGETVGAGLVGDERVKGVMFTGSTEVARLLQRNVAGRLDNQgrpIPLIAETGGQNAMIVDSSALTEQ 898 
                                          **********************************************9999*********************** PP

                           TIGR01238  290 vvadvlasafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidaeakqnllahie 362 
                                          vv+dv++safdsaGqrcsalrvlc+qed adrv++++kGam e ++g p rl  d+Gpvidaeak  +++hi+
  lcl|FitnessBrowser__Putida:PP_4947  899 VVIDVVSSAFDSAGQRCSALRVLCLQEDSADRVIEMLKGAMAESRLGCPDRLAVDIGPVIDAEAKAGIEKHIQ 971 
                                          ************************************************************************* PP

                           TIGR01238  363 kmkakakkvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkvvdkinakGyglt 435 
                                           m++k++ v+qv  +d  e+++gtfv ptl+eld++delk+e+fGpvlhvvry++++ld+++++in++Gyglt
  lcl|FitnessBrowser__Putida:PP_4947  972 GMREKGRPVYQVAIADAAEIKRGTFVMPTLIELDSFDELKREIFGPVLHVVRYNRRNLDQLIEQINNSGYGLT 1044
                                          ************************************************************************* PP

                           TIGR01238  436 lGvhsrieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrltrvr 499 
                                          lGvh+ri+et++++ + a++Gn+yvnrn+vGavvGvqpfGGeGlsGtGpkaGGplylyrl+++r
  lcl|FitnessBrowser__Putida:PP_4947 1045 LGVHTRIDETIAKVVETANAGNMYVNRNIVGAVVGVQPFGGEGLSGTGPKAGGPLYLYRLLSTR 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: 00:00:00.03
# Mc/sec: 16.69
//
[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