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))

Software error:

../bin/blast/fastacmd -i /tmp/list.6190.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.6190.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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