GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA in Paraburkholderia bryophila 376MFSha3.1

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate H281DRAFT_02404 H281DRAFT_02404 L-proline dehydrogenase /delta-1-pyrroline-5-carboxylate dehydrogenase

Query= reanno::Cup4G11:RR42_RS20125
         (1333 letters)



>FitnessBrowser__Burk376:H281DRAFT_02404
          Length = 1312

 Score = 1759 bits (4557), Expect = 0.0
 Identities = 917/1345 (68%), Positives = 1065/1345 (79%), Gaps = 45/1345 (3%)

Query: 1    MATTTLGVKLDDASRERLKRVAQSIDRTPHWLIKQAIFTYLEQVERGNIPHETSAAGTGS 60
            MA+TTLGVK+DD  R RL+  A  ++RTPHWLIKQAIF YLE++E+G +P E S      
Sbjct: 1    MASTTLGVKVDDLLRSRLRDAATRLERTPHWLIKQAIFAYLEKIEQGQLPPELS------ 54

Query: 61   EGAADGADAFDGAA----SDGAIQPFLEFAQSVQPQSVLRAAITAAYRRPESECVPVLLE 116
             G A  AD  DGA+     DGA  PFL+FAQ+VQPQSVLRAAITAAYRRPE ECVP LL 
Sbjct: 55   -GVAGSADMADGASVEPDEDGAAHPFLDFAQNVQPQSVLRAAITAAYRRPEPECVPFLLG 113

Query: 117  QARLPHQQAEAALAMARTLATRLRERKVGTGREGLVQGLIQEFSLSSQEGVALMCLAEAL 176
            QARLP   A    A+A  L   LR +  G G    V+GLI EFSLSSQEGVALMCLAEAL
Sbjct: 114  QARLPANLAGDVQALAAKLVETLRGKSKGGG----VEGLIHEFSLSSQEGVALMCLAEAL 169

Query: 177  LRIPDKATRDALIRDKISGANWQSHLGQSPSVFVNAATWGLLFTGKLVATHTEAGLSKAL 236
            LRIPD+ATRDALIRDKIS  +W+SH+GQ+PS+FVNAATWGL+ TGKLV T++E  LS AL
Sbjct: 170  LRIPDRATRDALIRDKISKGDWKSHVGQAPSLFVNAATWGLMITGKLVTTNSETNLSSAL 229

Query: 237  TRIIGKGGEPLIRKGVDMAMRLMGEQFVTGETISEALANARKYEAEGFRYSYDMLGEAAM 296
            TR+IGKGGEPLIRKGVDMAMRLMGEQFVTGE ISEALAN+RKYEA GFRYSYDMLGEAA 
Sbjct: 230  TRLIGKGGEPLIRKGVDMAMRLMGEQFVTGENISEALANSRKYEARGFRYSYDMLGEAAT 289

Query: 297  TEADAQRYLASYEQAINAIGQASRGRGIYEGPGISIKLSALHPRYSRAQHERVIGELYGR 356
            TEADAQRY ASYEQAI+AIG+A+ GRGIYEGPGISIKLSALHPRYSR+Q ER + EL  R
Sbjct: 290  TEADAQRYYASYEQAIHAIGKAAGGRGIYEGPGISIKLSALHPRYSRSQQERTMSELLPR 349

Query: 357  LKSLTLLARQYDIGINIDAEEADRLEISLDLLERLCFEPELAGWNGIGFVVQGYQKRCPF 416
            ++SL +LAR+YDIG+NIDAEEADRLEISLDLLE LCF+PELAGWNGIGFVVQ YQKRCPF
Sbjct: 350  VRSLAILARRYDIGLNIDAEEADRLEISLDLLEALCFDPELAGWNGIGFVVQAYQKRCPF 409

Query: 417  VIDYLIDLARRSRHRLMIRLVKGAYWDSEIKRAQVDGLEGYPVYTRKVYTDVSYVACARK 476
            VI+Y++DLARRSRHR+M+RLVKGAYWD+EIKRAQVDGLEGYPVYTRK+YTDVSY+ACA+K
Sbjct: 410  VIEYIVDLARRSRHRIMVRLVKGAYWDTEIKRAQVDGLEGYPVYTRKIYTDVSYLACAKK 469

Query: 477  LLSVPDVIYPQFATHNAHTLAAIYQIAGHNYYPGQYEFQCLHGMGEPLYDQVVGPLADGK 536
            LL  PD +YPQFATHNAHTL+AIY +AG+NYYPGQYEFQCLHGMGEPLY++V GPL+ GK
Sbjct: 470  LLGAPDAVYPQFATHNAHTLSAIYHLAGNNYYPGQYEFQCLHGMGEPLYEEVTGPLSAGK 529

Query: 537  FNRPCRIYAPVGTHETLLAYLVRRLLENGANTSFVNRIADDTISLDELVADPVAVVEQMH 596
             NRPCR+YAPVGTHETLLAYLVRRLLENGANTSFVNRIAD+ +++ +L+ADPV    ++ 
Sbjct: 530  LNRPCRVYAPVGTHETLLAYLVRRLLENGANTSFVNRIADENVAIQDLIADPVEEASKI- 588

Query: 597  ADEGALGLPHPRIAQPRTLYGESRANSAGIDLSNEHRLASLSSALLAGTSEAVSAVPLLG 656
                 LG PH +I  PR LYG  R NS G+DLSNEHRLASLSSALLA  +    A P+L 
Sbjct: 589  ---VPLGAPHAKIPLPRNLYGAERLNSMGLDLSNEHRLASLSSALLASANHPWRAAPMLA 645

Query: 657  TEAAAGEDVNQPAPVRNPSDQRDVVGHVTEASMAEVEAALQAAVNAAPIWQATPADVRAA 716
             +      +     VRNP+D RD+VG V EAS   V AAL  AV AAPIWQATP + RA 
Sbjct: 646  DDQIV---LGNARDVRNPADHRDLVGTVVEASAEHVSAALAHAVAAAPIWQATPVEARAD 702

Query: 717  ALERAAELMEAQMQSLMGIIVREAGKTFSNAIAEVREAVDFLRYYAAQVRETFSSDTHRP 776
             L RAA+L+EAQM +LMG++VREAGK+ +NA++E+REA+DFLRYY+ Q+R  FS+DTHRP
Sbjct: 703  CLARAADLLEAQMHTLMGLVVREAGKSLANAVSEIREAIDFLRYYSTQIRSEFSNDTHRP 762

Query: 777  LGPVVCISPWNFPLAIFTGQVAAALAAGNTVLAKPAEQTPLIAAQAVRLLREAGVPAGAV 836
            LGPVVCISPWNFPLAIF GQVAAALAAGNTVLAKPAEQTPLIAAQAVR+LREAGVPAGAV
Sbjct: 763  LGPVVCISPWNFPLAIFMGQVAAALAAGNTVLAKPAEQTPLIAAQAVRILREAGVPAGAV 822

Query: 837  QLLPGRGETVGAALVGDARVKGVMFTGSTEVARLLQRSVAGRLDAAGRPVPLIAETGGQN 896
            QLLPG GETVGAALV D R + VMFTGSTEVARL+ ++++GRLD  G+P+PLIAETGGQN
Sbjct: 823  QLLPGDGETVGAALVADPRTRAVMFTGSTEVARLINKTLSGRLDPEGKPIPLIAETGGQN 882

Query: 897  AMIVDSSALAEQVVGDVVNSAFDSAGQRCSALRVLCLQEEVADRVLEMLKGAMDELTMGN 956
            AMIVDSSALAEQVV DV+ S+FDSAGQRCSALRVLCLQ++VADR LEML GAM ELT+GN
Sbjct: 883  AMIVDSSALAEQVVADVMQSSFDSAGQRCSALRVLCLQDDVADRTLEMLTGAMRELTVGN 942

Query: 957  PDRLSTDVGPVIDEEARGNIVRHIDAMRAKGRRVHQADPNGALSAACRNGTFVSPTLIEL 1016
            PDRLSTDVGPVID +A+  I  HI AMR KGR+V Q      +   C  GTFV PTLIEL
Sbjct: 943  PDRLSTDVGPVIDVDAKRGIDAHIAAMREKGRKVEQL----PMPEGCAQGTFVPPTLIEL 998

Query: 1017 DSIEELQREVFGPVLHVVRYPRAGLDTLLAQINGTGYGLTMGIHTRIDETIEHIVERAEV 1076
            DSI+EL+REVFGPVLHVVRY R+ LD LL QI  TGYGLT+GIHTRIDETI H++ RA V
Sbjct: 999  DSIDELKREVFGPVLHVVRYRRSQLDQLLEQIRTTGYGLTLGIHTRIDETIAHVISRAHV 1058

Query: 1077 GNLYVNRNIVGAVVGVQPFGGEGLSGTGPKAGGPLYLHRLLSVCPLDAVARVVRASDT-V 1135
            GN+YVNRN++GAVVGVQPFGGEGLSGTGPKAGG LYL RLL+  P      + +A    V
Sbjct: 1059 GNIYVNRNVIGAVVGVQPFGGEGLSGTGPKAGGALYLQRLLATRPAGLPKSLAQALIVDV 1118

Query: 1136 GGADETGPVRRTLTETLATLKEW--AQRESAALPGLVAACERFAAASAAGLSVTLPGPTG 1193
              A E G      +  L  L++W  A+RE    P L A C+ + +   AG +  L GPTG
Sbjct: 1119 PQAAEKGD---NPSAALTALRDWLIAERE----PQLAARCDGYLSHMPAGATAVLSGPTG 1171

Query: 1194 ERNTYTLLPRAAVLCLAQQETDLAVQLAAVLAAGSQAVWVESPMARALFARLPKAVQSRV 1253
            ERNTYTL  R  VLC+A   +    Q AAVLA G++A++ E      L  +LP +++S  
Sbjct: 1172 ERNTYTLGARGTVLCIASTASGARAQFAAVLATGNRALF-EGAAGEQLVTQLPASLKSYA 1230

Query: 1254 RLVADWSAGDTGFDAVLHHGDSDQLRAVCEQLATRPGPIISVQGLA-----HGEPNIAIE 1308
             +  +    +T FDAVL  GDSD+L  + +++A RPGPI+SVQG+A      G+ + A+E
Sbjct: 1231 SVRKN---AETPFDAVLFEGDSDELLTLVKEVAKRPGPIVSVQGVASRALESGDEDYALE 1287

Query: 1309 RLLIERSLSVNTAAAGGNASLMTIG 1333
            RLL ERS+SVNTAAAGGNA+LMTIG
Sbjct: 1288 RLLTERSVSVNTAAAGGNANLMTIG 1312


Lambda     K      H
   0.318    0.133    0.383 

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: 4000
Number of extensions: 153
Number of successful extensions: 10
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: 1333
Length of database: 1312
Length adjustment: 49
Effective length of query: 1284
Effective length of database: 1263
Effective search space:  1621692
Effective search space used:  1621692
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 H281DRAFT_02404 H281DRAFT_02404 (L-proline dehydrogenase /delta-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.14050.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.14050.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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