GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA in Magnetospirillum magneticum AMB-1

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_011384888.1 AMB_RS12610 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA

Query= reanno::HerbieS:HSERO_RS00905
         (1230 letters)



>NCBI__GCF_000009985.1:WP_011384888.1
          Length = 1039

 Score =  926 bits (2394), Expect = 0.0
 Identities = 534/1028 (51%), Positives = 668/1028 (64%), Gaps = 41/1028 (3%)

Query: 21   LPTPSPLRAAITAAYRRDEREAVQWLLQQVQEEQPWKDATQQLARKLVQQVREKRTRSSG 80
            LP P P R AI  A    E + V  L   +  E   +      A  LV   R  R R+ G
Sbjct: 7    LPAPDPERQAIHRAAGTSEADLVSGLSAGIPLEDEARRRIVNRAVNLVDGARRNR-RTLG 65

Query: 81   VDALMHEFSLSSEEGVALMCLAEALLRIPDRQTADRLIADKISKGDWRKHLGESPSLFVN 140
            +D L++E+ LS+ EGV LMCLAEALLRIPD  T D LI DKI+  DW  HLG SPS+FVN
Sbjct: 66   LDGLLNEYRLSTREGVVLMCLAEALLRIPDDHTVDLLIKDKIASADWDGHLGHSPSVFVN 125

Query: 141  AATWGLLITGKLVSTSSESGLTQAITRLIGKGGEPLIRKGVDLAMRMLGNQFVTGQTIEE 200
            A+TW L++  +L+    +      + R+ G+ GE ++R+ +  AM ++G QFV G+TI E
Sbjct: 126  ASTWALVLGDRLLHLEEDG--RAVLGRMAGRLGEAVVRRALRHAMGLMGRQFVLGRTIAE 183

Query: 201  ALDNSRENEKRGYRYSYDMLGEAALTMHDADAYYQSYESAIHAIGRASNGRGIKDGPGIS 260
            ALDN+R  E RGYR+S+DMLGEAA     A  Y ++Y  AI A+GR + G G   GPG+S
Sbjct: 184  ALDNARAWEARGYRHSFDMLGEAARCEQAAQDYLRAYAGAIEALGRHAKGAGPIAGPGLS 243

Query: 261  VKLSALHPRYSRAQHARVMSELLPRLKQLLLLAKQYDIGLNIDAEEADRLELSLDMMEVL 320
            VKLSALHPR+  AQ  RV+ EL+PRL+ L   A+   IGL IDAEEADRL++SLD+ME  
Sbjct: 244  VKLSALHPRFEMAQRQRVLGELVPRLRDLCHRARDAGIGLTIDAEEADRLDISLDVMEAA 303

Query: 321  VADPDLAGFDGLGFVVQGYQKRCPFVIDYLVDLARRNGRRLMIRLVKGAYWDSEIKRAQV 380
            +ADP L G+DG G  VQ YQKR   VI +   LA R  +RLMIRLVKGAYWD E+KRAQ 
Sbjct: 304  LADPALDGWDGFGMAVQAYQKRARPVIAWAGALAARRQQRLMIRLVKGAYWDGEVKRAQE 363

Query: 381  DGLEGYPVYTRKVHTDLSYLTCAQKLLAATDVIYPQFATHNAHTLAAIYHWARQHQIDNY 440
             GL G+PV+T K  TD+SYL CA  LLA  D+ YPQFATHNAHT AA+          ++
Sbjct: 364  RGLGGFPVFTTKEATDVSYLACAADLLARPDLFYPQFATHNAHTAAAVMEMT--GGAGDW 421

Query: 441  EFQCLHGMGETLYDQVVGPDNLGKACRVYAPVGSHQTLLAYLVRRLLENGANSSFVNQIV 500
            EFQ LHGMGE LY Q+V P+     CR YAPVGSHQ LL YLVRRLLENGANSSFV+++ 
Sbjct: 422  EFQRLHGMGEALYAQLV-PE---FPCRTYAPVGSHQELLPYLVRRLLENGANSSFVSRLA 477

Query: 501  DEAVPLDRLVGDPIETVRAQGGLPHPAIAVPHRLYGEERKNSAGIDLSNEDRLQQLGQLF 560
            DE +P   +  DP+    A G +    +A P  L+G  R+NS G+DLS+   L QL    
Sbjct: 478  DEEIPAHVVAADPL---AALGRITPQLVAEPSALFGPSRRNSGGLDLSSPAVLAQLDLAL 534

Query: 561  ISMADRQWQAAPLLAADTAAQSAQAAQLVRNPADLREVVGQVSEATVADVDTALRAATDY 620
             ++A  + ++AP++  D   +  QAA+ V +PAD R VVG+V +A+ ADV+ AL +A   
Sbjct: 535  AAVATPE-RSAPIV--DGRERENQAAKPVLDPADHRRVVGEVVDASPADVEAALASARAA 591

Query: 621  APQWQSTPATERAAMLERAADLLEEHIAELMALAVREAGKSLPNAIAEVREAVDFLRYYA 680
             P W       RA++LERAAD LE   A  MALA+REAGK++P+A++EVREAVDFLR+YA
Sbjct: 592  FPAWDDLGGEARASILERAADRLEADRARFMALAIREAGKTIPDALSEVREAVDFLRFYA 651

Query: 681  --IASRHDGNVLAWGPV--------------VCISPWNFPLAIFIGEVSAALAAGNVVLA 724
                +R    V   GPV               CISPWNFPLAIF+G+V+AALAAGN V+A
Sbjct: 652  AEARARFSQPVRLPGPVGESNELMLGGRGVFACISPWNFPLAIFVGQVAAALAAGNAVVA 711

Query: 725  KPAEQTALIAHRAVQLLHEAGIPRAALQLLPGRGETVGAALTSDVRVKGVIFTGSTEVAQ 784
            KPA QT L+A  AV+LLH+AG+P  AL L+PG G  +G ALT +  V  + FTGST  A+
Sbjct: 712  KPAPQTPLMAAAAVRLLHQAGVPPQALHLVPG-GPAIGEALTVNPLVDAIAFTGSTATAR 770

Query: 785  LINRTLAQRQHDDGDGSGEHGEVPLIAETGGQNALIVDSSALAEQVVQDVLSSAFDSAGQ 844
             INR  A     DG         PLIAETGG NA+IVDSSAL EQVV D L SAF SAGQ
Sbjct: 771  HINRLRAAM---DGP------LAPLIAETGGLNAMIVDSSALPEQVVADCLESAFRSAGQ 821

Query: 845  RCSALRILCLQEDIADRTLAMLKGAMAELRVGRPDRLSIDIGPVIDAEARQNLLDHIERM 904
            RCSALR+  +Q +   R   +L GAMAEL +G P  LS D+GPVID  +R+ LL H  R+
Sbjct: 822  RCSALRVAFIQREAWTRIQPLLAGAMAELSLGDPALLSTDVGPVIDEASRRRLLAHGGRL 881

Query: 905  RASARAVHQLPLGEECQHGTFVAPTVIEIDDLAQLQREVFGPVLHVLRYRRDALPQLIDA 964
            R + R + Q     +C+ GTF AP   ++D+L  LQ EVFGP+LHV+ +    L Q++D 
Sbjct: 882  RHAGRMIGQSACPPDCRVGTFFAPMAHQLDNLDLLQSEVFGPILHVIPWEAGRLEQVLDC 941

Query: 965  INATGYGLTLGVHSRIDETIEFVAQRAHVGNIYVNRNIVGAVVGVQPFGGEGKSGTGPKA 1024
            + AT YGLTLG+HSRID TI  V  RA +GNIYVNR ++GAVVG QPFGG G SGTG KA
Sbjct: 942  VAATSYGLTLGIHSRIDATIAQVIARARIGNIYVNRTMIGAVVGSQPFGGLGLSGTGAKA 1001

Query: 1025 GGPLYLKR 1032
            GGP  L R
Sbjct: 1002 GGPNTLIR 1009



 Score = 38.9 bits (89), Expect = 2e-06
 Identities = 63/234 (26%), Positives = 86/234 (36%), Gaps = 51/234 (21%)

Query: 999  NRNIVGAVVGVQPFGGEGKSGTGPKA-------GGPLYLKRLQRNAQLHEE--------L 1043
            +R +VG VV   P   E    +   A       GG      L+R A   E          
Sbjct: 566  HRRVVGEVVDASPADVEAALASARAAFPAWDDLGGEARASILERAADRLEADRARFMALA 625

Query: 1044 TRAQPADVPNALLD--SLLDWARTHGHERLAANGQRYHRDSLLQRSLVLPGPTGERNTLG 1101
             R     +P+AL +    +D+ R +  E  A   Q             LPGP GE N L 
Sbjct: 626  IREAGKTIPDALSEVREAVDFLRFYAAEARARFSQPVR----------LPGPVGESNELM 675

Query: 1102 FAPRGLVLCAAG---SVGTLLNQLAAAFATGN---------TALVDERSAAIL-PSGLP- 1147
               RG+  C +     +   + Q+AAA A GN         T L+   +  +L  +G+P 
Sbjct: 676  LGGRGVFACISPWNFPLAIFVGQVAAALAAGNAVVAKPAPQTPLMAAAAVRLLHQAGVPP 735

Query: 1148 -----APVRAAIRRASQLDAEPLQAALV---DSHQAAHWRARLAAREGALVPLI 1193
                  P   AI  A  L   PL  A+     +  A H     AA +G L PLI
Sbjct: 736  QALHLVPGGPAIGEA--LTVNPLVDAIAFTGSTATARHINRLRAAMDGPLAPLI 787



 Score = 27.3 bits (59), Expect = 0.007
 Identities = 13/24 (54%), Positives = 16/24 (66%)

Query: 1203 LWRLLAERALCINTTAAGGNASLM 1226
            L R   ER L +NT AAGG+ +LM
Sbjct: 1007 LIRYGVERCLSVNTAAAGGDVALM 1030


Lambda     K      H
   0.319    0.134    0.389 

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: 3106
Number of extensions: 164
Number of successful extensions: 12
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 1230
Length of database: 1039
Length adjustment: 46
Effective length of query: 1184
Effective length of database: 993
Effective search space:  1175712
Effective search space used:  1175712
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 58 (26.9 bits)

Align candidate WP_011384888.1 AMB_RS12610 (bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA)
to HMM TIGR01238 (delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88))

Software error:

../bin/blast/fastacmd -i /tmp/list.26540.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.26540.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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