GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysA in Desulfovibrio vulgaris Miyazaki F

Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (uncharacterized)
to candidate 8500253 DvMF_1010 diaminopimelate decarboxylase (RefSeq)

Query= curated2:O27390
         (428 letters)



>FitnessBrowser__Miya:8500253
          Length = 421

 Score =  280 bits (715), Expect = 8e-80
 Identities = 169/403 (41%), Positives = 239/403 (59%), Gaps = 17/403 (4%)

Query: 22  ELADEYGTPLYVIDEMRIRENYRRLYRAFSGEYSRFQVFYACKANTNLAVMRILEEEGSG 81
           ELA  +G+PLYV  E  +R+  R + +A S  +  F V Y+ KANTNL+++RI+ EEG  
Sbjct: 22  ELAAAFGSPLYVYSEALLRKRCRDM-KALSS-HPGFFVNYSAKANTNLSLLRIVREEGLV 79

Query: 82  IDAVSPGEIYTALMAGFDPDRILYTGNNVRDDELQFALDSGVRINVDSRSQLLRLSEIAP 141
           +DA+SPGEI+    AGF PD+ILY  NNV + EL  A+  G+ ++VDS SQL  L  +  
Sbjct: 80  VDAMSPGEIHVNKAAGFTPDQILYVCNNVSEAELANAVSHGLLVSVDSLSQLETLGRV-N 138

Query: 142 EGLRISFRVNPLVGAGHHEHCITGGEMSKFGVMEREA--PEVYRMAMDLGFEPVGIHAHI 199
            G ++  R NP +GAGHH+  +T G+ +KFGV   EA   E+  +         GI+ HI
Sbjct: 139 RGGKVMVRFNPGIGAGHHQKVVTAGKATKFGVDPSEASLAELRAILARHDMTLAGINQHI 198

Query: 200 GSGILDPEPFMLAVETLMDIAGRVHEATGVEFEFIDFGGGLGIPYTP-EEEP-LDIDEFA 257
           GS  L+PE ++ A + L+ +A +         E IDFGGG GIPY   E++P LD+   A
Sbjct: 199 GSLFLEPEGYVAAADFLLSVAEKFDTV-----EVIDFGGGFGIPYRKYEDQPRLDLAATA 253

Query: 258 SKITGLFKDKLSEYGLGRPMMCLEPGRYIVGDASYLLTRVNTIKES-YRKFAGVDAGFNT 316
            ++  L        G  +    +EPGRY+V +   LL  V+  K +   ++ G D GFN 
Sbjct: 254 ERLHALISGWSERTGY-KGRFYIEPGRYVVAECGLLLGTVHATKNNGPTRYVGTDLGFNV 312

Query: 317 LLRPAMYGSYHHILVAER--PLDEPSEKMDVAGNVCESGDLFARDRQLPEINEGDVLAIM 374
           L RP MY ++H I V       D       V GN+CESGD+ AR+RQLP I EGD+L ++
Sbjct: 313 LARPVMYDAHHDIEVYRNNGTPDAALHPQTVVGNICESGDIMARERQLPAIQEGDILGVL 372

Query: 375 NAGAYSFSMSSQYNSRPRPAEVLV-REGKVDVVRERETFSDLL 416
           +AGAY ++MSS YN R RPAEVL+  +G+  ++R RE  +DL+
Sbjct: 373 DAGAYGYAMSSTYNQRLRPAEVLIGLDGEPRLIRRREELADLM 415


Lambda     K      H
   0.320    0.140    0.408 

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: 531
Number of extensions: 25
Number of successful extensions: 8
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: 428
Length of database: 421
Length adjustment: 32
Effective length of query: 396
Effective length of database: 389
Effective search space:   154044
Effective search space used:   154044
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: 51 (24.3 bits)

Align candidate 8500253 DvMF_1010 (diaminopimelate decarboxylase (RefSeq))
to HMM TIGR01048 (lysA: diaminopimelate decarboxylase (EC 4.1.1.20))

Software error:

../bin/blast/fastacmd -i /tmp/list.16011.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.16011.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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