RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1913
(535 letters)
>gnl|CDD|223411 COG0334, GdhA, Glutamate dehydrogenase/leucine dehydrogenase [Amino
acid transport and metabolism].
Length = 411
Score = 334 bits (860), Expect = e-110
Identities = 149/441 (33%), Positives = 218/441 (49%), Gaps = 67/441 (15%)
Query: 96 EIQF--PFRRDSGEYELIQCYRCHHCTHKSPTKGGIRYALDVNPDEVKALAALMTYKNSC 153
IQ P R D G ++ + YR H + P KGG+R+ V +EVKAL+ MT KN+
Sbjct: 34 VIQVRIPVRMDDGSVKVFRGYRVQHNSALGPYKGGVRFHPYVTLEEVKALSFWMTLKNAL 93
Query: 154 SNVPFGGAKGGIRIDPSKYNNRELERITRKFALELIKKNYVGPGIDVPAPDYNTSAREMS 213
+ +P+GG KGGI +DP ++ ELER++R F + + +GP D+PAPD T+ ++M+
Sbjct: 94 AGLPYGGGKGGIIVDPKGLSDGELERLSRAFGRAIYR--LIGPDTDIPAPDVGTNPQDMA 151
Query: 214 WFYDAYAKTLGSTNINALGMVTGKPLFLGGIRGRESATGRGVFTAAEILVNNEEYMCEIG 273
W D Y+K +G +A G+ TGKPL LGG GR ATG GVF A
Sbjct: 152 WMMDEYSKIVG---NSAPGVFTGKPLELGGSLGRSEATGYGVFYAIREA----LKALGDD 204
Query: 274 LEPCMENKTYIVQGFGNVGFHAARYFRRGRAKCLAIVEHDTAIVPDKGTEINYKDLHTYK 333
LE VQGFGNVG +AA AK +A+ + I + G ++ + L K
Sbjct: 205 LE----GARVAVQGFGNVGQYAAEKLHELGAKVVAVSDSKGGIYDEDG--LDVEALLELK 258
Query: 334 ITKGTIKGYPGTKSAPTDIMFD-KVDILVPAAIEKVIRKSNADKVQAKIIVEAANGPLTP 392
+G++ Y G + + + + DIL+P A+E VI + NAD+++AKI+VE ANGP TP
Sbjct: 259 ERRGSVAEYAGAEYITNEELLEVDCDILIPCALENVITEDNADQLKAKIVVEGANGPTTP 318
Query: 393 AAHAMLLKKNVLIIPDIFANAGGVTVSYFEWLKNISHSSLGRMSFGYDKEISDLLLSSID 452
A +LL++ +L++PDI ANAGGV VSY EW++N +
Sbjct: 319 EADEILLERGILVVPDILANAGGVIVSYLEWVQN-------AQGLYWT------------ 359
Query: 453 TSLSDTFNKKIRIQKSAMYEDRISNATEKDIVQSSLTHSMQRAGRDILEYAEKSDNKLDL 512
E+ V L M A + + A++ +DL
Sbjct: 360 -------------------EEE---------VDEKLERIMVNAFEAVYQAAKE--YGVDL 389
Query: 513 RNAAYCSALFKIFKTYEEAGL 533
R AAY A ++ + G
Sbjct: 390 RTAAYILAFERVADAMKARGW 410
>gnl|CDD|178095 PLN02477, PLN02477, glutamate dehydrogenase.
Length = 410
Score = 318 bits (816), Expect = e-104
Identities = 148/338 (43%), Positives = 202/338 (59%), Gaps = 26/338 (7%)
Query: 100 PFR---------RDSGEYELIQCYRCHHCTHKSPTKGGIRYALDVNPDEVKALAALMTYK 150
PFR +D G +R H + P KGGIRY +V+PDEV ALA LMT+K
Sbjct: 31 PFREIKVECTIPKDDGTLASFVGFRVQHDNARGPMKGGIRYHPEVDPDEVNALAQLMTWK 90
Query: 151 NSCSNVPFGGAKGGIRIDPSKYNNRELERITRKFALELIKKNYVGPGIDVPAPDYNTSAR 210
+ +N+P+GGAKGGI DP + ELER+TR F ++ + +G DVPAPD T+A+
Sbjct: 91 TAVANIPYGGAKGGIGCDPRDLSESELERLTRVFTQKI--HDLIGIHTDVPAPDMGTNAQ 148
Query: 211 EMSWFYDAYAKTLGSTNINALGMVTGKPLFLGGIRGRESATGRGVFTAAEILVNNEEYMC 270
M+W D Y+K G + +VTGKP+ LGG GRE+ATGRGV A E L+ E+
Sbjct: 149 TMAWILDEYSKFHGFSP----AVVTGKPIDLGGSLGREAATGRGVVFATEALLA--EHGK 202
Query: 271 EIGLEPCMENKTYIVQGFGNVGFHAARYFRRGRAKCLAIVEHDTAIVPDKGTEINYKDLH 330
I +T+++QGFGNVG AA+ K +A+ + A+ + G +I L
Sbjct: 203 SI------AGQTFVIQGFGNVGSWAAQLIHEKGGKIVAVSDITGAVKNENGLDIP--ALR 254
Query: 331 TYKITKGTIKGYPGTKSA-PTDIMFDKVDILVPAAIEKVIRKSNADKVQAKIIVEAANGP 389
+ G +KG+PG P DI+ + D+L+PAA+ VI K NA V+AK IVEAAN P
Sbjct: 255 KHVAEGGGLKGFPGGDPIDPDDILVEPCDVLIPAALGGVINKENAADVKAKFIVEAANHP 314
Query: 390 LTPAAHAMLLKKNVLIIPDIFANAGGVTVSYFEWLKNI 427
P A +L KK V+++PDI+AN+GGVTVSYFEW++NI
Sbjct: 315 TDPEADEILRKKGVVVLPDIYANSGGVTVSYFEWVQNI 352
>gnl|CDD|133445 cd01076, NAD_bind_1_Glu_DH, NAD(P) binding domain of glutamate
dehydrogenase, subgroup 1. Amino acid dehydrogenase
(DH) is a widely distributed family of enzymes that
catalyzes the oxidative deamination of an amino acid to
its keto acid and ammonia with concomitant reduction of
NADP+. Glutamate DH is a multidomain enzyme that
catalyzes the reaction from glutamate to 2-oxyoglutarate
and ammonia in the presence of NAD or NADP. It is
present in all organisms. Enzymes involved in ammonia
assimilation are typically NADP+-dependent, while those
involved in glutamate catabolism are generally
NAD+-dependent. Amino acid DH-like NAD(P)-binding
domains are members of the Rossmann fold superfamily and
include glutamate, leucine, and phenylalanine DHs,
methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase, Shikimate
DH-like proteins, malate oxidoreductases, and glutamyl
tRNA reductase. Amino acid DHs catalyze the deamination
of amino acids to keto acids with NAD(P)+ as a cofactor.
The NAD(P)-binding Rossmann fold superfamily includes a
wide variety of protein families including NAD(P)-
binding domains of alcohol DHs, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate DH,
lactate/malate DHs, formate/glycerate DHs, siroheme
synthases, 6-phosphogluconate DH, amino acid DHs,
repressor rex, NAD-binding potassium channel domain,
CoA-binding, and ornithine cyclodeaminase-like domains.
These domains have an alpha -beta-alpha configuration.
NAD binding involves numerous hydrogen and van der Waals
contacts.
Length = 227
Score = 246 bits (631), Expect = 6e-79
Identities = 104/286 (36%), Positives = 139/286 (48%), Gaps = 60/286 (20%)
Query: 242 GGIRGRESATGRGVFTAAEILVNNEEYMCEIGLEPCMENKTYIVQGFGNVGFHAARYFRR 301
GG GRE ATGRGV A + IGL +QGFGNVG HAAR+
Sbjct: 1 GGSLGREEATGRGVAYATREALKK----LGIGLA----GARVAIQGFGNVGSHAARFLHE 52
Query: 302 GRAKCLAIVEHDTAIVPDKGTEINYKDLHTYKITKGTIKGYPG-TKSAPTDIMFDKVDIL 360
AK +A+ + D I G ++ L YK G++ G+PG + +++ DIL
Sbjct: 53 AGAKVVAVSDSDGTIYNPDG--LDVPALLAYKKEHGSVLGFPGAERITNEELLELDCDIL 110
Query: 361 VPAAIEKVIRKSNADKVQAKIIVEAANGPLTPAAHAMLLKKNVLIIPDIFANAGGVTVSY 420
+PAA+E I NAD+++AKIIVEAANGP TP A +L ++ VL++PDI ANAGGVTVSY
Sbjct: 111 IPAALENQITADNADRIKAKIIVEAANGPTTPEADEILHERGVLVVPDILANAGGVTVSY 170
Query: 421 FEWLKNISHSSLGRMSFGYDKEISDLLLSSIDTSLSDTFNKKIRIQKSAMYEDRISNATE 480
FEW++N+ Y D
Sbjct: 171 FEWVQNLQG----------------------------------------FYWDE------ 184
Query: 481 KDIVQSSLTHSMQRAGRDILEYAEKSDNKLDLRNAAYCSALFKIFK 526
+ V S L M+ A +LE AEK +DLR AAY AL ++ +
Sbjct: 185 -EEVNSRLETKMREAFEAVLETAEKYG--VDLRTAAYVLALERVAE 227
>gnl|CDD|202408 pfam02812, ELFV_dehydrog_N, Glu/Leu/Phe/Val dehydrogenase,
dimerisation domain.
Length = 131
Score = 174 bits (445), Expect = 9e-53
Identities = 61/127 (48%), Positives = 79/127 (62%), Gaps = 2/127 (1%)
Query: 95 LEIQFPFRRDSGEYELIQCYRCHHCTHKSPTKGGIRYALDVNPDEVKALAALMTYKNSCS 154
++++ P R D GE E ++ YR H T P KGGIR+ V +EVK LA MTYKN+ +
Sbjct: 5 IQVRVPVRMDDGEVEGLRGYRVQHNTALGPAKGGIRFHPYVTLEEVKRLAFGMTYKNALA 64
Query: 155 NVPFGGAKGGIRIDPSKYNNRELERITRKFALELIKKNYVGPGIDVPAPDYNTSAREMSW 214
+PFGG KGGI DP ++ ELER+TR F EL +GPG D+PAPD T REM+W
Sbjct: 65 GLPFGGGKGGIIGDPKGLSDAELERLTRAFGRELES--IIGPGRDIPAPDVGTGPREMAW 122
Query: 215 FYDAYAK 221
D Y +
Sbjct: 123 IADEYRR 129
>gnl|CDD|215789 pfam00208, ELFV_dehydrog, Glutamate/Leucine/Phenylalanine/Valine
dehydrogenase.
Length = 237
Score = 171 bits (437), Expect = 4e-50
Identities = 72/194 (37%), Positives = 101/194 (52%), Gaps = 13/194 (6%)
Query: 242 GGIRGRESATGRGVFTAAEILVNNEEYMCEIGLEPCMENKTYIVQGFGNVGFHAARYFRR 301
GG GR ATG GV E E + ++G + +E KT VQGFGNVG +AA
Sbjct: 1 GGSLGRPEATGYGVVYFVE------EALKKLGGDS-LEGKTVAVQGFGNVGSYAAEKLLE 53
Query: 302 GRAKCLAIVEHDTAIVPDKGTEINY-KDLHTYKITKGTIKGYPGTKS---APTDIMFDKV 357
AK +A+ + I G +I +L + G + Y G+ + + ++
Sbjct: 54 LGAKVVAVSDSSGYIYDPNGIDIEELLEL--KEEGGGRVVEYAGSGAEYISGEELWEIDC 111
Query: 358 DILVPAAIEKVIRKSNADKVQAKIIVEAANGPLTPAAHAMLLKKNVLIIPDIFANAGGVT 417
DILVP A + I + NA ++AK +VE AN P TP A +L ++ +L PD ANAGGVT
Sbjct: 112 DILVPCATQNEINEENAKLIKAKAVVEGANMPTTPEADEILEERGILYAPDKAANAGGVT 171
Query: 418 VSYFEWLKNISHSS 431
VSY E ++N S S
Sbjct: 172 VSYLEMVQNSSRLS 185
>gnl|CDD|185433 PTZ00079, PTZ00079, NADP-specific glutamate dehydrogenase;
Provisional.
Length = 454
Score = 137 bits (348), Expect = 2e-35
Identities = 110/357 (30%), Positives = 158/357 (44%), Gaps = 36/357 (10%)
Query: 91 YSSLLE--------IQF--PFRRDSGEYELIQCYRCHHCTHKSPTKGGIRYALDVNPDEV 140
Y +LE IQF P+ D GE + + +R + + P KGG+R+ VN +
Sbjct: 52 YLGVLERLVEPERVIQFRVPWVDDKGEQRVNRGFRVQYNSALGPYKGGLRFHPSVNLSIL 111
Query: 141 KALAALMTYKNSCSNVPFGGAKGGIRIDPSKYNNRELERITRKFALELIKKNYVGPGIDV 200
K L +KNS + +P GG KGG DP ++ E+ R + F EL + ++GP DV
Sbjct: 112 KFLGFEQIFKNSLTTLPMGGGKGGSDFDPKGKSDNEVMRFCQSFMTELYR--HIGPDTDV 169
Query: 201 PAPDYNTSAREMSWFYDAYAKTLGSTNINALGMVTGKPLFLGGIRGRESATGRG-VFTAA 259
PA D RE+ + + Y K + G +TGK + GG R ATG G V+
Sbjct: 170 PAGDIGVGGREIGYLFGQYKKLRNNFE----GTLTGKNVKWGGSNIRPEATGYGLVYFVL 225
Query: 260 EILVNNEEYMCEIGLEPCMENKTYIVQGFGNVGFHAARYFRRGRAKCLAIVEHDTAIVPD 319
E+L + +E KT +V G GNV +A + AK L + + D I
Sbjct: 226 EVLKKLND---------SLEGKTVVVSGSGNVAQYAVEKLLQLGAKVLTMSDSDGYIHEP 276
Query: 320 KG-TEINYKDLHTYKITK-GTIKGY----PGTKSAPTDIMFD-KVDILVPAAIEKVIRKS 372
G T+ L K K G +K Y K P ++ DI P A + I
Sbjct: 277 NGFTKEKLAYLMDLKNVKRGRLKEYAKHSSTAKYVPGKKPWEVPCDIAFPCATQNEINLE 336
Query: 373 NADKVQA---KIIVEAANGPLTPAAHAMLLKKNVLIIPDIFANAGGVTVSYFEWLKN 426
+A + K++ E AN P T A + K V+ P ANAGGV +S E +N
Sbjct: 337 DAKLLIKNGCKLVAEGANMPTTIEATHLFKKNGVIFCPGKAANAGGVAISGLEMSQN 393
>gnl|CDD|184463 PRK14030, PRK14030, glutamate dehydrogenase; Provisional.
Length = 445
Score = 135 bits (341), Expect = 1e-34
Identities = 111/362 (30%), Positives = 160/362 (44%), Gaps = 26/362 (7%)
Query: 81 RNGIIMLMQNYSSLLEIQFPFRRDSGEYELIQCYRCHHCTHKSPTKGGIRYALDVNPDEV 140
+ II + + + P+ D GE ++ YR P KGGIR+ VN +
Sbjct: 43 KAKIIERIVEPDRIFTFRVPWVDDKGEVQVNLGYRVQFNNAIGPYKGGIRFHPSVNLSIL 102
Query: 141 KALAALMTYKNSCSNVPFGGAKGGIRIDPSKYNNRELERITRKFALELIKKNYVGPGIDV 200
K L T+KN+ + +P GG KGG P ++ E+ R + F LEL + ++GP DV
Sbjct: 103 KFLGFEQTFKNALTTLPMGGGKGGSDFSPRGKSDAEIMRFCQAFMLELWR--HIGPDTDV 160
Query: 201 PAPDYNTSAREMSWFYDAYAKTLGSTNINALGMVTGKPLFLGGIRGRESATGRGVFTAAE 260
PA D RE+ + + Y K L G +TGK L GG R ATG G A
Sbjct: 161 PAGDIGVGGREVGYMFGMY-KKLTREFT---GTLTGKGLEFGGSLIRPEATGFG----AL 212
Query: 261 ILVNNEEYMCE-IGLEPCMENKTYIVQGFGNVGFHAARYFRRGRAKCLAIVEHDTAI-VP 318
V+ M E G++ ++ KT + GFGNV + AA AK + I D I P
Sbjct: 213 YFVHQ---MLETKGID--IKGKTVAISGFGNVAWGAATKATELGAKVVTISGPDGYIYDP 267
Query: 319 D--KGTEINYK-DLHTY--KITKGTIKGYPGTKSAPTDIMFD-KVDILVPAAIEKVIRKS 372
D G +I+Y +L I + +PG+ ++ KVDI +P A + +
Sbjct: 268 DGISGEKIDYMLELRASGNDIVAPYAEKFPGSTFFAGKKPWEQKVDIALPCATQNELNGE 327
Query: 373 NADKVQA---KIIVEAANGPLTPAAHAMLLKKNVLIIPDIFANAGGVTVSYFEWLKNISH 429
+ADK+ + E +N T A + L P NAGGV S E +N H
Sbjct: 328 DADKLIKNGVLCVAEVSNMGCTAEAIDKFIAAKQLFAPGKAVNAGGVATSGLEMSQNAMH 387
Query: 430 SS 431
S
Sbjct: 388 LS 389
>gnl|CDD|133450 cd05211, NAD_bind_Glu_Leu_Phe_Val, NAD(P) binding domain of
glutamate dehydrogenase, leucine dehydrogenase,
phenylalanine dehydrogenase, and valine dehydrogenase.
Amino acid dehydrogenase (DH) is a widely distributed
family of enzymes that catalyzes the oxidative
deamination of an amino acid to its keto acid and
ammonia with concomitant reduction of NAD(P)+. This
subfamily includes glutamate, leucine, phenylalanine,
and valine DHs. Glutamate DH is a multi-domain enzyme
that catalyzes the reaction from glutamate to
2-oxyoglutarate and ammonia in the presence of NAD or
NADP. It is present in all organisms. Enzymes involved
in ammonia assimilation are typically NADP+-dependent,
while those involved in glutamate catabolism are
generally NAD+-dependent. As in other NAD+-dependent
DHs, monomers in this family have 2 domains separated by
a deep cleft. Here the c-terminal domain contains a
modified NAD-binding Rossmann fold with 7 rather than
the usual 6 beta strands and one strand anti-parrallel
to the others. Amino acid DH-like NAD(P)-binding domains
are members of the Rossmann fold superfamily and include
glutamate, leucine, and phenylalanine DHs, methylene
tetrahydrofolate DH, methylene-tetrahydromethanopterin
DH, methylene-tetrahydropholate DH/cyclohydrolase,
Shikimate DH-like proteins, malate oxidoreductases, and
glutamyl tRNA reductase. Amino acid DHs catalyze the
deamination of amino acids to keto acids with NAD(P)+ as
a cofactor. The NAD(P)-binding Rossmann fold superfamily
includes a wide variety of protein families including
NAD(P)- binding domains of alcohol DHs,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DH, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 217
Score = 124 bits (312), Expect = 1e-32
Identities = 64/182 (35%), Positives = 87/182 (47%), Gaps = 16/182 (8%)
Query: 250 ATGRGVFTAAEILVNNEEYMCEIGLEPCMENKTYIVQGFGNVGFHAARYFRRGRAKCLAI 309
ATG GV A + M +G E T VQG GNVG+ A+ K LA+
Sbjct: 1 ATGYGVVVAMK------AAMKHLGDSL--EGLTVAVQGLGNVGWGLAKKLAEEGGKVLAV 52
Query: 310 VEHDTAIVPDKGTE---INYKDLHTYKITKGTIKGYPGTKSAPTDIMFDKVDILVPAAIE 366
+ D I T INY G+ + I+ VDI P A+
Sbjct: 53 SDPDGYIYDPGITTEELINYAVALG-----GSARVKVQDYFPGEAILGLDVDIFAPCALG 107
Query: 367 KVIRKSNADKVQAKIIVEAANGPLTPAAHAMLLKKNVLIIPDIFANAGGVTVSYFEWLKN 426
VI NA K++AK++ E AN P T A +L ++ +++ PDI ANAGGV VSYFEW++N
Sbjct: 108 NVIDLENAKKLKAKVVAEGANNPTTDEALRILHERGIVVAPDIVANAGGVIVSYFEWVQN 167
Query: 427 IS 428
+
Sbjct: 168 LQ 169
>gnl|CDD|184464 PRK14031, PRK14031, glutamate dehydrogenase; Provisional.
Length = 444
Score = 126 bits (319), Expect = 1e-31
Identities = 102/333 (30%), Positives = 148/333 (44%), Gaps = 25/333 (7%)
Query: 104 DSGEYELIQCYRCHHCTHKSPTKGGIRYALDVNPDEVKALAALMTYKNSCSNVPFGGAKG 163
D G + YR H P KGGIR+ VN +K LA T+KNS + +P GG KG
Sbjct: 66 DKGNVQTNMGYRVQHNNAIGPYKGGIRFHASVNLGILKFLAFEQTFKNSLTTLPMGGGKG 125
Query: 164 GIRIDPSKYNNRELERITRKFALELIKKNYVGPGIDVPAPDYNTSAREMSWFYDAYAKTL 223
G P +N E+ R + F LEL ++GP DVPA D RE+ + + Y K
Sbjct: 126 GSDFSPRGKSNAEVMRFCQAFMLELW--RHIGPETDVPAGDIGVGGREVGFMFGMYKKL- 182
Query: 224 GSTNINALGMVTGKPLFLGGIRGRESATGRG-VFTAAEILVNNEEYMCEIGLEPCMENKT 282
++ G TGK GG R ATG G ++ E+L G + ++ K
Sbjct: 183 --SHEFT-GTFTGKGREFGGSLIRPEATGYGNIYFLMEMLKTK-------GTD--LKGKV 230
Query: 283 YIVQGFGNVGFHAARYFRRGRAKCLAIVEHDTAIVPDKGTEINYKD--LHTYKITKGTIK 340
+V G GNV + A K + + + D I G + D + + +G I+
Sbjct: 231 CLVSGSGNVAQYTAEKVLELGGKVVTMSDSDGYIYDPDGIDREKLDYIMELKNLYRGRIR 290
Query: 341 GYP---GTKSAPTDIMF-DKVDILVPAAIEKVIRKSNADKVQAK---IIVEAANGPLTPA 393
Y G K + +K DI +P+A + + +A ++ A + E AN P TP
Sbjct: 291 EYAEKYGCKYVEGARPWGEKGDIALPSATQNELNGDDARQLVANGVIAVSEGANMPSTPE 350
Query: 394 AHAMLLKKNVLIIPDIFANAGGVTVSYFEWLKN 426
A + +L P ANAGGV+VS E +N
Sbjct: 351 AIKVFQDAKILYAPGKAANAGGVSVSGLEMTQN 383
>gnl|CDD|181834 PRK09414, PRK09414, glutamate dehydrogenase; Provisional.
Length = 445
Score = 123 bits (311), Expect = 2e-30
Identities = 102/320 (31%), Positives = 148/320 (46%), Gaps = 32/320 (10%)
Query: 124 PTKGGIRYALDVNPDEVKALAALMTYKNSCSNVPFGGAKGGIRIDPSKYNNRELERITRK 183
P KGG+R+ VN +K L +KN+ + +P GG KGG DP ++ E+ R +
Sbjct: 90 PYKGGLRFHPSVNLSILKFLGFEQIFKNALTGLPIGGGKGGSDFDPKGKSDAEIMRFCQS 149
Query: 184 FALELIKKNYVGPGIDVPAPDYNTSAREMSWFYDAYAKTLGSTNINALGMVTGKPLFLGG 243
F EL + ++GP DVPA D RE+ + + Y K L TN G++TGK L GG
Sbjct: 150 FMTELYR--HIGPDTDVPAGDIGVGGREIGYLFGQY-KRL--TN-RFEGVLTGKGLSFGG 203
Query: 244 IRGRESATGRG-VFTAAEILVNNEEYMCEIGLEPCMENKTYIVQGFGNVGFHAARYFRRG 302
R ATG G V+ A E+L + E K +V G GNV +A ++
Sbjct: 204 SLIRTEATGYGLVYFAEEMLKARGD---------SFEGKRVVVSGSGNVAIYAIEKAQQL 254
Query: 303 RAKCLAIVEHDTAIVPDKGTEINYKDLHTYK-ITKGTIKGYPGTKSA-------PTDIMF 354
AK + + + ++G I+ + L K + +G I Y A P +
Sbjct: 255 GAKVVTCSDSSGYVYDEEG--IDLEKLKEIKEVRRGRISEYAEEFGAEYLEGGSPWSV-- 310
Query: 355 DKVDILVPAAIEKVIRKSNADKVQA---KIIVEAANGPLTPAAHAMLLKKNVLIIPDIFA 411
DI +P A + + + +A + A K + E AN P TP A + L+ VL P A
Sbjct: 311 -PCDIALPCATQNELDEEDAKTLIANGVKAVAEGANMPSTPEAIEVFLEAGVLFAPGKAA 369
Query: 412 NAGGVTVSYFEWLKNISHSS 431
NAGGV S E +N S S
Sbjct: 370 NAGGVATSGLEMSQNASRLS 389
>gnl|CDD|214847 smart00839, ELFV_dehydrog, Glutamate/Leucine/Phenylalanine/Valine
dehydrogenase. Glutamate, leucine, phenylalanine and
valine dehydrogenases are structurally and functionally
related. They contain a Gly-rich region containing a
conserved Lys residue, which has been implicated in the
catalytic activity, in each case a reversible oxidative
deamination reaction.
Length = 102
Score = 110 bits (277), Expect = 4e-29
Identities = 39/106 (36%), Positives = 58/106 (54%), Gaps = 9/106 (8%)
Query: 356 KVDILVPAAIEKVIRKSNADKVQAKIIVEAANGPLTPAAHAMLLKKNVLIIPDIFANAGG 415
DI +P A++ VI ++NA+++ AKII E AN PLT A +L + VL PD ANAGG
Sbjct: 2 NCDIFIPCALQNVINEANANRLGAKIIAEGANMPLTDEADDILEDRGVLYAPDFAANAGG 61
Query: 416 VTVSYFEWLKNISHSSLGRMSFGYDKEISDLLLSSIDTSLSDTFNK 461
V VS E L+N++ + +E+ L + +L + F
Sbjct: 62 VIVSALEMLQNLART---------AEEVFTDLSEIMRNALEEIFET 98
>gnl|CDD|133444 cd01075, NAD_bind_Leu_Phe_Val_DH, NAD(P) binding domain of leucine
dehydrogenase, phenylalanine dehydrogenase, and valine
dehydrogenase. Amino acid dehydrogenase (DH) is a
widely distributed family of enzymes that catalyzes the
oxidative deamination of an amino acid to its keto acid
and ammonia with concomitant reduction of NADP+. For
example, leucine DH catalyzes the reversible oxidative
deamination of L-leucine and several other straight or
branched chain amino acids to the corresponding
2-oxoacid derivative. Amino acid DH -like NAD(P)-binding
domains are members of the Rossmann fold superfamily and
include glutamate, leucine, and phenylalanine DHs,
methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase, Shikimate
DH-like proteins, malate oxidoreductases, and glutamyl
tRNA reductase. Amino acid DHs catalyze the deamination
of amino acids to keto acids with NAD(P)+ as a cofactor.
The NAD(P)-binding Rossmann fold superfamily includes a
wide variety of protein families including NAD(P)-
binding domains of alcohol DHs, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate DH,
lactate/malate DHs, formate/glycerate DHs, siroheme
synthases, 6-phosphogluconate DH, amino acid DHs,
repressor rex, NAD-binding potassium channel domain,
CoA-binding, and ornithine cyclodeaminase-like domains.
These domains have an alpha-beta-alpha configuration.
NAD binding involves numerous hydrogen and van der Waals
contacts.
Length = 200
Score = 85.7 bits (213), Expect = 3e-19
Identities = 48/171 (28%), Positives = 66/171 (38%), Gaps = 34/171 (19%)
Query: 251 TGRGVFT----AAEILVNNEEYMCEIGLEPCMENKTYIVQGFGNVGFHAARYFRRGRAKC 306
T GVF AAE L+ + +E KT VQG G VG+ A + AK
Sbjct: 5 TAYGVFLGMKAAAEHLLGTDS----------LEGKTVAVQGLGKVGYKLAEHLLEEGAKL 54
Query: 307 LAIVEHDTAIVPDKGTEINYKDLHTYKITKGTIKGYPGTKSAPTDIMFDKVDILVPAAIE 366
IV I + + + T AP +I D+ P A+
Sbjct: 55 --IV---ADINEEAVARA--------------AELFGATVVAPEEIYSVDADVFAPCALG 95
Query: 367 KVIRKSNADKVQAKIIVEAANGPLTPAAHAMLLK-KNVLIIPDIFANAGGV 416
VI +++AK I AAN L H +L + +L PD NAGG+
Sbjct: 96 GVINDDTIPQLKAKAIAGAANNQLADPRHGQMLHERGILYAPDYVVNAGGL 146
>gnl|CDD|133455 cd05313, NAD_bind_2_Glu_DH, NAD(P) binding domain of glutamate
dehydrogenase, subgroup 2. Amino acid dehydrogenase
(DH) is a widely distributed family of enzymes that
catalyzes the oxidative deamination of an amino acid to
its keto acid and ammonia with concomitant reduction of
NADP+. Glutamate DH is a multidomain enzyme that
catalyzes the reaction from glutamate to 2-oxyoglutarate
and ammonia in the presence of NAD or NADP. It is
present in all organisms. Enzymes involved in ammonia
asimilation are typically NADP+-dependent, while those
involved in glutamate catabolism are generally
NAD+-dependent. Amino acid DH-like NAD(P)-binding
domains are members of the Rossmann fold superfamily and
include glutamate, leucine, and phenylalanine DHs,
methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase, Shikimate
DH-like proteins, malate oxidoreductases, and glutamyl
tRNA reductase. Amino acid DHs catalyze the deamination
of amino acids to keto acids with NAD(P)+ as a cofactor.
The NAD(P)-binding Rossmann fold superfamily includes a
wide variety of protein families including NAD(P)-
binding domains of alcohol DHs, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate DH,
lactate/malate DHs, formate/glycerate DHs, siroheme
synthases, 6-phosphogluconate DH, amino acid DHs,
repressor rex, NAD-binding potassium channel domain,
CoA-binding, and ornithine cyclodeaminase-like domains.
These domains have an alpha -beta-alpha configuration.
NAD binding involves numerous hydrogen and van der Waals
contacts.
Length = 254
Score = 75.3 bits (186), Expect = 3e-15
Identities = 60/216 (27%), Positives = 81/216 (37%), Gaps = 36/216 (16%)
Query: 235 TGKPLFLGGIRGRESATGRG-VFTAAEIL-VNNEEYMCEIGLEPCMENKTYIVQGFGNVG 292
TGK L GG R ATG G V+ E+L NE + K + G GNV
Sbjct: 1 TGKGLSWGGSLIRPEATGYGLVYFVEEMLKDRNETL----------KGKRVAISGSGNVA 50
Query: 293 FHAARYFRRGRAKCLAIVEHDTAIVPDKGTEINYKDLH--------------TYKITKGT 338
+AA AK + + + + G + L Y GT
Sbjct: 51 QYAAEKLLELGAKVVTLSDSKGYVYDPDG--FTGEKLAELKEIKEVRRGRVSEYAKKYGT 108
Query: 339 IKGYPGTKSAPTDIMFDKVDILVPAAIEKVIRKSNADKVQA---KIIVEAANGPLTPAAH 395
K + G K P ++ DI P A + + +A + K + E AN P T A
Sbjct: 109 AKYFEGKK--PWEV---PCDIAFPCATQNEVDAEDAKLLVKNGCKYVAEGANMPCTAEAI 163
Query: 396 AMLLKKNVLIIPDIFANAGGVTVSYFEWLKNISHSS 431
+ + VL P ANAGGV VS E +N S
Sbjct: 164 EVFRQAGVLFAPGKAANAGGVAVSGLEMSQNSQRLS 199
>gnl|CDD|225455 COG2902, COG2902, NAD-specific glutamate dehydrogenase [Amino acid
transport and metabolism].
Length = 1592
Score = 48.5 bits (116), Expect = 8e-06
Identities = 48/185 (25%), Positives = 72/185 (38%), Gaps = 23/185 (12%)
Query: 348 APTDIM-FDKVDILVPAAIE---KVIRKSN------ADKVQAKIIVEAANGPLTPAAHAM 397
AP D++ + V A+ E V ++N ++V+AK+I E AN +T
Sbjct: 1074 APVDLLWNGGIGTYVKASGETNADVGDRANDAIRVNGEEVRAKVIGEGANLGVTQRGRIE 1133
Query: 398 LLKKNVLIIPDIFANAGGVTVSYFEWLKNISHSSL---GRMSFGYDKEISDLLLSSID-- 452
I D N+ GV S E I+ +S G+++ G E + LL S D
Sbjct: 1134 FALAGGRINTDAIDNSAGVDCSDHEVNIKIALNSAVFAGKLTRG---ERNALLASMTDEV 1190
Query: 453 TSLSDTFNKKIRIQKSAMYEDRISNATEKDIVQSSLTHSMQRAGRDILEY-AEKSDNKLD 511
SL N Q A+ N + S +++ G E SD +L
Sbjct: 1191 ASLVLRNNYL---QTEAISLLERLNLSLITE-LSRFISTLEAKGLLDREVEFLPSDAELA 1246
Query: 512 LRNAA 516
RNAA
Sbjct: 1247 ERNAA 1251
>gnl|CDD|240359 PTZ00324, PTZ00324, glutamate dehydrogenase 2; Provisional.
Length = 1002
Score = 44.8 bits (106), Expect = 1e-04
Identities = 22/51 (43%), Positives = 28/51 (54%)
Query: 374 ADKVQAKIIVEAANGPLTPAAHAMLLKKNVLIIPDIFANAGGVTVSYFEWL 424
K++ KIIVE AN +T A L + V++ D AN GGVT S E L
Sbjct: 793 NGKLRFKIIVEGANLFITQDARLALEECGVILFKDASANKGGVTSSSLEVL 843
Score = 33.2 bits (76), Expect = 0.37
Identities = 35/143 (24%), Positives = 53/143 (37%), Gaps = 30/143 (20%)
Query: 126 KGGIRYALDVNP-----------DEVKALAALMTYKNSCSNVPFGGAKGGIRIDPSKYNN 174
+GG+R DE LA+ KN ++P GG+KG I + S+Y N
Sbjct: 498 RGGVRMIQSFKEQAYRRNKRSVFDENYNLASTQLLKNK--DIPEGGSKGTILLS-SRYLN 554
Query: 175 RELERITRKFAL-------------ELIKKNYVGPGIDVPAPDYNTSAREMSWFYDAYAK 221
+ + + L E + + I PD +T+ M W +AK
Sbjct: 555 KFAQVRCQHAFLQYIDALLDVMLPGEKVVDHLKQEEIIFLGPDEHTTGTLMDW-AALHAK 613
Query: 222 TLGSTNINALGMVTGKPLFLGGI 244
G + TGK +GGI
Sbjct: 614 KRGYPFWKSF--TTGKSPSMGGI 634
>gnl|CDD|192741 pfam11314, DUF3117, Protein of unknown function (DUF3117). This
family of proteins with unknown function appears to be
restricted to Actinobacteria.
Length = 51
Score = 28.5 bits (64), Expect = 0.94
Identities = 8/25 (32%), Positives = 13/25 (52%)
Query: 124 PTKGGIRYALDVNPDEVKALAALMT 148
P +GG R +++N DE L +
Sbjct: 24 PLEGGGRLVVEMNADEAAELGDALK 48
>gnl|CDD|182541 PRK10551, PRK10551, phage resistance protein; Provisional.
Length = 518
Score = 31.5 bits (72), Expect = 1.3
Identities = 10/37 (27%), Positives = 19/37 (51%)
Query: 307 LAIVEHDTAIVPDKGTEINYKDLHTYKITKGTIKGYP 343
+A++ +TA+ +N +L + + TI GYP
Sbjct: 185 IALIIGNTALSTFSSRLMNVNELPDMPLRETTIPGYP 221
>gnl|CDD|234301 TIGR03663, TIGR03663, TIGR03663 family protein. Members of this
protein family, uncommon and rather sporadically
distributed, are found almost always in the same genomes
as members of family TIGR03662, and frequently as a
nearby gene. Members show some N-terminal sequence
similarity with Pfam family pfam02366,
dolichyl-phosphate-mannose-protein mannosyltransferase.
The few invariant residues in this family, found toward
the N-terminus, include a dipeptide DE, a tripeptide
HGP, and two different Arg residues. Up to three members
may be found in a genome. The function is unknown.
Length = 439
Score = 30.9 bits (70), Expect = 2.0
Identities = 19/79 (24%), Positives = 34/79 (43%), Gaps = 9/79 (11%)
Query: 375 DKVQAKIIVEAANGPLTPAAHAMLLKKNVLIIPDIFANAGGVTVSYFEW--LKNISHSSL 432
D + + + AA + A A K+N +I IF GG+ Y +W + + +L
Sbjct: 142 DTGKRRYLFLAA----SALALAFTSKENAYLIILIF---GGLLAIYLDWKKERAGARETL 194
Query: 433 GRMSFGYDKEISDLLLSSI 451
R + + + DL+ S
Sbjct: 195 TRKRSLFWRWLRDLIGSVA 213
>gnl|CDD|187615 cd05357, PR_SDR_c, pteridine reductase (PR), classical (c) SDRs.
Pteridine reductases (PRs), members of the SDR family,
catalyzes the NAD-dependent reduction of folic acid,
dihydrofolate and related compounds. In Leishmania,
pteridine reductase (PTR1) acts to circumvent the
anti-protozoan drugs that attack dihydrofolate reductase
activity. Proteins in this subgroup have an N-terminal
NAD-binding motif and a YxxxK active site motif, but
have an Asp instead of the usual upstream catalytic Ser.
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRS are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes have a 3-glycine N-terminal NAD(P)(H)-binding
pattern (typically, TGxxxGxG in classical SDRs and
TGxxGxxG in extended SDRs), while substrate binding is
in the C-terminal region. A critical catalytic Tyr
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering), is often found in a
conserved YXXXK pattern. In addition to the Tyr and Lys,
there is often an upstream Ser (Ser-138, 15-PGDH
numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is not
generally found among SDRs.
Length = 234
Score = 30.3 bits (69), Expect = 2.0
Identities = 15/38 (39%), Positives = 21/38 (55%), Gaps = 3/38 (7%)
Query: 177 LERITRKFALEL---IKKNYVGPGIDVPAPDYNTSARE 211
LE +TR ALEL I+ N + PG+ + D + RE
Sbjct: 157 LEGLTRSAALELAPNIRVNGIAPGLILLPEDMDAEYRE 194
>gnl|CDD|235725 PRK06179, PRK06179, short chain dehydrogenase; Provisional.
Length = 270
Score = 29.5 bits (67), Expect = 3.8
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 5/44 (11%)
Query: 363 AAIEKVIRKSNADKVQAKIIVEAANGPL-----TPAAHAMLLKK 401
A+ K ++K++A +V A +V+AA GP T A LL K
Sbjct: 205 KAVAKAVKKADAPEVVADTVVKAALGPWPKMRYTAGGQASLLSK 248
>gnl|CDD|232981 TIGR00456, argS, arginyl-tRNA synthetase. This model recognizes
arginyl-tRNA synthetase in every completed genome to
date. An interesting feature of the alignment of all
arginyl-tRNA synthetases is a fairly deep split between
two families. One family includes archaeal, eukaryotic
and organellar, spirochete, E. coli, and Synechocystis
sp. The second, sharing a deletion of about 25 residues
in the central region relative to the first, includes
Bacillus subtilis, Aquifex aeolicus, the Mycoplasmas and
Mycobacteria, and the Gram-negative bacterium
Helicobacter pylori [Protein synthesis, tRNA
aminoacylation].
Length = 566
Score = 30.0 bits (68), Expect = 4.0
Identities = 38/256 (14%), Positives = 71/256 (27%), Gaps = 45/256 (17%)
Query: 63 FDVSIRARKFTDEDIALRRNGIIMLMQNYSSLLEIQFPFRRDSGEYEL---IQCYRCHHC 119
+ K +E+ L L S E + EY L + +
Sbjct: 192 EGFYVEINKRLEENEELE-EEARELFVKLESGDEEAIKLWKRLVEYSLEGIKETLARLNI 250
Query: 120 THKSPTKGGIRYALDVNPDEVKALAALM----TYKNSCSNVPFGGAKGGIRIDPSKYNNR 175
S G N K L L ++ G + +D + + ++
Sbjct: 251 HFDSFVWEGESV---KNGMVPKVLEDLKEKGLVVED-----------GALWLDLTLFGDK 296
Query: 176 ELERITRKFALELIKKN----YVGPGIDVPAPDYNTSAREMSWFYDA----YAKTLGSTN 227
+ +R+ L K + Y+ I +M + + + + +
Sbjct: 297 DKDRV-------LQKSDGTYLYLTRDIAYHLDKLERGFDKMIYVWGSDHHLHIAQFFAI- 348
Query: 228 INALGMVTGKPLF---LGGIRGRESATGRGVF-TAAEILVNNEEYMCEIGLEPCMENKTY 283
+ LG K L G + T RG + +L + + +
Sbjct: 349 LEKLGFYKKKELIHLNFGMVPLGSMKTRRGNVISLDNLLDEASKRAGNVITIKNDLEEED 408
Query: 284 IVQGFGNVGFHAARYF 299
+ VG A RYF
Sbjct: 409 VAD---AVGIGAVRYF 421
>gnl|CDD|167141 PRK01021, lpxB, lipid-A-disaccharide synthase; Reviewed.
Length = 608
Score = 29.4 bits (66), Expect = 5.2
Identities = 19/76 (25%), Positives = 29/76 (38%), Gaps = 4/76 (5%)
Query: 269 MCEIGLEPCMENKTYIVQGFGNVGFHAARYFRRGRAKCLAIVEHDTAIVPDKGTEINYKD 328
M G P + + V GF V + + R R I++ + V I++ D
Sbjct: 266 MRAEGFHPLFNMEEFQVSGFWEVLLALFKLWYRYRKLYKTILKTNPRTV----ICIDFPD 321
Query: 329 LHTYKITKGTIKGYPG 344
H I K +GY G
Sbjct: 322 FHFLLIKKLRKRGYKG 337
>gnl|CDD|187881 cd09750, Csa5_I-A, CRISPR/Cas system-associated protein Csa5.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Predicted transcriptional regulator of CRISPR/Cas
system; contains DNA binding HTH domain; also known as
Csa5 family.
Length = 101
Score = 27.9 bits (62), Expect = 5.3
Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 467 KSAMYEDRISNATEKDIVQSSLTHSMQRAGRDILEYAE 504
++ Y DRI NA K+ V+ L + QR R +E E
Sbjct: 6 ENPTYVDRIGNALSKEAVEKVL-YEAQRIFRSGIERGE 42
>gnl|CDD|223674 COG0601, DppB, ABC-type dipeptide/oligopeptide/nickel transport
systems, permease components [Amino acid transport and
metabolism / Inorganic ion transport and metabolism].
Length = 317
Score = 29.0 bits (66), Expect = 5.8
Identities = 13/36 (36%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 420 YFEWLKNISHSSLGRMSFGYDKEISDLLLSSIDTSL 455
Y +LKN+ H G SF Y + ++DL+L + +L
Sbjct: 65 YLNYLKNLLHGDFGT-SFVYKRPVADLILERLPATL 99
>gnl|CDD|118234 pfam09702, Cas_Csa5, CRISPR-associated protein (Cas_Csa5). CRISPR
is a term for Clustered, Regularly Interspaced Short
Palindromic Repeats. A number of protein families appear
only in association with these repeats and are
designated Cas (CRISPR-Associated) proteins. This entry
represents a minor family of Cas proteins found in
various species of Sulfolobus and Pyrococcus (all
archaeal). It is found with two different CRISPR loci in
Sulfolobus solfataricus.
Length = 105
Score = 27.5 bits (61), Expect = 6.0
Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 467 KSAMYEDRISNATEKDIVQSSLTHSMQRAGRDILEYAE 504
++ Y DRI NA K+ V+ L + QR R +E E
Sbjct: 6 ENPTYVDRIGNALSKEAVEKVL-YEAQRIVRSGIERGE 42
>gnl|CDD|192697 pfam11016, DUF2854, Protein of unknown function (DUF2854). This
family of proteins has no known function.
Length = 146
Score = 28.1 bits (63), Expect = 6.4
Identities = 9/31 (29%), Positives = 14/31 (45%), Gaps = 2/31 (6%)
Query: 214 WFYDAYAKTLGSTNINALGMVTGKPLFLGGI 244
+ AY N++ G G P+ LGG+
Sbjct: 1 VGFVAYF--TDGANLSLPGFFYGIPILLGGL 29
>gnl|CDD|183772 PRK12823, benD, 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate
dehydrogenase; Provisional.
Length = 260
Score = 28.4 bits (64), Expect = 7.9
Identities = 23/84 (27%), Positives = 33/84 (39%), Gaps = 28/84 (33%)
Query: 156 VPFGGAKGGIRIDPSKYNNRELERITRKFALEL----IKKNYVGPG-IDVP--------A 202
VP+ AKGG+ +T A E I+ N V PG + P A
Sbjct: 153 VPYSAAKGGV------------NALTASLAFEYAEHGIRVNAVAPGGTEAPPRRVPRNAA 200
Query: 203 PDYNTSAREMSWFYDAYAKTLGST 226
P S +E +W+ +TL S+
Sbjct: 201 PQ---SEQEKAWYQQIVDQTLDSS 221
>gnl|CDD|217368 pfam03100, CcmE, CcmE. CcmE is the product of one of a cluster of
Ccm genes that are necessary for cytochrome c
biosynthesis in eubacteria. Expression of these proteins
is induced when the organisms are grown under anaerobic
conditions with nitrate or nitrite as the final electron
acceptor.
Length = 130
Score = 27.4 bits (62), Expect = 8.2
Identities = 12/25 (48%), Positives = 14/25 (56%), Gaps = 5/25 (20%)
Query: 250 ATGR----GVFTAAEILVN-NEEYM 269
A GR GVF A E+L +E YM
Sbjct: 103 AEGRLDADGVFVADEVLAKHDENYM 127
>gnl|CDD|234022 TIGR02813, omega_3_PfaA, polyketide-type polyunsaturated fatty acid
synthase PfaA. Members of the seed for this alignment
are involved in omega-3 polyunsaturated fatty acid
biosynthesis, such as the protein PfaA from the
eicosapentaenoic acid biosynthesis operon in
Photobacterium profundum strain SS9. PfaA is encoded
together with PfaB, PfaC, and PfaD, and the functions of
the individual polypeptides have not yet been described.
More distant homologs of PfaA, also included with the
reach of this model, appear to be involved in
polyketide-like biosynthetic mechanisms of
polyunsaturated fatty acid biosynthesis, an alternative
to the more familiar iterated mechanism of chain
extension and desaturation, and in most cases are encoded
near genes for homologs of PfaB, PfaC, and/or PfaD.
Length = 2582
Score = 29.2 bits (65), Expect = 8.5
Identities = 40/157 (25%), Positives = 59/157 (37%), Gaps = 22/157 (14%)
Query: 323 EINYKDLHTYKITKGTIKGYPGTKSAPTDIMFDKVDILVPAAIEKVIRKSNAD------- 375
E+N +DL + T G I Y +K +PTD KV VPAA+E + R
Sbjct: 1672 ELNPEDLAECR-TLGEIVAYMQSKVSPTDATDPKVATTVPAAVEAIARTVETAVNLPPHS 1730
Query: 376 KVQAKIIVEAANGPLTPAAHAMLLKKNVLIIPDIFANAG---------GVTVSYFEWLKN 426
+V+ K + N L+I D NAG G V+
Sbjct: 1731 EVELKKLPAVNKLVQDVTGEGKQSGANALVIDDDGHNAGVLAEKLIAAGWQVAVVRSPWV 1790
Query: 427 ISHSSLGRMSFGYDKEISDLLLSSIDTSLSDTFNKKI 463
+SHS+ I+ + L +ID + + K I
Sbjct: 1791 VSHSAS-----PLASAIASVTLGTIDDTSIEAVIKDI 1822
>gnl|CDD|183343 PRK11861, PRK11861, bifunctional prephenate
dehydrogenase/3-phosphoshikimate
1-carboxyvinyltransferase; Provisional.
Length = 673
Score = 28.5 bits (63), Expect = 9.6
Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 5/61 (8%)
Query: 295 AARYFRRGR-AKCLAIVEHDTAIVPDKGTEINYKDLHTYKITKGTIKGYPGTKSAPTDIM 353
AAR R R AK V DT G+ + + DL + +GT++ PG+KS ++
Sbjct: 213 AARAAWRERGAKPAPAVRSDT---SGTGSHMEHLDLGPFSHAQGTVR-LPGSKSISNRVL 268
Query: 354 F 354
Sbjct: 269 L 269
>gnl|CDD|222865 PHA02543, regA, translation repressor protein; Provisional.
Length = 125
Score = 27.3 bits (61), Expect = 9.7
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 17/60 (28%)
Query: 71 KFTDEDIALRRNGIIMLMQNYSSLLEIQFP-----------FR----RDSGEYELIQCYR 115
T+EDI RRN I L++++ L+EI P FR + GE+ L+ YR
Sbjct: 65 DLTEEDI-QRRNNIAKLLEDW-GLIEIVDPDQMEEVSPTNNFRVISHKQKGEWTLVPKYR 122
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.317 0.135 0.392
Gapped
Lambda K H
0.267 0.0780 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 27,654,633
Number of extensions: 2764498
Number of successful extensions: 2643
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2601
Number of HSP's successfully gapped: 45
Length of query: 535
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 433
Effective length of database: 6,413,494
Effective search space: 2777042902
Effective search space used: 2777042902
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 (21.6 bits)
S2: 61 (27.2 bits)