RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780263|ref|YP_003064676.1| translation elongation factor
Tu [Candidatus Liberibacter asiaticus str. psy62]
(392 letters)
>gnl|CDD|177010 CHL00071, tufA, elongation factor Tu.
Length = 409
Score = 544 bits (1403), Expect = e-155
Identities = 226/410 (55%), Positives = 291/410 (70%), Gaps = 19/410 (4%)
Query: 1 MVEKRYVRNKESLGLSTIGHVDHGKTTLTAAIT----KYYSEEKKEYGDIDSAPEEKLRG 56
M +++ R K + + TIGHVDHGKTTLTAAIT + K+Y +IDSAPEEK RG
Sbjct: 1 MAREKFERKKPHVNIGTIGHVDHGKTTLTAAITMTLAAKGGAKAKKYDEIDSAPEEKARG 60
Query: 57 ITIATAHVSYETDKRFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHI 116
ITI TAHV YET+ R Y+H+DCPGHADYVKNMITGA Q DGAILV +A DGP PQT+EHI
Sbjct: 61 ITINTAHVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTKEHI 120
Query: 117 LLARQIGISSIVVYMNKVDAVDDDELLDISEYEIRDLLKEHKY-SDDTPIIRGSALCAL- 174
LLA+Q+G+ +IVV++NK D VDD+ELL++ E E+R+LL ++ + DD PI+ GSAL AL
Sbjct: 121 LLAKQVGVPNIVVFLNKEDQVDDEELLELVELEVRELLSKYDFPGDDIPIVSGSALLALE 180
Query: 175 ---QGTNKELGE----DSIHALMKAVDTHIPTPQRSLDAPFLMHIEGSCGIEGRGTVVTG 227
+ + GE D I+ LM AVD++IPTP+R D PFLM IE I GRGTV TG
Sbjct: 181 ALTENPKIKRGENKWVDKIYNLMDAVDSYIPTPERDTDKPFLMAIEDVFSITGRGTVATG 240
Query: 228 CIKRGRIKAGSDVEIIGMGGKKLKVKCTDVEMFRKKLDEAIAGDNVGLLLRGVNRADVPR 287
I+RG +K G VEI+G+ K T +EMF+K LDE +AGDNVG+LLRG+ + D+ R
Sbjct: 241 RIERGTVKVGDTVEIVGLRETKT-TTVTGLEMFQKTLDEGLAGDNVGILLRGIQKEDIER 299
Query: 288 GRVVCAPGSIQEYSRFRASVYILTASEGGRTTGFMDNYRPQFFMDTADVTGRI---ILSP 344
G V+ PG+I +++F A VYILT EGGR T F YRPQF++ T DVTG+I
Sbjct: 300 GMVLAKPGTITPHTKFEAQVYILTKEEGGRHTPFFPGYRPQFYVRTTDVTGKIESFTADD 359
Query: 345 GSQA--VMPGDRVDLEVELIYPIAMEPNQTFSMREGGKTVGAGLILEIIE 392
GS+ VMPGDR+ + VELIYPIA+E F++REGG+TVGAG++ +I++
Sbjct: 360 GSKTEMVMPGDRIKMTVELIYPIAIEKGMRFAIREGGRTVGAGVVSKILK 409
>gnl|CDD|35681 KOG0460, KOG0460, KOG0460, Mitochondrial translation elongation
factor Tu [Translation, ribosomal structure and
biogenesis].
Length = 449
Score = 523 bits (1348), Expect = e-149
Identities = 227/395 (57%), Positives = 290/395 (73%), Gaps = 6/395 (1%)
Query: 3 EKRYVRNKESLGLSTIGHVDHGKTTLTAAITKYYSEEK----KEYGDIDSAPEEKLRGIT 58
+ +VR+K + + TIGHVDHGKTTLTAAITK +E+ K+Y +ID APEEK RGIT
Sbjct: 45 KAVFVRDKPHVNVGTIGHVDHGKTTLTAAITKILAEKGGAKFKKYDEIDKAPEEKARGIT 104
Query: 59 IATAHVSYETDKRFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILL 118
I AHV YET KR Y+H DCPGHADY+KNMITGA Q DGAILV AA DGP PQTREH+LL
Sbjct: 105 INAAHVEYETAKRHYAHTDCPGHADYIKNMITGAAQMDGAILVVAATDGPMPQTREHLLL 164
Query: 119 ARQIGISSIVVYMNKVDAVDDDELLDISEYEIRDLLKEHKYS-DDTPIIRGSALCALQGT 177
ARQ+G+ IVV++NKVD VDD E+L++ E EIR+LL E + D+TP+IRGSALCAL+G
Sbjct: 165 ARQVGVKHIVVFINKVDLVDDPEMLELVEMEIRELLSEFGFDGDNTPVIRGSALCALEGR 224
Query: 178 NKELGEDSIHALMKAVDTHIPTPQRSLDAPFLMHIEGSCGIEGRGTVVTGCIKRGRIKAG 237
E+G ++I L+ AVD++IPTP+R LD PFL+ IE I GRGTVVTG ++RG +K G
Sbjct: 225 QPEIGLEAIEKLLDAVDSYIPTPERDLDKPFLLPIEDVFSIPGRGTVVTGRLERGVLKKG 284
Query: 238 SDVEIIGMGGKKLKVKCTDVEMFRKKLDEAIAGDNVGLLLRGVNRADVPRGRVVCAPGSI 297
+VEI+G K LK T +EMFRK LDEA AGDN+G LLRG+ R DV RG V+ PGS+
Sbjct: 285 DEVEIVG-HNKTLKTTVTGIEMFRKSLDEAQAGDNLGALLRGIKREDVKRGMVLAKPGSV 343
Query: 298 QEYSRFRASVYILTASEGGRTTGFMDNYRPQFFMDTADVTGRIILSPGSQAVMPGDRVDL 357
+ +++F A +YIL+ EGGR F+ YRPQ F T DVTGR+ + P + VMPG+ V +
Sbjct: 344 KPHNKFEAQLYILSKEEGGRHKPFVSGYRPQMFSRTWDVTGRVDIPPEKEMVMPGENVKV 403
Query: 358 EVELIYPIAMEPNQTFSMREGGKTVGAGLILEIIE 392
EV LI P+ +E Q F++REGG+TVG G++ + +
Sbjct: 404 EVTLIRPMPLEKGQRFTLREGGRTVGTGVVTDTLP 438
>gnl|CDD|30399 COG0050, TufB, GTPases - translation elongation factors
[Translation, ribosomal structure and biogenesis].
Length = 394
Score = 519 bits (1337), Expect = e-148
Identities = 239/397 (60%), Positives = 292/397 (73%), Gaps = 8/397 (2%)
Query: 1 MVEKRYVRNKESLGLSTIGHVDHGKTTLTAAITKYYSE----EKKEYGDIDSAPEEKLRG 56
M ++++ R K + + TIGHVDHGKTTLTAAIT ++ E K Y ID+APEEK RG
Sbjct: 1 MAKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKKGGAEAKAYDQIDNAPEEKARG 60
Query: 57 ITIATAHVSYETDKRFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHI 116
ITI TAHV YET R Y+H+DCPGHADYVKNMITGA Q DGAILV AA DGP PQTREHI
Sbjct: 61 ITINTAHVEYETANRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHI 120
Query: 117 LLARQIGISSIVVYMNKVDAVDDDELLDISEYEIRDLLKEHKYS-DDTPIIRGSALCALQ 175
LLARQ+G+ IVV++NKVD VDD+ELL++ E E+R+LL E+ + DDTPIIRGSAL AL+
Sbjct: 121 LLARQVGVPYIVVFLNKVDMVDDEELLELVEMEVRELLSEYGFPGDDTPIIRGSALKALE 180
Query: 176 GTNKELGEDSIHALMKAVDTHIPTPQRSLDAPFLMHIEGSCGIEGRGTVVTGCIKRGRIK 235
G K E I LM AVD++IPTP+R +D PFLM +E I GRGTVVTG ++RG +K
Sbjct: 181 GDAK--WEAKIEELMDAVDSYIPTPERDIDKPFLMPVEDVFSISGRGTVVTGRVERGILK 238
Query: 236 AGSDVEIIGMGGKKLKVKCTDVEMFRKKLDEAIAGDNVGLLLRGVNRADVPRGRVVCAPG 295
G +VEI+G + K T VEMFRK LDE AGDNVG+LLRGV R DV RG+V+ PG
Sbjct: 239 VGEEVEIVG-IKETQKTTVTGVEMFRKLLDEGQAGDNVGVLLRGVKREDVERGQVLAKPG 297
Query: 296 SIQEYSRFRASVYILTASEGGRTTGFMDNYRPQFFMDTADVTGRIILSPGSQAVMPGDRV 355
SI+ +++F A VY+L+ EGGR T F YRPQF+ T DVTG I L G + VMPGD V
Sbjct: 298 SIKPHTKFEAEVYVLSKEEGGRHTPFFHGYRPQFYFRTTDVTGAITLPEGVEMVMPGDNV 357
Query: 356 DLEVELIYPIAMEPNQTFSMREGGKTVGAGLILEIIE 392
+ VELI+PIAME F++REGG+TVGAG++ +IIE
Sbjct: 358 KMVVELIHPIAMEEGLRFAIREGGRTVGAGVVTKIIE 394
>gnl|CDD|133284 cd01884, EF_Tu, EF-Tu subfamily. This subfamily includes orthologs
of translation elongation factor EF-Tu in bacteria,
mitochondria, and chloroplasts. It is one of several
GTP-binding translation factors found in the larger
family of GTP-binding elongation factors. The
eukaryotic counterpart, eukaryotic translation
elongation factor 1 (eEF-1 alpha), is excluded from this
family. EF-Tu is one of the most abundant proteins in
bacteria, as well as, one of the most highly conserved,
and in a number of species the gene is duplicated with
identical function. When bound to GTP, EF-Tu can form a
complex with any (correctly) aminoacylated tRNA except
those for initiation and for selenocysteine, in which
case EF-Tu is replaced by other factors. Transfer RNA
is carried to the ribosome in these complexes for
protein translation.
Length = 195
Score = 339 bits (872), Expect = 7e-94
Identities = 117/189 (61%), Positives = 147/189 (77%), Gaps = 5/189 (2%)
Query: 17 TIGHVDHGKTTLTAAITKYYSE----EKKEYGDIDSAPEEKLRGITIATAHVSYETDKRF 72
TIGHVDHGKTTLTAAITK ++ + K+Y +ID APEEK RGITI TAHV YET R
Sbjct: 7 TIGHVDHGKTTLTAAITKVLAKKGGAKFKKYDEIDKAPEEKARGITINTAHVEYETANRH 66
Query: 73 YSHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISSIVVYMN 132
Y+H+DCPGHADY+KNMITGA Q DGAILV +A DGP PQTREH+LLARQ+G+ IVV++N
Sbjct: 67 YAHVDCPGHADYIKNMITGAAQMDGAILVVSATDGPMPQTREHLLLARQVGVPYIVVFLN 126
Query: 133 KVDAVDDDELLDISEYEIRDLLKEHKY-SDDTPIIRGSALCALQGTNKELGEDSIHALMK 191
K D VDD+ELL++ E E+R+LL ++ + D+TPI+RGSAL AL+G + I L+
Sbjct: 127 KADMVDDEELLELVEMEVRELLSKYGFDGDNTPIVRGSALKALEGDDPNKWVKKILELLD 186
Query: 192 AVDTHIPTP 200
A+D++IPTP
Sbjct: 187 ALDSYIPTP 195
>gnl|CDD|143801 pfam00009, GTP_EFTU, Elongation factor Tu GTP binding domain. This
domain contains a P-loop motif, also found in several
other families such as pfam00071, pfam00025 and
pfam00063. Elongation factor Tu consists of three
structural domains, this plus two C-terminal beta barrel
domains.
Length = 185
Score = 221 bits (566), Expect = 2e-58
Identities = 89/191 (46%), Positives = 122/191 (63%), Gaps = 17/191 (8%)
Query: 15 LSTIGHVDHGKTTLTAAITKY-----YSEEKKEYGDIDSAPEEKLRGITIATAHVSYETD 69
+ IGHVDHGKTTLT A+ E K+ G++D EE+ RGITI A VS+ET
Sbjct: 6 IGIIGHVDHGKTTLTDALLYVTGAIDKRGEVKQEGELDRLKEERERGITIKIAAVSFETK 65
Query: 70 KRFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISSIVV 129
KR + ID PGH D+ K MI GA QADGAILV A +G PQTREH+LLA+Q+G+ I+V
Sbjct: 66 KRHINIIDTPGHVDFTKEMIRGAAQADGAILVVDAVEGVMPQTREHLLLAKQLGV-PIIV 124
Query: 130 YMNKVDAVDDDELLDISEYEIRDLLKEHKYS-DDTPIIRGSALCALQGTNKELGEDSIHA 188
++NK+D VDD EL ++ E R+LL+++ + + P+I GS AL G I
Sbjct: 125 FINKMDRVDDAELDEVVEEISRELLEKYGFGGETIPVIPGS---ALTGEG-------IDT 174
Query: 189 LMKAVDTHIPT 199
L++A+D ++P+
Sbjct: 175 LLEALDLYLPS 185
>gnl|CDD|34853 COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 428
Score = 217 bits (555), Expect = 4e-57
Identities = 147/435 (33%), Positives = 208/435 (47%), Gaps = 63/435 (14%)
Query: 10 KESLGLSTIGHVDHGKTTLT-----------AAITKYYSEEKKEYGD--------IDSAP 50
K L L IGHVD GK+TL + +E KE G +D
Sbjct: 5 KPHLNLVFIGHVDAGKSTLVGRLLYDLGEIDKRTMEKLEKEAKELGKESFKFAWVLDKTK 64
Query: 51 EEKLRGITIATAHVSYETDKRFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDG--- 107
EE+ RG+TI AH +ETDK ++ ID PGH D+VKNMITGA+QAD A+LV A DG
Sbjct: 65 EERERGVTIDVAHSKFETDKYNFTIIDAPGHRDFVKNMITGASQADVAVLVVDARDGEFE 124
Query: 108 ----PKPQTREHILLARQIGISSIVVYMNKVDAVD-DDELLDISEYEIRDLLKEHKY-SD 161
QTREH LAR +GI ++V +NK+D V D+E + E+ LLK Y
Sbjct: 125 AGFGVGGQTREHAFLARTLGIKQLIVAVNKMDLVSWDEERFEEIVSEVSKLLKMVGYNPK 184
Query: 162 DTPIIRGSALCALQGTN-KELGEDS----IHALMKAVDTHIPTPQRSLDAPFLMHIEGSC 216
D P I S +G N + E+ L++A+D + P+R LD P + I+
Sbjct: 185 DVPFIPIS---GFKGDNLTKKSENMPWYKGPTLLEALDQ-LEPPERPLDKPLRLPIQDVY 240
Query: 217 GIEGRGTVVTGCIKRGRIKAGSDVEIIGMGGKKLKVKCTDVEMFRKKLDEAIAGDNVGLL 276
I G GTV G ++ G IK G V G +VK +EM +++ +A GDNVG
Sbjct: 241 SISGIGTVPVGRVESGVIKPGQKV-TFMPAGVVGEVK--SIEMHHEEISQAEPGDNVGFN 297
Query: 277 LRGVNRADVPRGRVVCAPGSIQEYSRFRASVYILTASEGGRTTGFMDNYRPQFFMDTADV 336
+RGV + D+ RG V+ + S + I+ G T+G Y P TA V
Sbjct: 298 VRGVEKNDIRRGDVIGHSDNPPTVSPEFTAQIIVLWHPGIITSG----YTPVLHAHTAQV 353
Query: 337 TGRII-----LSPGS--------QAVMPGDRVDLEVELIYPIAMEPNQ------TFSMRE 377
RI L P + Q + GD +++E P+ +E F++R+
Sbjct: 354 ACRIAELLSKLDPRTGKKLEENPQFLKRGDAAIVKIEPEKPLCLEKVSEIPQLGRFALRD 413
Query: 378 GGKTVGAGLILEIIE 392
G+T+ AG +LE+ +
Sbjct: 414 MGQTIAAGKVLEVKK 428
>gnl|CDD|133257 cd00881, GTP_translation_factor, GTP translation factor family.
This family consists primarily of translation
initiation, elongation, and release factors, which play
specific roles in protein translation. In addition, the
family includes Snu114p, a component of the U5 small
nuclear riboprotein particle which is a component of the
spliceosome and is involved in excision of introns,
TetM, a tetracycline resistance gene that protects the
ribosome from tetracycline binding, and the unusual
subfamily CysN/ATPS, which has an unrelated function
(ATP sulfurylase) acquired through lateral transfer of
the EF1-alpha gene and development of a new function.
Length = 189
Score = 162 bits (413), Expect = 1e-40
Identities = 70/199 (35%), Positives = 104/199 (52%), Gaps = 26/199 (13%)
Query: 16 STIGHVDHGKTTLTAAITKYYSEEKK----EYGDIDSAPEEKLRGITIATAHVSYETDKR 71
GHVDHGKTTLT + + ++ E +D EE+ RGITI + ++E R
Sbjct: 3 GIAGHVDHGKTTLTERLLYVTGDIERDGTVEETFLDVLKEERERGITIKSGVATFEWPDR 62
Query: 72 FYSHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISSIVVYM 131
+ ID PGH D+ +I G + +DGAILV A +G +PQTREH+ +AR+ G+ I+V +
Sbjct: 63 RVNFIDTPGHEDFSSEVIRGLSVSDGAILVVDANEGVQPQTREHLRIAREGGL-PIIVAI 121
Query: 132 NKVDAVDDDELLDISEYEIRDLLKE----------HKYSDDTPIIRGSALCALQGTNKEL 181
NK+D V +E L+ EI++LL + PI+ GSAL
Sbjct: 122 NKIDRV-GEEDLEEVLREIKELLGLIGFISTKEEGTRNGLLVPIVPGSALTG-------- 172
Query: 182 GEDSIHALMKAVDTHIPTP 200
+ L++A+ H+P P
Sbjct: 173 --IGVEELLEAIVEHLPPP 189
>gnl|CDD|33087 COG3276, SelB, Selenocysteine-specific translation elongation
factor [Translation, ribosomal structure and
biogenesis].
Length = 447
Score = 155 bits (394), Expect = 2e-38
Identities = 95/326 (29%), Positives = 157/326 (48%), Gaps = 31/326 (9%)
Query: 17 TIGHVDHGKTTLTAAITKYYSEEKKEYGDIDSAPEEKLRGITIATAHVSYETDKRFYSHI 76
T GH+DHGKTTL A+T G D PEEK RGITI + + I
Sbjct: 5 TAGHIDHGKTTLLKALT---------GGVTDRLPEEKKRGITIDLGFYYRKLEDGVMGFI 55
Query: 77 DCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISSIVVYMNKVDA 136
D PGH D++ N++ G D A+LV AA++G QT EH+L+ +GI + ++ + K D
Sbjct: 56 DVPGHPDFISNLLAGLGGIDYALLVVAADEGLMAQTGEHLLILDLLGIKNGIIVLTKADR 115
Query: 137 VDDDELLDISEYEIRDLLKEHKYSDDTPIIRGSALCALQGTNKELGEDSIHALMKAVDTH 196
VD+ + E +I+ +L + + + I + SA + G I L +
Sbjct: 116 VDEARI----EQKIKQILADLSLA-NAKIFKTSA---------KTGRG-IEELKNELIDL 160
Query: 197 IPTPQRSLDAPFLMHIEGSCGIEGRGTVVTGCIKRGRIKAGSDVEIIGMGGKKLKVKCTD 256
+ +R PF + I+ + ++G GTVVTG + G +K G + + + K+++V+
Sbjct: 161 LEEIERDEQKPFRIAIDRAFTVKGVGTVVTGTVLSGEVKVGDKLYLSPI-NKEVRVR--S 217
Query: 257 VEMFRKKLDEAIAGDNVGLLLRGVNRADVPRGRVVCAPGSIQEYSRFRASVYILTASEGG 316
++ ++EA AG VGL L+GV + ++ RG + P ++ +R + I +
Sbjct: 218 IQAHDVDVEEAKAGQRVGLALKGVEKEEIERGDWLLKPEPLEVTTRLIVELEIDPLFK-- 275
Query: 317 RTTGFMDNYRPQFFMDTADVTGRIIL 342
+T + VTGRI+
Sbjct: 276 KTLKQGQPV--HIHVGLRSVTGRIVP 299
>gnl|CDD|133283 cd01883, EF1_alpha, Eukaryotic elongation factor 1 (EF1) alpha
subfamily. EF1 is responsible for the GTP-dependent
binding of aminoacyl-tRNAs to the ribosomes. EF1 is
composed of four subunits: the alpha chain which binds
GTP and aminoacyl-tRNAs, the gamma chain that probably
plays a role in anchoring the complex to other cellular
components and the beta and delta (or beta') chains.
This subfamily is the alpha subunit, and represents the
counterpart of bacterial EF-Tu for the archaea
(aEF1-alpha) and eukaryotes (eEF1-alpha). eEF1-alpha
interacts with the actin of the eukaryotic cytoskeleton
and may thereby play a role in cellular transformation
and apoptosis. EF-Tu can have no such role in bacteria.
In humans, the isoform eEF1A2 is overexpressed in 2/3
of breast cancers and has been identified as a putative
oncogene. This subfamily also includes Hbs1, a G
protein known to be important for efficient growth and
protein synthesis under conditions of limiting
translation initiation in yeast, and to associate with
Dom34. It has been speculated that yeast Hbs1 and Dom34
proteins may function as part of a complex with a role
in gene expression.
Length = 219
Score = 149 bits (379), Expect = 1e-36
Identities = 73/194 (37%), Positives = 95/194 (48%), Gaps = 39/194 (20%)
Query: 18 IGHVDHGKTTLTA------------AITKYYSEEKKEYGD--------IDSAPEEKLRGI 57
IGHVD GK+T T I KY +E KE G +D+ EE+ RG+
Sbjct: 5 IGHVDAGKSTTTGHLLYLLGGVDKRTIEKY-EKEAKEMGKGSFKYAWVLDTLKEERERGV 63
Query: 58 TIATAHVSYETDKRFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDG-------PKP 110
TI +ET+K ++ +D PGH D+V NMITGA+QAD A+LV A G
Sbjct: 64 TIDVGLAKFETEKYRFTILDAPGHRDFVPNMITGASQADVAVLVVDARKGEFEAGFEKGG 123
Query: 111 QTREHILLARQIGISSIVVYMNKVDAVDDDELLDISEY-EIRD-----LLKEHKYSDDTP 164
QTREH LLAR +G+ ++V +NK+D V + Y EI+ L K D P
Sbjct: 124 QTREHALLARTLGVKQLIVAVNKMDDVTVN--WSEERYDEIKKELSPFLKKVGYNPKDVP 181
Query: 165 IIRGSALCALQGTN 178
I S L G N
Sbjct: 182 FIPIS---GLTGDN 192
>gnl|CDD|35682 KOG0461, KOG0461, KOG0461, Selenocysteine-specific elongation
factor [Translation, ribosomal structure and
biogenesis].
Length = 522
Score = 147 bits (373), Expect = 4e-36
Identities = 86/300 (28%), Positives = 160/300 (53%), Gaps = 30/300 (10%)
Query: 12 SLGLSTIGHVDHGKTTLTAAITKYYSEEKKEYGDIDSAPEEKLRGITI----------AT 61
+L L +GHVD GKTTL A+++ S D P+ RGIT+ +
Sbjct: 7 NLNLGILGHVDSGKTTLARALSELGSTAA-----FDKHPQSTERGITLDLGFSTMTVLSP 61
Query: 62 AHVSYETDKRFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQ 121
A + + ++ ++ +DCPGHA ++ +I GA D ILV + G + QT E +++ +
Sbjct: 62 ARLP-QGEQLQFTLVDCPGHASLIRTIIGGAQIIDLMILVIDVQKGKQTQTAECLIIG-E 119
Query: 122 IGISSIVVYMNKVDAVDDDEL---LDISEYEIRDLLKEHKYSDDTPIIRGSALCALQGTN 178
+ +VV +NK+D + +++ ++ S ++R L+ + ++PI+ + A G
Sbjct: 120 LLCKKLVVVINKIDVLPENQRASKIEKSAKKVRKTLESTGFDGNSPIV---EVSAADGYF 176
Query: 179 KELGEDSIHALMKAVDTHIPTPQRSLDAPFLMHIEGSCGIEGRGTVVTGCIKRGRIKAGS 238
KE I L +A+++ I P+R + PFLM ++ I+G+GTV+TG + RG ++ +
Sbjct: 177 KEEM---IQELKEALESRIFEPKRDEEGPFLMAVDHCFAIKGQGTVLTGTVLRGVLRLNT 233
Query: 239 DVEIIGMGGKKLKVKCTDVEMFRKKLDEAIAGDNVGLLLRGVNRADVPRGRVVCAPGSIQ 298
++E + K+ KVK ++MF++++ A AGD G + + + RG + PG+++
Sbjct: 234 EIEFPALNEKR-KVK--SLQMFKQRVTSAAAGDRAGFCVTQFDEKLLERG-ICGPPGTLK 289
>gnl|CDD|58073 cd03707, EFTU_III, Domain III of elongation factor (EF) Tu. Ef-Tu
consists of three structural domains, designated I, II
and III. Domain III adopts a beta barrel structure.
Domain III is involved in binding to both charged tRNA
and binding to elongation factor Ts (EF-Ts). EF-Ts is
the guanine-nucleotide-exchange factor for EF-Tu. EF-Tu
and EF-G participate in the elongation phase during
protein biosynthesis on the ribosome. Their functional
cycles depend on GTP binding and its hydrolysis. The
EF-Tu complexed with GTP and aminoacyl-tRNA delivers
tRNA to the ribosome, whereas EF-G stimulates
translocation, a process in which tRNA and mRNA
movements occur in the ribosome. Crystallographic
studies revealed structural similarities ("molecular
mimicry") between tertiary structures of EF-G and the
EF-Tu-aminoacyl-tRNA ternary complex. Domains III, IV,
and V of EF-G mimic the tRNA structure in the EF-Tu
ternary complex; domains III, IV and V can be related to
the acceptor stem, anticodon helix and T stem of tRNA
respectively..
Length = 90
Score = 146 bits (371), Expect = 8e-36
Identities = 50/90 (55%), Positives = 66/90 (73%)
Query: 298 QEYSRFRASVYILTASEGGRTTGFMDNYRPQFFMDTADVTGRIILSPGSQAVMPGDRVDL 357
+ +++F A VY+LT EGGR T F YRPQF++ T DVTG I L G++ VMPGD V +
Sbjct: 1 KPHTKFEAEVYVLTKEEGGRHTPFFSGYRPQFYIRTTDVTGSITLPEGTEMVMPGDNVKM 60
Query: 358 EVELIYPIAMEPNQTFSMREGGKTVGAGLI 387
VELI+PIA+E F++REGG+TVGAG+I
Sbjct: 61 TVELIHPIALEKGLRFAIREGGRTVGAGVI 90
>gnl|CDD|35679 KOG0458, KOG0458, KOG0458, Elongation factor 1 alpha [Translation,
ribosomal structure and biogenesis].
Length = 603
Score = 146 bits (370), Expect = 1e-35
Identities = 110/437 (25%), Positives = 184/437 (42%), Gaps = 62/437 (14%)
Query: 10 KESLGLSTIGHVDHGKTTL------------TAAITKYYSEEKKEYGD--------IDSA 49
K+ L L +GHVD GK+TL + ++ K E K G +D
Sbjct: 175 KDHLNLVVLGHVDAGKSTLMGHLLYDLGEISSRSMHKL-ERESKNLGKSSFAYAWILDET 233
Query: 50 PEEKLRGITIATAHVSYETDKRFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDG-- 107
EE+ RG+T+ +E+ + + ID PGH D++ NMI+GA+QAD A+LV A G
Sbjct: 234 KEERERGVTMDVKTTWFESKSKIVTLIDAPGHKDFIPNMISGASQADVAVLVVDASTGEF 293
Query: 108 -----PKPQTREHILLARQIGISSIVVYMNKVDAVD-DDELLDISEYEIRDLLKEH-KYS 160
P QTREH LL R +GIS ++V +NK+D V + + + ++ LKE +
Sbjct: 294 ESGFDPGGQTREHALLLRSLGISQLIVAINKMDLVSWSQDRFEEIKNKLSSFLKESCGFK 353
Query: 161 DD----TPI--IRGSALCALQGTNKELGEDSIHALMKAVDTHIPTPQRSLDAPFLMHIEG 214
+ PI + G L ++ N+ L+ +D+ P+R +D P + I
Sbjct: 354 ESSVKFIPISGLSGENLIKIEQENELSQWYKGPTLLSQIDS-FKIPERPIDKPLRLTISD 412
Query: 215 SCGIEGRGTVVTGCIKRGRIKAGSDVEIIGMGGKKLKVKCTDVEMFRKKLDEAIAGDNVG 274
+ G ++G I+ G I+ G + I + + + A+AGDNV
Sbjct: 413 IYPLPSSGVSISGKIESGYIQPGQKLYI---MTSREDATVKGLTSNDEPKTWAVAGDNVS 469
Query: 275 LLLRGVNRADVPRGRVVCA--PGSIQEYSRFRASVYILTAS-----------EGGRTTGF 321
L L G+ V G + + I + +RF A + + G +
Sbjct: 470 LKLPGILPNLVQVGDIADSGPQFPISKTTRFVARITTFDINLPITKGSPLILHFGSLSEP 529
Query: 322 MDNYRPQFFMDTADVTGRIILSPGSQAVMPGDRVDLEVELIYPIAMEPNQT------FSM 375
+ + + + I+ + + +E+E PI +E +
Sbjct: 530 AVLKK---LTSSINKSTGEIVKKKPRCLTSNQSAIVELETERPICLETFAENRALGRVVL 586
Query: 376 REGGKTVGAGLILEIIE 392
R+ G T+ AG + EII+
Sbjct: 587 RKSGSTIAAGKVTEIIQ 603
>gnl|CDD|34854 COG5257, GCD11, Translation initiation factor 2, gamma subunit
(eIF-2gamma; GTPase) [Translation, ribosomal structure
and biogenesis].
Length = 415
Score = 140 bits (355), Expect = 6e-34
Identities = 114/412 (27%), Positives = 191/412 (46%), Gaps = 82/412 (19%)
Query: 12 SLGLSTIGHVDHGKTTLTAAITKYYSEEKKEYGDIDSAPEEKLRGITI----ATAHV--- 64
+ + +GHVDHGKTTLT A++ ++ D EE RGITI A A +
Sbjct: 10 EVNIGMVGHVDHGKTTLTKALSGVWT---------DRHSEELKRGITIKLGYADAKIYKC 60
Query: 65 -------SYETDK------------RFYSHIDCPGHADYVKNMITGATQADGAILVCAA- 104
Y T+ R S +D PGH + M++GA DGA+LV AA
Sbjct: 61 PECYRPECYTTEPKCPNCGAETELVRRVSFVDAPGHETLMATMLSGAALMDGALLVIAAN 120
Query: 105 EDGPKPQTREHILLARQIGISSIVVYMNKVDAVDDDELLDISEYEIRDLLKEHKYSDDTP 164
E P+PQTREH++ IGI +I++ NK+D V + L+ + +I++ +K +++ P
Sbjct: 121 EPCPQPQTREHLMALEIIGIKNIIIVQNKIDLVSRERALE-NYEQIKEFVKG-TVAENAP 178
Query: 165 IIRGSALCALQGTNKELGEDSIHALMKAVDTHIPTPQRSLDAPFLMHIEGSCGI------ 218
II S A N I AL++A++ +IPTP+R LD P M++ S +
Sbjct: 179 IIPIS---AQHKAN-------IDALIEAIEKYIPTPERDLDKPPRMYVARSFDVNKPGTP 228
Query: 219 --EGRGTVVTGCIKRGRIKAGSDVEI-----IGMGGK----KLKVKCTDVEMFRKKLDEA 267
E +G V+ G + +G ++ G ++EI + GGK + + ++ + ++EA
Sbjct: 229 PEELKGGVIGGSLVQGVLRVGDEIEIRPGIVVEKGGKTVWEPITTEIVSLQAGGEDVEEA 288
Query: 268 IAGDNVGL---LLRGVNRADVPRGRVVCAPGSIQE-YSRFRASVYILTASEGGRTTGFMD 323
G VG+ L + +AD G+VV PG++ ++ R ++L G + ++
Sbjct: 289 RPGGLVGVGTKLDPTLTKADALVGQVVGKPGTLPPVWTSIRIEYHLLERVVGTKEELKVE 348
Query: 324 NYRPQ----FFMDTADVTGRIILSPGSQAVMPGDRVDLEVELIYPIAMEPNQ 371
+ + TA G + + + EV+L P+ E +
Sbjct: 349 PIKTNEVLMLNVGTATTVGVVTSAKKDEI---------EVKLKRPVCAEIGE 391
>gnl|CDD|133371 cd04171, SelB, SelB subfamily. SelB is an elongation factor needed
for the co-translational incorporation of
selenocysteine. Selenocysteine is coded by a UGA stop
codon in combination with a specific downstream mRNA
hairpin. In bacteria, the C-terminal part of SelB
recognizes this hairpin, while the N-terminal part binds
GTP and tRNA in analogy with elongation factor Tu
(EF-Tu). It specifically recognizes the selenocysteine
charged tRNAsec, which has a UCA anticodon, in an EF-Tu
like manner. This allows insertion of selenocysteine at
in-frame UGA stop codons. In E. coli SelB binds GTP,
selenocysteyl-tRNAsec, and a stem-loop structure
immediately downstream of the UGA codon (the SECIS
sequence). The absence of active SelB prevents the
participation of selenocysteyl-tRNAsec in translation.
Archaeal and animal mechanisms of selenocysteine
incorporation are more complex. Although the SECIS
elements have different secondary structures and
conserved elements between archaea and eukaryotes, they
do share a common feature. Unlike in E. coli, these
SECIS elements are located in the 3' UTRs. This group
contains bacterial SelBs, as well as, one from archaea.
Length = 164
Score = 131 bits (331), Expect = 4e-31
Identities = 67/156 (42%), Positives = 88/156 (56%), Gaps = 14/156 (8%)
Query: 17 TIGHVDHGKTTLTAAITKYYSEEKKEYGDIDSAPEEKLRGITI--ATAHVSYETDKRFYS 74
T GH+DHGKTTL A+T + D PEEK RGITI A++ + KR
Sbjct: 5 TAGHIDHGKTTLIKALTGI---------ETDRLPEEKKRGITIDLGFAYLDLPSGKRL-G 54
Query: 75 HIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISSIVVYMNKV 134
ID PGH ++KNM+ GA D +LV AA++G PQTREH+ + +GI +V + K
Sbjct: 55 FIDVPGHEKFIKNMLAGAGGIDLVLLVVAADEGIMPQTREHLEILELLGIKRGLVVLTKA 114
Query: 135 DAVDDDELLDISEYEIRDLLKEHKYSDDTPIIRGSA 170
D VD+D L + E EIR+LL + D PI SA
Sbjct: 115 DLVDEDWLELVEE-EIRELLAGTFLA-DAPIFPVSA 148
>gnl|CDD|31410 COG1217, TypA, Predicted membrane GTPase involved in stress
response [Signal transduction mechanisms].
Length = 603
Score = 130 bits (329), Expect = 6e-31
Identities = 91/290 (31%), Positives = 136/290 (46%), Gaps = 22/290 (7%)
Query: 18 IGHVDHGKTTLTAAITK----YYSEEKKEYGDIDSAPEEKLRGITIATAHVSYETDKRFY 73
I HVDHGKTTL A+ K + E+ +DS EK RGITI + + +
Sbjct: 11 IAHVDHGKTTLVDALLKQSGTFREREEVAERVMDSNDLEKERGITILAKNTAVNYNGTRI 70
Query: 74 SHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISSIVVYMNK 133
+ +D PGHAD+ + + DG +L+ A +GP PQTR + A +G+ IVV +NK
Sbjct: 71 NIVDTPGHADFGGEVERVLSMVDGVLLLVDASEGPMPQTRFVLKKALALGLKPIVV-INK 129
Query: 134 VD--AVDDDELLDISEYEIRDLLKEHKYSD---DTPIIRGSALCALQGTNKELGEDSIHA 188
+D DE++D E+ DL E +D D PI+ SA + E D +
Sbjct: 130 IDRPDARPDEVVD----EVFDLFVELGATDEQLDFPIVYASARNGTASLDPEDEADDMAP 185
Query: 189 LMKAVDTHIPTPQRSLDAPFLMHIEGSCGIEGRGTVVTGCIKRGRIKAGSDVEIIGMGGK 248
L + + H+P P+ LD P M + G + G I RG +K V +I G
Sbjct: 186 LFETILDHVPAPKGDLDEPLQMQVTQLDYNSYVGRIGIGRIFRGTVKPNQQVALIKSDGT 245
Query: 249 KLKVKCTDVEMF----RKKLDEAIAGDNVGLLLRGVNRADVPRGRVVCAP 294
+ T + F R +++EA AGD V + G+ ++ G +C P
Sbjct: 246 TENGRITKLLGFLGLERIEIEEAEAGDIVA--IAGLEDINI--GDTICDP 291
>gnl|CDD|35680 KOG0459, KOG0459, KOG0459, Polypeptide release factor 3
[Translation, ribosomal structure and biogenesis].
Length = 501
Score = 129 bits (326), Expect = 1e-30
Identities = 108/445 (24%), Positives = 189/445 (42%), Gaps = 63/445 (14%)
Query: 1 MVEKRYVRN-KESLGLSTIGHVDHGKTTLTAAITKY-----------YSEEKKEYGD--- 45
+V K KE + IGHVD GK+T+ I Y E KE
Sbjct: 67 VVVKSCGEYPKEHVNAVFIGHVDAGKSTIGGNILFLTGMVDKRTLEKYEREAKEKNRESW 126
Query: 46 -----IDSAPEEKLRGITIATAHVSYETDKRFYSHIDCPGHADYVKNMITGATQADGAIL 100
+D+ EE+ +G T+ +ET+ + ++ +D PGH +V NMI GA+QAD A+L
Sbjct: 127 YLSWALDTNGEERDKGKTVEVGRAYFETENKRFTILDAPGHKSFVPNMIGGASQADLAVL 186
Query: 101 VCAAEDGP-------KPQTREHILLARQIGISSIVVYMNKVD---AVDDDELLDISEYEI 150
V +A G QTREH +LA+ G+ ++V +NK+D +E + + ++
Sbjct: 187 VISARKGEFETGFEKGGQTREHAMLAKTAGVKHLIVLINKMDDPTVNWSNERYEECKEKL 246
Query: 151 RDLLKEHKYSDDTPI--IRGSALCAL---QGTNKELGEDSIHALMKAVDTHIPTPQRSLD 205
+ L++ ++ + S L T+ ++ +D +P +R L+
Sbjct: 247 QPFLRKLGFNPKPDKHFVPVSGLTGANVKDRTDSVCPWYKGPIFLEYLDE-LPHLERILN 305
Query: 206 APFLMHIEGSCGIEGRGTVVTGCIKRGRIKAGSDVEIIGMGGKKLKVKCTDVEMFRKKLD 265
P + + GTVV G ++ G IK G + ++ K V+ + + D
Sbjct: 306 GPIRCPVANK--YKDMGTVVGGKVESGSIKKGQQLVVM---PNKTNVEVLGIYSDDVETD 360
Query: 266 EAIAGDNVGLLLRGVNRADVPRGRVVCAPGS-IQEYSRFRASVYILTASEGGR--TTGF- 321
G+NV L L+G+ D+ G ++C+P + + F A + IL E G+
Sbjct: 361 RVAPGENVKLRLKGIEEEDISPGFILCSPNNPCKSGRTFDAQIVIL---EHKSIICAGYS 417
Query: 322 --------MDNYRPQFFMDTADVTGRIILSPGSQAVMPGDRVDLEVELIYPIAMEPNQT- 372
++ + TG + V G + +E PI +E +
Sbjct: 418 CVLHIHTAVEEVEIKLIHLIDKKTGEKSKKR-PRFVKQGQKCIARLETEGPICLETFKDY 476
Query: 373 -----FSMREGGKTVGAGLILEIIE 392
F++R+ GKT+ G +L+++E
Sbjct: 477 PQMGRFTLRDEGKTIAIGKVLKVVE 501
>gnl|CDD|111981 pfam03143, GTP_EFTU_D3, Elongation factor Tu C-terminal domain.
Elongation factor Tu consists of three structural
domains, this is the third domain. This domain adopts a
beta barrel structure. This the third domain is involved
in binding to both charged tRNA and binding to EF-Ts
pfam00889.
Length = 97
Score = 127 bits (322), Expect = 5e-30
Identities = 47/97 (48%), Positives = 65/97 (67%), Gaps = 1/97 (1%)
Query: 296 SIQEYSRFRASVYILTASEGGRTTGFMDNYRPQFFMDTADVTGRIILSP-GSQAVMPGDR 354
I+ +++F+A VYIL EGG T F D Y PQF+ T DVTG+I + G + VMPGD
Sbjct: 1 PIKPHTKFKAQVYILNHPEGGGYTPFFDGYTPQFYCRTTDVTGKIKVLEEGPEFVMPGDN 60
Query: 355 VDLEVELIYPIAMEPNQTFSMREGGKTVGAGLILEII 391
+ VELI PIA+EP F++REGG+TV G++ E++
Sbjct: 61 AIVTVELIKPIAVEPGGRFAIREGGRTVAVGVVTEVL 97
>gnl|CDD|34855 COG5258, GTPBP1, GTPase [General function prediction only].
Length = 527
Score = 122 bits (307), Expect = 2e-28
Identities = 115/435 (26%), Positives = 180/435 (41%), Gaps = 75/435 (17%)
Query: 10 KESLGLSTIGHVDHGKTTLTAAITKYYSEEKK--EYGDIDSAPEEKLRGITIATAHVSY- 66
E + + GHVDHGK+TL + ++ +D E RG++ + Y
Sbjct: 115 PEHVLVGVAGHVDHGKSTLVGVLVTGRLDDGDGATRSYLDVQKHEVERGLSADISLRVYG 174
Query: 67 ----------------------ETDKRFYSHIDCPGHADYVKNMITG--ATQADGAILVC 102
+ + S +D GH +++ I G + D +LV
Sbjct: 175 FDDGKVVRLKNPLDEAEKAAVVKRADKLVSFVDTVGHEPWLRTTIRGLLGQKVDYGLLVV 234
Query: 103 AAEDGPKPQTREHILLARQIGISSIVVYMNKVDAVDDDELLDISEYEIRDLLK------- 155
AA+DG T+EH+ +A + + IVV + K+D V DD + E EI LLK
Sbjct: 235 AADDGVTKMTKEHLGIALAMELPVIVV-VTKIDMVPDDRFQGVVE-EISALLKRVGRIPL 292
Query: 156 EHKYSDD--------------TPIIRGSALCALQGTNKELGEDSIHALMKAVDTHIPTPQ 201
K +DD PI S++ T + L L+ +P +
Sbjct: 293 IVKDTDDVVLAAKAMKAGRGVVPIFYTSSV-----TGEGL------DLLDEFFLLLP-KR 340
Query: 202 RSLDA--PFLMHIEGSCGIEGRGTVVTGCIKRGRIKAGSDVEIIG--MGGKKLKVKCTDV 257
R D PFLM+I+ + G GTVV+G +K G + G V ++G GK +V +
Sbjct: 341 RRWDDEGPFLMYIDKIYSVTGVGTVVSGSVKSGILHVGDTV-LLGPFKDGKFREVVVKSI 399
Query: 258 EMFRKKLDEAIAGDNVGLLLRGVNRADVPRGRVVCAPGSIQEYSRFRASVYILTASEGGR 317
EM ++D A AG +G+ L+GV + ++ RG V+ A + F A V +L
Sbjct: 400 EMHHYRVDSAKAGSIIGIALKGVEKEELERGMVLSAGADPKAVREFDAEVLVLR-----H 454
Query: 318 TTGFMDNYRPQFFMDTADVTGRIILSPGSQAVMPGDRVDLEVELIY-PIAMEPNQTFSMR 376
T Y P F +T +MPGDR + + Y P +E Q F R
Sbjct: 455 PTTIRAGYEPVFHYETIREAVYFE-EIDKGFLMPGDRGVVRMRFKYRPHHVEEGQKFVFR 513
Query: 377 EGGKTVGAGLILEII 391
E G++ G G ++ +
Sbjct: 514 E-GRSKGVGRVIRVD 527
>gnl|CDD|32720 COG2895, CysN, GTPases - Sulfate adenylate transferase subunit 1
[Inorganic ion transport and metabolism].
Length = 431
Score = 120 bits (303), Expect = 6e-28
Identities = 93/330 (28%), Positives = 148/330 (44%), Gaps = 42/330 (12%)
Query: 8 RNKESLGLSTIGHVDHGKTTLT---------------AAITKYYSEEKKEYGDIDSA--- 49
++K L T G VD GK+TL A++ + + + ID A
Sbjct: 2 QHKSLLRFITCGSVDDGKSTLIGRLLYDTKAIYEDQLASLERDSKRKGTQGEKIDLALLV 61
Query: 50 ---PEEKLRGITIATAHVSYETDKRFYSHIDCPGHADYVKNMITGATQADGAILVCAAED 106
E+ +GITI A+ + T+KR + D PGH Y +NM TGA+ AD AIL+ A
Sbjct: 62 DGLEAEREQGITIDVAYRYFSTEKRKFIIADTPGHEQYTRNMATGASTADLAILLVDARK 121
Query: 107 GPKPQTREHILLARQIGISSIVVYMNKVDAVD-DDELLDISEYEIRDLLKEHKYSDDTPI 165
G QTR H +A +GI +VV +NK+D VD +E+ + + + D I
Sbjct: 122 GVLEQTRRHSFIASLLGIRHVVVAVNKMDLVDYSEEVFEAIVADYLAFAAQLGLKDVRFI 181
Query: 166 IRGSALCALQGTNKELGEDSI-----HALMKAVDTHIPTPQRSLDAPFLMHIE--GSCGI 218
+ AL G N +++ L++ ++T RS F ++ +
Sbjct: 182 ----PISALLGDNVVSKSENMPWYKGPTLLEILETVEIADDRSAK-AFRFPVQYVNRPNL 236
Query: 219 EGRGTVVTGCIKRGRIKAGSDVEIIGMGGKKLKVKCTDVEMFRKKLDEAIAGDNVGLLLR 278
+ RG G I G +K G +V ++ GK +VK + F +L +A AG+ V L+L
Sbjct: 237 DFRG--YAGTIASGSVKVGDEVVVLP-SGKTSRVK--RIVTFDGELAQASAGEAVTLVLA 291
Query: 279 GVNRADVPRGRVVCAPGSIQEYSR-FRASV 307
+ D+ RG ++ A + + F A V
Sbjct: 292 --DEIDISRGDLIVAADAPPAVADAFDADV 319
>gnl|CDD|58088 cd03697, EFTU_II, EFTU_II: Elongation factor Tu domain II.
Elongation factors Tu (EF-Tu) are three-domain GTPases
with an essential function in the elongation phase of
mRNA translation. The GTPase center of EF-Tu is in the
N-terminal domain (domain I), also known as the
catalytic or G-domain. The G-domain is composed of about
200 amino acid residues, arranged into a predominantly
parallel six-stranded beta-sheet core surrounded by
seven a-helices. Non-catalytic domains II and III are
beta-barrels of seven and six, respectively,
antiparallel beta-strands that share an extended
interface. Either non-catalytic domain is composed of
about 100 amino acid residues. EF-Tu proteins exist in
two principal conformations: in a compact one,
EF-Tu*GTP, with tight interfaces between all three
domains and a high affinity for aminoacyl-tRNA, and in
an open one, EF-Tu*GDP, with essentially no
G-domain-domain II interactions and a low affinity for
aminoacyl-tRNA. EF-Tu has approximately a 100-fold
higher affinity for GDP than for GTP..
Length = 87
Score = 119 bits (300), Expect = 1e-27
Identities = 56/88 (63%), Positives = 63/88 (71%), Gaps = 1/88 (1%)
Query: 208 FLMHIEGSCGIEGRGTVVTGCIKRGRIKAGSDVEIIGMGGKKLKVKCTDVEMFRKKLDEA 267
FLM IE I GRGTVVTG I+RG IK G +VEI+G G + LK T +EMFRK LDEA
Sbjct: 1 FLMPIEDVFSIPGRGTVVTGRIERGTIKVGDEVEIVGFG-ETLKTTVTGIEMFRKTLDEA 59
Query: 268 IAGDNVGLLLRGVNRADVPRGRVVCAPG 295
AGDNVG+LLRGV R DV RG V+ PG
Sbjct: 60 EAGDNVGVLLRGVKREDVERGMVLAKPG 87
>gnl|CDD|133366 cd04166, CysN_ATPS, CysN_ATPS subfamily. CysN, together with
protein CysD, form the ATP sulfurylase (ATPS) complex in
some bacteria and lower eukaryotes. ATPS catalyzes the
production of ATP sulfurylase (APS) and pyrophosphate
(PPi) from ATP and sulfate. CysD, which catalyzes ATP
hydrolysis, is a member of the ATP pyrophosphatase (ATP
PPase) family. CysN hydrolysis of GTP is required for
CysD hydrolysis of ATP; however, CysN hydrolysis of GTP
is not dependent on CysD hydrolysis of ATP. CysN is an
example of lateral gene transfer followed by acquisition
of new function. In many organisms, an ATPS exists
which is not GTP-dependent and shares no sequence or
structural similarity to CysN.
Length = 208
Score = 112 bits (282), Expect = 2e-25
Identities = 60/183 (32%), Positives = 84/183 (45%), Gaps = 26/183 (14%)
Query: 17 TIGHVDHGKTTL-------TAAI-----TKYYSEEKKEYGD-------IDSAPEEKLRGI 57
T G VD GK+TL + +I S+ G+ +D E+ +GI
Sbjct: 4 TCGSVDDGKSTLIGRLLYDSKSIFEDQLAALESKSCGTGGEPLDLALLVDGLQAEREQGI 63
Query: 58 TIATAHVSYETDKRFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHIL 117
TI A+ + T KR + D PGH Y +NM+TGA+ AD AIL+ A G QTR H
Sbjct: 64 TIDVAYRYFSTPKRKFIIADTPGHEQYTRNMVTGASTADLAILLVDARKGVLEQTRRHSY 123
Query: 118 LARQIGISSIVVYMNKVDAVDDDE--LLDISEYEIRDLLKEHKYSDDTPIIRGSALCALQ 175
+ +GI +VV +NK+D VD E +I + + D T I + AL
Sbjct: 124 ILSLLGIRHVVVAVNKMDLVDYSEEVFEEIVA-DYLAFAAKLGIEDITFI----PISALD 178
Query: 176 GTN 178
G N
Sbjct: 179 GDN 181
>gnl|CDD|133288 cd01888, eIF2_gamma, eIF2-gamma (gamma subunit of initiation factor
2). eIF2 is a heterotrimeric translation initiation
factor that consists of alpha, beta, and gamma subunits.
The GTP-bound gamma subunit also binds initiator
methionyl-tRNA and delivers it to the 40S ribosomal
subunit. Following hydrolysis of GTP to GDP, eIF2:GDP
is released from the ribosome. The gamma subunit has no
intrinsic GTPase activity, but is stimulated by the
GTPase activating protein (GAP) eIF5, and GDP/GTP
exchange is stimulated by the guanine nucleotide
exchange factor (GEF) eIF2B. eIF2B is a heteropentamer,
and the epsilon chain binds eIF2. Both eIF5 and
eIF2B-epsilon are known to bind strongly to eIF2-beta,
but have also been shown to bind directly to eIF2-gamma.
It is possible that eIF2-beta serves simply as a
high-affinity docking site for eIF5 and eIF2B-epsilon,
or that eIF2-beta serves a regulatory role. eIF2-gamma
is found only in eukaryotes and archaea. It is closely
related to SelB, the selenocysteine-specific elongation
factor from eubacteria. The translational factor
components of the ternary complex, IF2 in eubacteria and
eIF2 in eukaryotes are not the same protein (despite
their unfortunately similar names). Both factors are
GTPases; however, eubacterial IF-2 is a single
polypeptide, while eIF2 is heterotrimeric. eIF2-gamma
is a member of the same family as eubacterial IF2, but
the two proteins are only distantly related. This
family includes translation initiation, elongation, and
release factors.
Length = 203
Score = 108 bits (273), Expect = 2e-24
Identities = 67/222 (30%), Positives = 101/222 (45%), Gaps = 55/222 (24%)
Query: 15 LSTIGHVDHGKTTLTAAITKYYSEEKKEYGDIDSAPEEKLRGITI----ATAHV------ 64
+ TIGHV HGK+TL A++ ++ KE E R ITI A A +
Sbjct: 3 IGTIGHVAHGKSTLVKALSGVWTVRFKE---------ELERNITIKLGYANAKIYKCPNC 53
Query: 65 -------------SYETD----------KRFYSHIDCPGHADYVKNMITGATQADGAILV 101
S E + R S +DCPGH + M++GA DGA+L+
Sbjct: 54 GCPRPYCYRSKEDSPECECPGCGGETKLVRHVSFVDCPGHEILMATMLSGAAVMDGALLL 113
Query: 102 CAA-EDGPKPQTREHILLARQIGISSIVVYMNKVDAVDDDELLDISEYEIRDLLKEHKYS 160
AA E P+PQT EH+ +G+ I++ NK+D V +++ L+ E +I+ +K
Sbjct: 114 IAANEPCPQPQTSEHLAALEIMGLKHIIIVQNKIDLVKEEQALENYE-QIKKFVKGTIA- 171
Query: 161 DDTPIIRGSALCALQGTNKELGEDSIHALMKAVDTHIPTPQR 202
++ PII + A N I L++ + IPTP R
Sbjct: 172 ENAPII---PISAQLKYN-------IDVLLEYIVKKIPTPPR 203
>gnl|CDD|133291 cd01891, TypA_BipA, TypA (tyrosine phosphorylated protein A)/BipA
subfamily. BipA is a protein belonging to the
ribosome-binding family of GTPases and is widely
distributed in bacteria and plants. BipA was originally
described as a protein that is induced in Salmonella
typhimurium after exposure to
bactericidal/permeability-inducing protein (a cationic
antimicrobial protein produced by neutrophils), and has
since been identified in E. coli as well. The
properties thus far described for BipA are related to
its role in the process of pathogenesis by
enteropathogenic E. coli. It appears to be involved in
the regulation of several processes important for
infection, including rearrangements of the cytoskeleton
of the host, bacterial resistance to host defense
peptides, flagellum-mediated cell motility, and
expression of K5 capsular genes. It has been proposed
that BipA may utilize a novel mechanism to regulate the
expression of target genes. In addition, BipA from
enteropathogenic E. coli has been shown to be
phosphorylated on a tyrosine residue, while BipA from
Salmonella and from E. coli K12 strains is not
phosphorylated under the conditions assayed. The
phosphorylation apparently modifies the rate of
nucleotide hydrolysis, with the phosphorylated form
showing greatly increased GTPase activity.
Length = 194
Score = 98.4 bits (246), Expect = 3e-21
Identities = 65/198 (32%), Positives = 96/198 (48%), Gaps = 26/198 (13%)
Query: 18 IGHVDHGKTTLTAAITKYYSE--EKKEYGD--IDSAPEEKLRGITIATAHVSYETDKRFY 73
I HVDHGKTTL A+ K E +E + +DS E+ RGITI + +
Sbjct: 8 IAHVDHGKTTLVDALLKQSGTFRENEEVEERVMDSNDLERERGITILAKNTAVTYKDTKI 67
Query: 74 SHIDCPGHADY------VKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISSI 127
+ +D PGHAD+ V +M DG +L+ A +GP PQTR + A ++G+ I
Sbjct: 68 NIVDTPGHADFGGEVERVLSM------VDGVLLLVDASEGPMPQTRFVLKKALELGLKPI 121
Query: 128 VVYMNKVDAVDD--DELLDISEYEIRDL---LKEHKYSDDTPIIRGSALCALQGTNKELG 182
VV +NK+D D +E++D E+ DL L + D P++ SA N E
Sbjct: 122 VV-INKIDRPDARPEEVVD----EVFDLFIELGATEEQLDFPVLYASAKNGWASLNLEDP 176
Query: 183 EDSIHALMKAVDTHIPTP 200
+ + L + H+P P
Sbjct: 177 SEDLEPLFDTIIEHVPAP 194
>gnl|CDD|35683 KOG0462, KOG0462, KOG0462, Elongation factor-type GTP-binding
protein [Translation, ribosomal structure and
biogenesis].
Length = 650
Score = 97.7 bits (243), Expect = 5e-21
Identities = 77/264 (29%), Positives = 117/264 (44%), Gaps = 31/264 (11%)
Query: 7 VRNKESLGLSTIGHVDHGKTTLTAAI---TKYYSEEKKEYGDIDSAPEEKLRGITIA--T 61
+RN S I HVDHGK+TL + T + +D E+ RGITI T
Sbjct: 60 IRN-----FSIIAHVDHGKSTLADRLLELTGTIDNNIGQEQVLDKLQVERERGITIKAQT 114
Query: 62 AHVSYETDKRFYSH-IDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLAR 120
A + Y+ + + + ID PGH D+ + DGA+LV A G + QT + LA
Sbjct: 115 ASIFYKDGQSYLLNLIDTPGHVDFSGEVSRSLAACDGALLVVDASQGVQAQTVANFYLAF 174
Query: 121 QIGISSIVVYMNKVDAVDDDELLDISEYEIRDLLKEHKYSDDTPIIRGSALCALQGTNKE 180
+ G++ I V +NK+D D + E ++ +L +I SA G N E
Sbjct: 175 EAGLAIIPV-LNKIDLPSAD--PERVENQLFELFDI----PPAEVIYVSAK---TGLNVE 224
Query: 181 LGEDSIHALMKAVDTHIPTPQRSLDAPFLMHIEGSCGIEGRGTVVTGCIKRGRIKAGSDV 240
L++A+ +P P+ DAP M I S E RG + + G ++ G V
Sbjct: 225 -------ELLEAIIRRVPPPKGIRDAPLRMLIFDSEYDEYRGVIALVRVVDGVVRKGDKV 277
Query: 241 EIIGMGGKKLKVKCTDVEMFRKKL 264
+ GK +VK V + R ++
Sbjct: 278 QSAA-TGKSYEVK--VVGVMRPEM 298
>gnl|CDD|58072 cd03706, mtEFTU_III, Domain III of mitochondrial EF-TU (mtEF-TU).
mtEF-TU is highly conserved and is 55-60% identical to
bacterial EF-TU. The overall structure is similar to
that observed in the Escherichia coli and Thermus
aquaticus EF-TU. However, compared with that observed in
prokaryotic EF-TU the nucleotide-binding domain (domain
I) of EF-TUmt is in a different orientation relative to
the rest of the structure. Furthermore, domain III is
followed by a short 11-amino acid extension that forms
one helical turn. This extension seems to be specific to
the mitochondrial factors and has not been observed in
any of the prokaryotic factors..
Length = 93
Score = 94.9 bits (236), Expect = 4e-20
Identities = 36/89 (40%), Positives = 55/89 (61%)
Query: 302 RFRASVYILTASEGGRTTGFMDNYRPQFFMDTADVTGRIILSPGSQAVMPGDRVDLEVEL 361
+ A VYIL+ +EGGR F+ N++PQ F T D RI L PG + VMPG+ + + L
Sbjct: 5 KVEAQVYILSKAEGGRHKPFVSNFQPQMFSLTWDCAARIDLPPGKEMVMPGEDTKVTLIL 64
Query: 362 IYPIAMEPNQTFSMREGGKTVGAGLILEI 390
P+ +E Q F++R+G +T+G GL+ +
Sbjct: 65 RRPMVLEKGQRFTLRDGNRTIGTGLVTDT 93
>gnl|CDD|133289 cd01889, SelB_euk, SelB subfamily. SelB is an elongation factor
needed for the co-translational incorporation of
selenocysteine. Selenocysteine is coded by a UGA stop
codon in combination with a specific downstream mRNA
hairpin. In bacteria, the C-terminal part of SelB
recognizes this hairpin, while the N-terminal part binds
GTP and tRNA in analogy with elongation factor Tu
(EF-Tu). It specifically recognizes the selenocysteine
charged tRNAsec, which has a UCA anticodon, in an EF-Tu
like manner. This allows insertion of selenocysteine at
in-frame UGA stop codons. In E. coli SelB binds GTP,
selenocysteyl-tRNAsec and a stem-loop structure
immediately downstream of the UGA codon (the SECIS
sequence). The absence of active SelB prevents the
participation of selenocysteyl-tRNAsec in translation.
Archaeal and animal mechanisms of selenocysteine
incorporation are more complex. Although the SECIS
elements have different secondary structures and
conserved elements between archaea and eukaryotes, they
do share a common feature. Unlike in E. coli, these
SECIS elements are located in the 3' UTRs. This group
contains eukaryotic SelBs and some from archaea.
Length = 192
Score = 88.9 bits (221), Expect = 2e-18
Identities = 40/137 (29%), Positives = 65/137 (47%), Gaps = 20/137 (14%)
Query: 19 GHVDHGKTTLTAAITKYYSEEKKEYGDIDSAPEEKLRGITI--------------ATAHV 64
GHVD GKT+L A++ E D P+ + RGIT+ +
Sbjct: 7 GHVDSGKTSLAKALS-----EIASTAAFDKNPQSQERGITLDLGFSSFYVDKPKHLRELI 61
Query: 65 SYETDKRFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGI 124
+ + + +DCPGHA ++ +I GA D +LV A G + QT E +++ +
Sbjct: 62 NPGEENLQITLVDCPGHASLIRTIIGGAQIIDLMLLVVDATKGIQTQTAECLVIGEILCK 121
Query: 125 SSIVVYMNKVDAVDDDE 141
IVV +NK+D + ++E
Sbjct: 122 KLIVV-LNKIDLIPEEE 137
>gnl|CDD|35275 KOG0052, KOG0052, KOG0052, Translation elongation factor EF-1
alpha/Tu [Translation, ribosomal structure and
biogenesis].
Length = 391
Score = 86.6 bits (214), Expect = 1e-17
Identities = 94/326 (28%), Positives = 131/326 (40%), Gaps = 78/326 (23%)
Query: 10 KESLGLSTIGHVDHGKTTLTA----AITKYYSE----EKKEYG--------DIDSAPEEK 53
K + + IGHVD GK+T T I K E E E G +D E+
Sbjct: 5 KIHINIVVIGHVDSGKSTTTGYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAER 64
Query: 54 LRGITIATAHVSYETDKRFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDG------ 107
RGITI A +ET K + + ID PGH D++KNMITG +QAD A+L+ AA G
Sbjct: 65 ERGITIDIALWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEAGI 124
Query: 108 -PKPQTREHILLARQIGISSIVVYMNKVDAVDDDELLDISEYEIRDLLKEHKYSDDTPII 166
QTREH LLA +G+ ++V +NK+D+ E YS+
Sbjct: 125 SKNGQTREHALLAFTLGVKQLIVGVNKMDST------------------EPPYSEAR--- 163
Query: 167 RGSALCALQGTNKELGEDSIHALMKAVDTHIPTPQRSLDAPFLMHIEGSCGIEGRGTVVT 226
+ E S + +K + + D + I GI G VT
Sbjct: 164 ----------YEEIKKEVSSY--IKKIGYNPAAV--LQDVYKIGGIGVETGISEPGMDVT 209
Query: 227 GCIKRGRIKAGSDVEIIGMGGKKLKVKCTDVEMFRKKLDEAIAGDNVGLLLRGVNRADVP 286
G +VK V++ + E + GDNVG ++ V+ D+
Sbjct: 210 ----------------FAPSGVTTEVKS--VKVHHEAGSEDLPGDNVGFNVKNVSVKDID 251
Query: 287 RGRVVCAPGSIQEYSR--FRASVYIL 310
RG VV + F A V IL
Sbjct: 252 RGNVVGDSKNDPPVEAAGFTAQVIIL 277
>gnl|CDD|36360 KOG1145, KOG1145, KOG1145, Mitochondrial translation initiation
factor 2 (IF-2; GTPase) [Translation, ribosomal
structure and biogenesis].
Length = 683
Score = 86.2 bits (213), Expect = 2e-17
Identities = 83/261 (31%), Positives = 117/261 (44%), Gaps = 29/261 (11%)
Query: 18 IGHVDHGKTTLTAAITKYYSEEKKEYGDIDSAPEEKLRGIT--IATAHVSYETDKRFYSH 75
+GHVDHGKTTL A+ K S E G GIT I V+ + K +
Sbjct: 159 MGHVDHGKTTLLDALRKS-SVAAGEAG-----------GITQHIGAFTVTLPSGKSI-TF 205
Query: 76 IDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISSIVVYMNKVD 135
+D PGHA + GA D +LV AA+DG PQT E I A+ + IVV +NK+D
Sbjct: 206 LDTPGHAAFSAMRARGANVTDIVVLVVAADDGVMPQTLEAIKHAKSANV-PIVVAINKID 264
Query: 136 AVDDDELLDISEYEIRDLLKEHKYSDDTPIIRGSALCALQGTNKELGEDSIHALMKAVDT 195
+ E + ++ E D +I S AL G N +L E++I L + +D
Sbjct: 265 KPGANPEKVKRELLSQGIVVE-DLGGDVQVIPIS---ALTGENLDLLEEAILLLAEVMDL 320
Query: 196 HIPTPQRSLDAPFLMHIEGSCGIEGRGTVVTGCIKRGRIKAGSDVEIIGMGGKKLKVKCT 255
+ P + S +GRG V T +KRG +K GS V + G K++
Sbjct: 321 -----KADPKGPAEGWVIESSVDKGRGPVATVIVKRGTLKKGS-VLVAGKSWCKVR---A 371
Query: 256 DVEMFRKKLDEAIAGDNVGLL 276
+ K +DEA V +L
Sbjct: 372 LFDHNGKPIDEATPSQPVEVL 392
>gnl|CDD|35687 KOG0466, KOG0466, KOG0466, Translation initiation factor 2, gamma
subunit (eIF-2gamma; GTPase) [Translation, ribosomal
structure and biogenesis].
Length = 466
Score = 84.6 bits (209), Expect = 4e-17
Identities = 95/374 (25%), Positives = 163/374 (43%), Gaps = 81/374 (21%)
Query: 7 VRNKESLGLSTIGHVDHGKTTLTAAITKYYSEEKKEYGDIDSAPEEKLRGITI----ATA 62
+ + ++ + TIGHV HGK+T+ AI+ ++ K E R ITI A A
Sbjct: 33 ISRQATINIGTIGHVAHGKSTVVKAISGVHTVRFKN---------ELERNITIKLGYANA 83
Query: 63 HV---------------SYETDK------------------RFYSHIDCPGHADYVKNMI 89
+ S+ + K R S +DCPGH + M+
Sbjct: 84 KIYKCDDPKCPRPGCYRSFGSSKEDRPPCDRPGCEGKMKLVRHVSFVDCPGHDILMATML 143
Query: 90 TGATQADGAILVCAA-EDGPKPQTREHILLARQIGISSIVVYMNKVDAVDDDELLDISEY 148
GA D A+L+ A E P+PQT EH+ + + I++ NK+D + + + L+ E
Sbjct: 144 NGAAVMDAALLLIAGNESCPQPQTSEHLAAVEIMKLKHIIILQNKIDLIKESQALEQHE- 202
Query: 149 EIRDLLKEHKYSDDTPIIRGSALCALQGTNKELGEDSIHALMKAVDTHIPTPQRSLDAP- 207
+I+ ++ ++ PII SA +L + I + + + IP P R +P
Sbjct: 203 QIQKFIQ-GTVAEGAPIIPISA---------QLKYN-IDVVCEYIVKKIPVPVRDFTSPP 251
Query: 208 -------FLMHIEGSCGIEGRGTVVTGCIKRGRIKAGSDVEI---IGMGGKKLKVKCTD- 256
F ++ GS + +G V G I +G +K G ++EI I + +KC
Sbjct: 252 RLIVIRSFDVNKPGSEVDDLKGGVAGGSILKGVLKVGQEIEIRPGIVTKDENGNIKCRPI 311
Query: 257 ----VEMFRKK--LDEAIAGDNVGL---LLRGVNRADVPRGRVVCAPGSIQE-YSRFRAS 306
V +F ++ L A+ G +G+ + + RAD G+V+ A G++ + ++ S
Sbjct: 312 FSRIVSLFAEQNDLQFAVPGGLIGVGTKMDPTLCRADRLVGQVLGAVGTLPDIFTELEIS 371
Query: 307 VYILTASEGGRTTG 320
++L G RT G
Sbjct: 372 YFLLRRLLGVRTKG 385
>gnl|CDD|133287 cd01887, IF2_eIF5B, IF2/eIF5B (initiation factors 2/ eukaryotic
initiation factor 5B) subfamily. IF2/eIF5B contribute
to ribosomal subunit joining and function as GTPases
that are maximally activated by the presence of both
ribosomal subunits. As seen in other GTPases, IF2/IF5B
undergoes conformational changes between its GTP- and
GDP-bound states. Eukaryotic IF2/eIF5Bs possess three
characteristic segments, including a divergent
N-terminal region followed by conserved central and
C-terminal segments. This core region is conserved
among all known eukaryotic and archaeal IF2/eIF5Bs and
eubacterial IF2s.
Length = 168
Score = 82.2 bits (204), Expect = 2e-16
Identities = 57/166 (34%), Positives = 75/166 (45%), Gaps = 34/166 (20%)
Query: 18 IGHVDHGKTTLTAAITKYYSEEKKEYGDID--------SAPEEKLRGITIATAHVSYETD 69
+GHVDHGKTTL I K + E G I A K+ GIT
Sbjct: 6 MGHVDHGKTTLLDKIRKT-NVAAGEAGGITQHIGAFEVPAEVLKIPGITF---------- 54
Query: 70 KRFYSHIDCPGHADYVKNMIT-GATQADGAILVCAAEDGPKPQTREHILLARQIGISSIV 128
ID PGH + NM GA+ D AILV AA+DG PQT E I LA+ + +
Sbjct: 55 ------IDTPGHEAF-TNMRARGASLTDIAILVVAADDGVMPQTIEAIKLAKAANV-PFI 106
Query: 129 VYMNKVDAVDDDE---LLDISEYEIRDLLKEHKYSDDTPIIRGSAL 171
V +NK+D + + ++SE L E ++ D I+ SA
Sbjct: 107 VALNKIDKPNANPERVKNELSEL---GLQGEDEWGGDVQIVPTSAK 149
>gnl|CDD|30878 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 81.7 bits (202), Expect = 3e-16
Identities = 75/243 (30%), Positives = 102/243 (41%), Gaps = 38/243 (15%)
Query: 19 GHVDHGKTTLTAAITKYYSEEKKEYGDIDSAPEEKLRGIT--IATAHVSYETDK-RFYSH 75
GHVDHGKTTL I K + A E GIT I V + K +
Sbjct: 12 GHVDHGKTTLLDKIRK-----------TNVAAGEAG-GITQHIGAYQVPLDVIKIPGITF 59
Query: 76 IDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISSIVVYMNKVD 135
ID PGH + GA+ D AILV AA+DG PQT E I A+ G+ IVV +NK+D
Sbjct: 60 IDTPGHEAFTAMRARGASVTDIAILVVAADDGVMPQTIEAINHAKAAGV-PIVVAINKID 118
Query: 136 AVDDDELLDISEYEIRDLLKEHKYSDDTPIIRGSALCALQGTNKELGEDSIHALMKAVDT 195
+ + E + L+ E ++ D + S A G + + I L
Sbjct: 119 KPEANPDKVKQELQEYGLVPE-EWGGDVIFVPVS---AKTGEGIDELLELILLL------ 168
Query: 196 HIPTPQRSLDAPFLMHIEGSCGIE-----GRGTVVTGCIKRGRIKAGSDVEIIGMGGKKL 250
L A G+ IE G G V T ++ G +K G +II GG+
Sbjct: 169 ---AEVLELKANPEGPARGTV-IEVKLDKGLGPVATVIVQDGTLKKG---DIIVAGGEYG 221
Query: 251 KVK 253
+V+
Sbjct: 222 RVR 224
>gnl|CDD|30828 COG0480, FusA, Translation elongation factors (GTPases)
[Translation, ribosomal structure and biogenesis].
Length = 697
Score = 81.4 bits (201), Expect = 4e-16
Identities = 39/126 (30%), Positives = 64/126 (50%), Gaps = 10/126 (7%)
Query: 18 IGHVDHGKTTLTAAITKYYSEEKKEYGDI-------DSAPEEKLRGITIATAHVSYET-D 69
+ H+D GKTTLT I +Y+ + G++ D +E+ RGITI +A +
Sbjct: 16 VAHIDAGKTTLTERI-LFYTGIISKIGEVHDGAATMDWMEQEQERGITITSAATTLFWKG 74
Query: 70 KRFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISSIVV 129
+ ID PGH D+ + DGA++V A +G +PQT A + G+ ++
Sbjct: 75 DYRINLIDTPGHVDFTIEVERSLRVLDGAVVVVDAVEGVEPQTETVWRQADKYGV-PRIL 133
Query: 130 YMNKVD 135
++NK+D
Sbjct: 134 FVNKMD 139
>gnl|CDD|133368 cd04168, TetM_like, Tet(M)-like subfamily. Tet(M), Tet(O), Tet(W),
and OtrA are tetracycline resistance genes found in
Gram-positive and Gram-negative bacteria. Tetracyclines
inhibit protein synthesis by preventing aminoacyl-tRNA
from binding to the ribosomal acceptor site. This
subfamily contains tetracycline resistance proteins that
function through ribosomal protection and are typically
found on mobile genetic elements, such as transposons or
plasmids, and are often conjugative. Ribosomal
protection proteins are homologous to the elongation
factors EF-Tu and EF-G. EF-G and Tet(M) compete for
binding on the ribosomes. Tet(M) has a higher affinity
than EF-G, suggesting these two proteins may have
overlapping binding sites and that Tet(M) must be
released before EF-G can bind. Tet(M) and Tet(O) have
been shown to have ribosome-dependent GTPase activity.
These proteins are part of the GTP translation factor
family, which includes EF-G, EF-Tu, EF2, LepA, and SelB.
Length = 237
Score = 76.5 bits (189), Expect = 1e-14
Identities = 53/155 (34%), Positives = 84/155 (54%), Gaps = 22/155 (14%)
Query: 17 TIG---HVDHGKTTLTAAITKYYSEEKKEYGDI-------DSAPEEKLRGITIATAHVSY 66
IG HVD GKTTLT ++ Y S ++ G + D+ E+ RGITI +A S+
Sbjct: 1 NIGILAHVDAGKTTLTESLL-YTSGAIRKLGSVDKGTTRTDTMELERQRGITIFSAVASF 59
Query: 67 ETDKRFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHIL--LARQIGI 124
+ + + ID PGH D++ + + DGAILV +A +G + QTR IL L R++ I
Sbjct: 60 QWEDTKVNLIDTPGHMDFIAEVERSLSVLDGAILVISAVEGVQAQTR--ILWRLLRKLNI 117
Query: 125 SSIVVYMNKVDA--VDDDELLDISEYEIRDLLKEH 157
+I +++NK+D D +++ EI++ L
Sbjct: 118 PTI-IFVNKIDRAGADLEKVYQ----EIKEKLSSD 147
>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional.
Length = 742
Score = 76.4 bits (188), Expect = 1e-14
Identities = 71/238 (29%), Positives = 111/238 (46%), Gaps = 25/238 (10%)
Query: 18 IGHVDHGKTTLTAAITKYYSEEKKEYGDIDSAPEEKLRGITIATAHVSYETDKRFYSHID 77
+GHVDHGKTTL I K +KE G I I Y+ + + +D
Sbjct: 250 LGHVDHGKTTLLDKIRKT-QIAQKEAGGITQK-------IGAYEVEFEYKDENQKIVFLD 301
Query: 78 CPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISSIVVYMNKVDAV 137
PGH + GA D AIL+ AA+DG KPQT E I + + I+V +NK+D
Sbjct: 302 TPGHEAFSSMRSRGANVTDIAILIIAADDGVKPQTIEAINYIQAANV-PIIVAINKIDKA 360
Query: 138 DDD-ELL--DISEYEIRDLLKEHKYSDDTPIIRGSALCALQGTNKELGEDSIHALMKAVD 194
+ + E + +++Y L+ E K+ DTP+I + A QGTN + ++I L + D
Sbjct: 361 NANTERIKQQLAKYN---LIPE-KWGGDTPMI---PISASQGTNIDKLLETILLLAEIED 413
Query: 195 THIPTPQRSLDAPFLMHIEGSCGIEGRGTVVTGCIKRGRIKAGSDVEIIGMGGKKLKV 252
Q + H++ + +G V T ++ G + G D+ +IG K++
Sbjct: 414 LKADPTQLAQGIILEAHLDKT-----KGPVATILVQNGTLHIG-DIIVIGTSYAKIRG 465
>gnl|CDD|30829 COG0481, LepA, Membrane GTPase LepA [Cell envelope biogenesis,
outer membrane].
Length = 603
Score = 75.2 bits (185), Expect = 3e-14
Identities = 82/302 (27%), Positives = 134/302 (44%), Gaps = 42/302 (13%)
Query: 1 MVEKRYVRNKESLGLSTIGHVDHGKTTLTAAI---TKYYSEEKKEYGDIDSAPEEKLRGI 57
++ +RN S I H+DHGK+TL + T SE + +DS E+ RGI
Sbjct: 3 FTPQKNIRN-----FSIIAHIDHGKSTLADRLLELTGGLSEREMRAQVLDSMDIERERGI 57
Query: 58 TI----ATAHVSYETDKRFYSH-IDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQT 112
TI + + + + + ID PGH D+ + +GA+LV A G + QT
Sbjct: 58 TIKAQAVRLNYKAKDGETYVLNLIDTPGHVDFSYEVSRSLAACEGALLVVDASQGVEAQT 117
Query: 113 REHILLARQIGISSIVVYMNKVD--AVDDDELLDISEYEIRDLLKEHKYSDDTPIIRGSA 170
++ LA + + I+ +NK+D A D + + EI D++ D + + SA
Sbjct: 118 LANVYLALENNL-EIIPVLNKIDLPAADPERVKQ----EIEDIIG----IDASDAVLVSA 168
Query: 171 LCALQGTNKELGEDSIHALMKAVDTHIPTPQRSLDAPFLMHIEGSCGIEGRGTVVTGCIK 230
+ I +++A+ IP P+ DAP I S G VV I
Sbjct: 169 KTGI----------GIEDVLEAIVEKIPPPKGDPDAPLKALIFDSWYDNYLGVVVLVRIF 218
Query: 231 RGRIKAGSDVEIIGMGGKKLKVKCTDVEMF---RKKLDEAIAGDNVGLLLRGV-NRADVP 286
G +K G + ++ GK+ +V +V +F K+DE AG+ VG ++ G+ + D
Sbjct: 219 DGTLKKGDKIRMMST-GKEYEV--DEVGIFTPKMVKVDELKAGE-VGYIIAGIKDVRDAR 274
Query: 287 RG 288
G
Sbjct: 275 VG 276
>gnl|CDD|133370 cd04170, EF-G_bact, Elongation factor G (EF-G) subfamily.
Translocation is mediated by EF-G (also called
translocase). The structure of EF-G closely resembles
that of the complex between EF-Tu and tRNA. This is an
example of molecular mimicry; a protein domain evolved
so that it mimics the shape of a tRNA molecule. EF-G in
the GTP form binds to the ribosome, primarily through
the interaction of its EF-Tu-like domain with the 50S
subunit. The binding of EF-G to the ribosome in this
manner stimulates the GTPase activity of EF-G. On GTP
hydrolysis, EF-G undergoes a conformational change that
forces its arm deeper into the A site on the 30S
subunit. To accommodate this domain, the peptidyl-tRNA
in the A site moves to the P site, carrying the mRNA and
the deacylated tRNA with it. The ribosome may be
prepared for these rearrangements by the initial binding
of EF-G as well. The dissociation of EF-G leaves the
ribosome ready to accept the next aminoacyl-tRNA into
the A site. This group contains only bacterial members.
Length = 268
Score = 70.7 bits (174), Expect = 7e-13
Identities = 40/130 (30%), Positives = 61/130 (46%), Gaps = 9/130 (6%)
Query: 18 IGHVDHGKTTLTAAITKYYSEEKKEYGDI-------DSAPEEKLRGITIATAHVSYETDK 70
+GH GKTTL A+ Y + G + D PEE R ++I+T+ E
Sbjct: 5 VGHSGSGKTTLAEALL-YATGAIDRLGSVEDGTTVSDYDPEEIKRKMSISTSVAPLEWKG 63
Query: 71 RFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISSIVVY 130
+ ID PG+AD+V AD A++V +A+ G + T + A + GI I+
Sbjct: 64 HKINLIDTPGYADFVGETRAALRAADAALVVVSAQSGVEVGTEKLWEFADEAGIPRIIF- 122
Query: 131 MNKVDAVDDD 140
+NK+D D
Sbjct: 123 INKMDRERAD 132
>gnl|CDD|133285 cd01885, EF2, EF2 (for archaea and eukarya). Translocation
requires hydrolysis of a molecule of GTP and is mediated
by EF-G in bacteria and by eEF2 in eukaryotes. The
eukaryotic elongation factor eEF2 is a GTPase involved
in the translocation of the peptidyl-tRNA from the A
site to the P site on the ribosome. The 95-kDa protein
is highly conserved, with 60% amino acid sequence
identity between the human and yeast proteins. Two
major mechanisms are known to regulate protein
elongation and both involve eEF2. First, eEF2 can be
modulated by reversible phosphorylation. Increased
levels of phosphorylated eEF2 reduce elongation rates
presumably because phosphorylated eEF2 fails to bind the
ribosomes. Treatment of mammalian cells with agents
that raise the cytoplasmic Ca2+ and cAMP levels reduce
elongation rates by activating the kinase responsible
for phosphorylating eEF2. In contrast, treatment of
cells with insulin increases elongation rates by
promoting eEF2 dephosphorylation. Second, the protein
can be post-translationally modified by
ADP-ribosylation. Various bacterial toxins perform this
reaction after modification of a specific histidine
residue to diphthamide, but there is evidence for
endogenous ADP ribosylase activity. Similar to the
bacterial toxins, it is presumed that modification by
the endogenous enzyme also inhibits eEF2 activity.
Length = 222
Score = 70.3 bits (173), Expect = 8e-13
Identities = 42/136 (30%), Positives = 66/136 (48%), Gaps = 19/136 (13%)
Query: 16 STIGHVDHGKTTLT-AAITKYYSEEKKEYGDI---DSAPEEKLRGITIATAHVS--YETD 69
I HVDHGKTTL+ + + +K G DS +E+ RGIT+ ++ +S +E +
Sbjct: 4 CIIAHVDHGKTTLSDSLLASAGIISEKLAGKARYMDSREDEQERGITMKSSAISLYFEYE 63
Query: 70 KRFYSH--------IDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQ 121
+ + ID PGH D+ + DGA++V A +G QT +L RQ
Sbjct: 64 EEDKADGNEYLINLIDSPGHVDFSSEVTAALRLCDGALVVVDAVEGVCVQT--ETVL-RQ 120
Query: 122 IGISSI--VVYMNKVD 135
+ V+ +NK+D
Sbjct: 121 ALKERVKPVLVINKID 136
>gnl|CDD|58087 cd03696, selB_II, selB_II: this subfamily represents the domain of
elongation factor SelB, homologous to domain II of
EF-Tu. SelB may function by replacing EF-Tu. In
prokaryotes, the incorporation of selenocysteine as the
21st amino acid, encoded by TGA, requires several
elements: SelC is the tRNA itself, SelD acts as a donor
of reduced selenium, SelA modifies a serine residue on
SelC into selenocysteine, and SelB is a
selenocysteine-specific translation elongation factor.
3' or 5' non-coding elements of mRNA have been found as
probable structures for directing selenocysteine
incorporation..
Length = 83
Score = 69.0 bits (169), Expect = 2e-12
Identities = 32/86 (37%), Positives = 54/86 (62%), Gaps = 3/86 (3%)
Query: 208 FLMHIEGSCGIEGRGTVVTGCIKRGRIKAGSDVEIIGMGGKKLKVKCTDVEMFRKKLDEA 267
F + I+ ++G+GTVVTG + G +K G VEI+ +G ++ +V+ +++ K ++EA
Sbjct: 1 FRLPIDRVFTVKGQGTVVTGTVLSGSVKVGDKVEILPLG-EETRVR--SIQVHGKDVEEA 57
Query: 268 IAGDNVGLLLRGVNRADVPRGRVVCA 293
AGD V L L GV+ D+ RG V+ +
Sbjct: 58 KAGDRVALNLTGVDAKDLERGDVLSS 83
>gnl|CDD|35686 KOG0465, KOG0465, KOG0465, Mitochondrial elongation factor
[Translation, ribosomal structure and biogenesis].
Length = 721
Score = 66.8 bits (163), Expect = 9e-12
Identities = 41/127 (32%), Positives = 62/127 (48%), Gaps = 13/127 (10%)
Query: 18 IGHVDHGKTTLTAAITKYYSEEKKEYGDI-------DSAPEEKLRGITIATAHVSYETDK 70
H+D GKTTLT + YY+ K G++ DS E+ RGITI +A +
Sbjct: 45 SAHIDAGKTTLTERML-YYTGRIKHIGEVRGGGATMDSMELERQRGITIQSAATYFTWRD 103
Query: 71 RFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISSI--V 128
+ ID PGH D+ + DGA+LV A G + QT + RQ+ ++ +
Sbjct: 104 YRINIIDTPGHVDFTFEVERALRVLDGAVLVLDAVAGVESQT---ETVWRQMKRYNVPRI 160
Query: 129 VYMNKVD 135
++NK+D
Sbjct: 161 CFINKMD 167
>gnl|CDD|33865 COG4108, PrfC, Peptide chain release factor RF-3 [Translation,
ribosomal structure and biogenesis].
Length = 528
Score = 66.8 bits (163), Expect = 1e-11
Identities = 48/170 (28%), Positives = 74/170 (43%), Gaps = 19/170 (11%)
Query: 18 IGHVDHGKTTLTAAITKYYSEEKKEYGDI-----------DSAPEEKLRGITIATAHVSY 66
I H D GKTTLT + + +E G + D EK RGI++ ++ + +
Sbjct: 18 ISHPDAGKTTLTEKLL-LFGGAIQEAGTVKGRKSGKHAKSDWMEIEKQRGISVTSSVMQF 76
Query: 67 ETDKRFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISS 126
+ + +D PGH D+ ++ T D A++V A G +PQT + + R I
Sbjct: 77 DYADCLVNLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKGIEPQTLKLFEVCRLRDI-P 135
Query: 127 IVVYMNKVDAVDDD--ELLDISEYEIRDLLKEHKYSDDTPIIRGSALCAL 174
I ++NK+D D ELLD EI + L PI G +
Sbjct: 136 IFTFINKLDREGRDPLELLD----EIEEELGIQCAPITWPIGMGKDFKGV 181
>gnl|CDD|145992 pfam03144, GTP_EFTU_D2, Elongation factor Tu domain 2. Elongation
factor Tu consists of three structural domains, this is
the second domain. This domain adopts a beta barrel
structure. This the second domain is involved in binding
to charged tRNA. This domain is also found in other
proteins such as elongation factor G and translation
initiation factor IF-2. This domain is structurally
related to pfam03143, and in fact has weak sequence
matches to this domain.
Length = 70
Score = 64.6 bits (158), Expect = 4e-11
Identities = 29/71 (40%), Positives = 40/71 (56%), Gaps = 1/71 (1%)
Query: 222 GTVVTGCIKRGRIKAGSDVEIIGMGGKKLKVKCTDVEMFRKKLDEAIAGDNVGLLLRGVN 281
GTV TG ++ G +K G V I G K K + T +EMF L EA+AG N G++L G+
Sbjct: 1 GTVATGRVESGTLKKGDKVVIGPNGTGK-KGRVTSLEMFHGDLREAVAGANAGIILAGIG 59
Query: 282 RADVPRGRVVC 292
D+ RG +
Sbjct: 60 LKDIKRGDTLT 70
>gnl|CDD|133367 cd04167, Snu114p, Snu114p subfamily. Snu114p is one of several
proteins that make up the U5 small nuclear
ribonucleoprotein (snRNP) particle. U5 is a component
of the spliceosome, which catalyzes the splicing of
pre-mRNA to remove introns. Snu114p is homologous to
EF-2, but typically contains an additional N-terminal
domain not found in Ef-2. This protein is part of the
GTP translation factor family and the Ras superfamily,
characterized by five G-box motifs.
Length = 213
Score = 63.8 bits (156), Expect = 8e-11
Identities = 36/131 (27%), Positives = 59/131 (45%), Gaps = 15/131 (11%)
Query: 18 IGHVDHGKTTLTAAITKYYSEEKKEYGDIDSAPE--------EKLRGITIATAHVSY-ET 68
GH+ HGKT+L + + + G P E+ RGI+I ++ +S
Sbjct: 6 AGHLHHGKTSLLDMLI-EQTHDLTPSGKDGWKPLRYTDIRKDEQERGISIKSSPISLVLP 64
Query: 69 DKRFYSH----IDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGI 124
D + S+ ID PGH +++ + +DG +LV +G T I A G+
Sbjct: 65 DSKGKSYLFNIIDTPGHVNFMDEVAAALRLSDGVVLVVDVVEGVTSNTERLIRHAILEGL 124
Query: 125 SSIVVYMNKVD 135
IV+ +NK+D
Sbjct: 125 -PIVLVINKID 134
>gnl|CDD|35688 KOG0467, KOG0467, KOG0467, Translation elongation factor 2/ribosome
biogenesis protein RIA1 and related proteins
[Translation, ribosomal structure and biogenesis].
Length = 887
Score = 63.9 bits (155), Expect = 8e-11
Identities = 38/137 (27%), Positives = 67/137 (48%), Gaps = 10/137 (7%)
Query: 3 EKRYVRNKESLGLSTIGHVDHGKTTLT----AAITKYYSEEKKEYGDIDSAPEEKLRGIT 58
+RN + + HVDHGKT+L A+ S + +D+ +E+ RGIT
Sbjct: 5 GSEGIRN-----ICLVAHVDHGKTSLADSLVASNGVISSRLAGKIRFLDTREDEQTRGIT 59
Query: 59 IATAHVSYETDKRFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILL 118
+ ++ +S + ID PGH D+ + + + +DGA+++ +G QT +
Sbjct: 60 MKSSAISLLHKDYLINLIDSPGHVDFSSEVSSASRLSDGALVLVDVVEGVCSQTYAVLRQ 119
Query: 119 ARQIGISSIVVYMNKVD 135
A G+ I+V +NK+D
Sbjct: 120 AWIEGLKPILV-INKID 135
>gnl|CDD|58084 cd03693, EF1_alpha_II, EF1_alpha_II: this family represents the
domain II of elongation factor 1-alpha (EF-1a) that is
found in archaea and all eukaryotic lineages. EF-1A is
very abundant in the cytosol, where it is involved in
the GTP-dependent binding of aminoacyl-tRNAs to the A
site of the ribosomes in the second step of translation
from mRNAs to proteins. Both domain II of EF1A and
domain IV of IF2/eIF5B have been implicated in
recognition of the 3'-ends of tRNA. More than 61% of
eukaryotic elongation factor 1A (eEF-1A) in cells is
estimated to be associated with actin cytoskeleton. The
binding of eEF1A to actin is a noncanonical function
that may link two distinct cellular processes,
cytoskeleton organization and gene expression..
Length = 91
Score = 62.8 bits (153), Expect = 2e-10
Identities = 32/91 (35%), Positives = 46/91 (50%), Gaps = 3/91 (3%)
Query: 205 DAPFLMHIEGSCGIEGRGTVVTGCIKRGRIKAGSDVEIIGMGGKKLKVKCTDVEMFRKKL 264
D P + I+ I G GTV G ++ G +K G V G +VK VEM + L
Sbjct: 2 DKPLRLPIQDVYKIGGIGTVPVGRVETGVLKPGMVV-TFAPAGVTGEVK--SVEMHHEPL 58
Query: 265 DEAIAGDNVGLLLRGVNRADVPRGRVVCAPG 295
+EA+ GDNVG ++ V++ D+ RG V
Sbjct: 59 EEALPGDNVGFNVKNVSKKDIKRGDVAGDSK 89
>gnl|CDD|35690 KOG0469, KOG0469, KOG0469, Elongation factor 2 [Translation,
ribosomal structure and biogenesis].
Length = 842
Score = 61.5 bits (149), Expect = 3e-10
Identities = 50/157 (31%), Positives = 73/157 (46%), Gaps = 30/157 (19%)
Query: 1 MVEKRYVRNKESLGLSTIGHVDHGKTTLT-AAITKYYSEEKKEYGD---IDSAPEEKLRG 56
M +K+ +RN +S I HVDHGK+TLT + + K + G+ D+ +E+ RG
Sbjct: 13 MDKKKNIRN-----MSVIAHVDHGKSTLTDSLVQKAGIISAAKAGETRFTDTRKDEQERG 67
Query: 57 ITIATAHVSY-----ETDKRFYSH-----------IDCPGHADYVKNMITGATQADGAIL 100
ITI + +S + D +F ID PGH D+ + DGA++
Sbjct: 68 ITIKSTAISLFFEMSDDDLKFIKQEGDGNGFLINLIDSPGHVDFSSEVTAALRVTDGALV 127
Query: 101 VCAAEDGPKPQTREHILLARQIGISSI--VVYMNKVD 135
V G QT E +L RQ I V+ MNK+D
Sbjct: 128 VVDCVSGVCVQT-ETVL--RQAIAERIKPVLVMNKMD 161
>gnl|CDD|58069 cd01513, Translation_factor_III, Domain III of Elongation factor
(EF) Tu (EF-TU) and EF-G. Elongation factors (EF) EF-Tu
and EF-G participate in the elongation phase during
protein biosynthesis on the ribosome. Their functional
cycles depend on GTP binding and its hydrolysis. The
EF-Tu complexed with GTP and aminoacyl-tRNA delivers
tRNA to the ribosome, whereas EF-G stimulates
translocation, a process in which tRNA and mRNA
movements occur in the ribosome. Experimental data
showed that: (1) intrinsic GTPase activity of EF-G is
influenced by excision of its domain III; (2) that EF-G
lacking domain III has a 1,000-fold decreased GTPase
activity on the ribosome and, a slightly decreased
affinity for GTP; and (3) EF-G lacking domain III does
not stimulate translocation, despite the physical
presence of domain IV which is also very important for
translocation. These findings indicate an essential
contribution of domain III to activation of GTP
hydrolysis. Domains III and V of EF-G have the same fold
(although they are not completely superimposable), the
double split beta-alpha-beta fold. This fold is observed
in a large number of ribonucleotide binding proteins and
is also referred to as the ribonucleoprotein (RNP) or
RNA recognition (RRM) motif. This domain III is found
in several elongation factors, as well as in peptide
chain release factors and in GT-1 family of GTPase
(GTPBP1)..
Length = 102
Score = 58.8 bits (142), Expect = 2e-09
Identities = 34/107 (31%), Positives = 49/107 (45%), Gaps = 22/107 (20%)
Query: 298 QEYSRFRASVYILTASEGGRTTGFMDNYRPQFFMDTADVTGRIILSP-----------GS 346
Q +F A +Y+L E Y+P + TA V GRI
Sbjct: 1 QAVDKFVAEIYVLDHPEP-----LSPGYKPVLNVGTAHVPGRIAKLLSKVDGKTEEKKPP 55
Query: 347 QAVMPGDRVDLEVELIYPIAME------PNQTFSMREGGKTVGAGLI 387
+ + G+R +EVEL P+A+E F++R+GG+TVGAGLI
Sbjct: 56 EFLKSGERGIVEVELQKPVALETFSENQEGGRFALRDGGRTVGAGLI 102
>gnl|CDD|133290 cd01890, LepA, LepA subfamily. LepA belongs to the GTPase family
of and exhibits significant homology to the translation
factors EF-G and EF-Tu, indicating its possible
involvement in translation and association with the
ribosome. LepA is ubiquitous in bacteria and eukaryota
(e.g. yeast GUF1p), but is missing from archaea. This
pattern of phyletic distribution suggests that LepA
evolved through a duplication of the EF-G gene in
bacteria, followed by early transfer into the eukaryotic
lineage, most likely from the promitochondrial
endosymbiont. Yeast GUF1p is not essential and mutant
cells did not reveal any marked phenotype.
Length = 179
Score = 57.5 bits (140), Expect = 6e-09
Identities = 42/135 (31%), Positives = 66/135 (48%), Gaps = 23/135 (17%)
Query: 16 STIGHVDHGKTTL-------TAAITKYYSEEKKEYGDIDSAPEEKLRGITI----ATAHV 64
S I H+DHGK+TL T ++K E K++ +DS E+ RGITI +
Sbjct: 4 SIIAHIDHGKSTLADRLLELTGTVSK--REMKEQV--LDSMDLERERGITIKAQTVRLNY 59
Query: 65 SYETDKRFYSH-IDCPGHADY---VKNMITGATQADGAILVCAAEDGPKPQTREHILLAR 120
+ + + + ID PGH D+ V + +GA+L+ A G + QT + LA
Sbjct: 60 KAKDGQEYLLNLIDTPGHVDFSYEVSRSLAA---CEGALLLVDATQGVEAQTLANFYLAL 116
Query: 121 QIGISSIVVYMNKVD 135
+ + I V +NK+D
Sbjct: 117 ENNLEIIPV-INKID 130
>gnl|CDD|35685 KOG0464, KOG0464, KOG0464, Elongation factor G [Translation,
ribosomal structure and biogenesis].
Length = 753
Score = 56.7 bits (136), Expect = 1e-08
Identities = 41/130 (31%), Positives = 60/130 (46%), Gaps = 13/130 (10%)
Query: 15 LSTIGHVDHGKTTLTAAITKYYSEEKKEYGDIDSA-------PEEKLRGITIATAHVSYE 67
+ I H+D GKTT T I Y + GD+D E+ RGITI +A V+++
Sbjct: 40 IGIIAHIDAGKTTTTERIL-YLAGAIHSAGDVDDGDTVTDFLAIERERGITIQSAAVNFD 98
Query: 68 TDKRFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISSI 127
+ ID PGH D+ + DGA+ V A G + QT + + RQ I
Sbjct: 99 WKGHRINLIDTPGHVDFRLEVERCLRVLDGAVAVFDASAGVEAQT---LTVWRQADKFKI 155
Query: 128 --VVYMNKVD 135
++NK+D
Sbjct: 156 PAHCFINKMD 165
>gnl|CDD|58078 cd01342, Translation_Factor_II_like, Translation_Factor_II_like:
Elongation factor Tu (EF-Tu) domain II-like proteins.
Elongation factor Tu consists of three structural
domains, this family represents the second domain.
Domain II adopts a beta barrel structure and is involved
in binding to charged tRNA. Domain II is found in other
proteins such as elongation factor G and translation
initiation factor IF-2. This group also includes the C2
subdomain of domain IV of IF-2 that has the same fold as
domain II of (EF-Tu). Like IF-2 from certain prokaryotes
such as Thermus thermophilus, mitochondrial IF-2 lacks
domain II, which is thought to be involved in binding
of E.coli IF-2 to 30S subunits..
Length = 83
Score = 55.3 bits (133), Expect = 2e-08
Identities = 27/86 (31%), Positives = 45/86 (52%), Gaps = 3/86 (3%)
Query: 208 FLMHIEGSCGIEGRGTVVTGCIKRGRIKAGSDVEIIGMGGKKLKVKCTDVEMFRKKLDEA 267
+ +GRGTV TG ++ G +K G V + GG K K ++ F+ ++DEA
Sbjct: 1 LRALVFKVFKDKGRGTVATGRVESGTLKKGDKVRVGPGGGGV-KGKVKSLKRFKGEVDEA 59
Query: 268 IAGDNVGLLLRGVNRADVPRGRVVCA 293
+AGD VG++L+ + D+ G +
Sbjct: 60 VAGDIVGIVLKDKD--DIKIGDTLTD 83
>gnl|CDD|133286 cd01886, EF-G, Elongation factor G (EF-G) subfamily. Translocation
is mediated by EF-G (also called translocase). The
structure of EF-G closely resembles that of the complex
between EF-Tu and tRNA. This is an example of molecular
mimicry; a protein domain evolved so that it mimics the
shape of a tRNA molecule. EF-G in the GTP form binds to
the ribosome, primarily through the interaction of its
EF-Tu-like domain with the 50S subunit. The binding of
EF-G to the ribosome in this manner stimulates the
GTPase activity of EF-G. On GTP hydrolysis, EF-G
undergoes a conformational change that forces its arm
deeper into the A site on the 30S subunit. To
accommodate this domain, the peptidyl-tRNA in the A site
moves to the P site, carrying the mRNA and the
deacylated tRNA with it. The ribosome may be prepared
for these rearrangements by the initial binding of EF-G
as well. The dissociation of EF-G leaves the ribosome
ready to accept the next aminoacyl-tRNA into the A site.
This group contains both eukaryotic and bacterial
members.
Length = 270
Score = 55.6 bits (135), Expect = 2e-08
Identities = 43/130 (33%), Positives = 63/130 (48%), Gaps = 19/130 (14%)
Query: 18 IGHVDHGKTTLTAAITKYYSEEKKEYGDI-------DSAPEEKLRGITIATAHVSYE-TD 69
I H+D GKTT T I YY+ + G++ D +E+ RGITI +A + D
Sbjct: 5 IAHIDAGKTTTTERIL-YYTGRIHKIGEVHGGGATMDFMEQERERGITIQSAATTCFWKD 63
Query: 70 KRFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQT----REHILLARQIGIS 125
R + ID PGH D+ + DGA+ V A G +PQT R+ A + +
Sbjct: 64 HRI-NIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVAGVEPQTETVWRQ----ADRYNVP 118
Query: 126 SIVVYMNKVD 135
I ++NK+D
Sbjct: 119 RI-AFVNKMD 127
>gnl|CDD|133369 cd04169, RF3, RF3 subfamily. Peptide chain release factor 3 (RF3)
is a protein involved in the termination step of
translation in bacteria. Termination occurs when class
I release factors (RF1 or RF2) recognize the stop codon
at the A-site of the ribosome and activate the release
of the nascent polypeptide. The class II release factor
RF3 then initiates the release of the class I RF from
the ribosome. RF3 binds to the RF/ribosome complex in
the inactive (GDP-bound) state. GDP/GTP exchange
occurs, followed by the release of the class I RF.
Subsequent hydrolysis of GTP to GDP triggers the release
of RF3 from the ribosome. RF3 also enhances the
efficiency of class I RFs at less preferred stop codons
and at stop codons in weak contexts.
Length = 267
Score = 53.7 bits (130), Expect = 8e-08
Identities = 47/151 (31%), Positives = 73/151 (48%), Gaps = 19/151 (12%)
Query: 18 IGHVDHGKTTLTAAITKYYSEEKKEYGDIDSAPE-----------EKLRGITIATAHVSY 66
I H D GKTTLT + + +E G + + EK RGI++ ++ + +
Sbjct: 8 ISHPDAGKTTLTEKLL-LFGGAIREAGAVKARKSRKHATSDWMEIEKQRGISVTSSVMQF 66
Query: 67 ETDKRFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISS 126
E + +D PGH D+ ++ T D A++V A G +PQTR+ + R GI
Sbjct: 67 EYRDCVINLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKGVEPQTRKLFEVCRLRGI-P 125
Query: 127 IVVYMNKVD--AVDDDELLDISEYEIRDLLK 155
I+ ++NK+D D ELLD EI + L
Sbjct: 126 IITFINKLDREGRDPLELLD----EIEEELG 152
>gnl|CDD|35689 KOG0468, KOG0468, KOG0468, U5 snRNP-specific protein [Translation,
ribosomal structure and biogenesis].
Length = 971
Score = 53.5 bits (128), Expect = 9e-08
Identities = 30/132 (22%), Positives = 54/132 (40%), Gaps = 15/132 (11%)
Query: 18 IGHVDHGKTTLTAAITKY-----YSEEKKEYGDIDSAPEEKLRGITIATAHVSY-----E 67
+GH+ HGKT L + + + + D+ E+ RG +I + V+ +
Sbjct: 134 VGHLHHGKTALMDLLVEQTHPDFSKNTEADLRYTDTLFYEQERGCSIKSTPVTLVLSDSK 193
Query: 68 TDKRFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISS- 126
+ +D PGH ++ +DG +LV +G T + + +
Sbjct: 194 GKSYLMNILDTPGHVNFSDETTASLRLSDGVVLVVDVAEGVMLNTE---RIIKHAIQNRL 250
Query: 127 -IVVYMNKVDAV 137
IVV +NKVD +
Sbjct: 251 PIVVVINKVDRL 262
>gnl|CDD|35684 KOG0463, KOG0463, KOG0463, GTP-binding protein GP-1 [General
function prediction only].
Length = 641
Score = 47.4 bits (112), Expect = 7e-06
Identities = 74/343 (21%), Positives = 130/343 (37%), Gaps = 28/343 (8%)
Query: 67 ETDKRFYSHIDCPGHADYVKNMITGAT--QADGAILVCAAEDGPKPQTREHILLARQIGI 124
E + + ID GH Y+K + G T D +L+ A G T+EH+ LA + +
Sbjct: 215 EDSAKVITFIDLAGHEKYLKTTVFGMTGHMPDFTMLMIGANAGIIGMTKEHLGLALALHV 274
Query: 125 SSIVVYMNKVDAVDDDELLDISEYEIRDLLKEHKYSDDTPIIRGSALCALQGTN------ 178
VV + K+D + +L + + LLK ++R N
Sbjct: 275 PVFVV-VTKIDMCPAN-ILQETMKLLTRLLKSPGCRKLPVLVRSMDDVVHAAVNFPSERV 332
Query: 179 ------KELGEDSIHALMKAVDTHIPTPQRSLDAPFLMHIEGSCGIEGRGTVVTGCIKRG 232
+ ++ L ++ Q + + P I+ + G GTVV+G + G
Sbjct: 333 CPIFQVSNVTGTNLPLLKMFLNLLSLRRQLNENDPAEFQIDDIYWVPGVGTVVSGTLLSG 392
Query: 233 RIKAGSDVEIIG--MGGKKLKVKCTDVEMFRKKLDEAIAGDNVGLLLRGVNRADVPRGRV 290
I+ +D+ ++G G + + + R + G L+ + R DV +G V
Sbjct: 393 TIRL-NDILLLGPDSNGDFMPIPIKSIHRKRMPVGIVRCGQTASFALKKIKRKDVRKGMV 451
Query: 291 VCAPG-SIQEYSRFRASVYILTASEGGRTTGFMDNYRPQFFMDTADVTGRIILSPGSQAV 349
+ +P Q F A + +L T Y+ + T I+ S G +
Sbjct: 452 MVSPKLKPQASWEFEAEILVLH-----HPTTISPRYQAMVHCGSIRQTATIV-SMGKDCL 505
Query: 350 MPGDRVDLEVELI-YPIAMEPNQTFSMREGGKTVGAGLILEII 391
GD+ ++ I P + P Q RE G+T G I ++
Sbjct: 506 RTGDKAKVQFRFIKQPEYIRPGQRLVFRE-GRTKAVGTISSVL 547
>gnl|CDD|133256 cd00880, Era_like, Era (E. coli Ras-like protein)-like. This
family includes several distinct subfamilies (TrmE/ThdF,
FeoB, YihA (EngG), Era, and EngA/YfgK) that generally
show sequence conservation in the region between the
Walker A and B motifs (G1 and G3 box motifs), to the
exclusion of other GTPases. TrmE is ubiquitous in
bacteria and is a widespread mitochondrial protein in
eukaryotes, but is absent from archaea. The yeast member
of TrmE family, MSS1, is involved in mitochondrial
translation; bacterial members are often present in
translation-related operons. FeoB represents an unusual
adaptation of GTPases for high-affinity iron (II)
transport. YihA (EngB) family of GTPases is typified by
the E. coli YihA, which is an essential protein involved
in cell division control. Era is characterized by a
distinct derivative of the KH domain (the pseudo-KH
domain) which is located C-terminal to the GTPase
domain. EngA and its orthologs are composed of two
GTPase domains and, since the sequences of the two
domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family.
Length = 163
Score = 44.6 bits (106), Expect = 5e-05
Identities = 21/87 (24%), Positives = 39/87 (44%), Gaps = 8/87 (9%)
Query: 92 ATQADGAILVCAAEDGPKPQTREHILLARQIGISSIVVYMNKVDAVDDDELLDISEYEIR 151
+AD + V A+ + + + L R+ G ++V NK+D + ++E ++ E +
Sbjct: 73 LERADLILFVVDADLRADEEEEKLLELLRERGKPVLLVL-NKIDLLPEEEEEELLELRLL 131
Query: 152 DLLKEHKYSDDTPIIRGSALCALQGTN 178
LL P+I A+ AL G
Sbjct: 132 ILLLLLGL----PVI---AVSALTGEG 151
>gnl|CDD|36359 KOG1144, KOG1144, KOG1144, Translation initiation factor 5B
(eIF-5B) [Translation, ribosomal structure and
biogenesis].
Length = 1064
Score = 42.7 bits (100), Expect = 2e-04
Identities = 44/148 (29%), Positives = 59/148 (39%), Gaps = 11/148 (7%)
Query: 18 IGHVDHGKTTLTAAITKYYSEEKKEYGDIDSA------PEEKLRGIT-IATAHVSYETDK 70
+GHVD GKT L I +E E G I P E +R T
Sbjct: 481 LGHVDTGKTKLLDKIRGTNVQEG-EAGGITQQIGATYFPAENIREKTKELKKDAKKRLKV 539
Query: 71 RFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISSIVVY 130
ID PGH + G++ D AILV G +PQT E I L R + +V
Sbjct: 540 PGLLVIDTPGHESFTNLRSRGSSLCDLAILVVDIMHGLEPQTIESINLLRMRK-TPFIVA 598
Query: 131 MNKVDAVDDDELLDISEYEIRDLLKEHK 158
+NK+D + + I + LK+ K
Sbjct: 599 LNKIDRLYGWK--SCPNAPIVEALKKQK 624
>gnl|CDD|31354 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 41.3 bits (97), Expect = 5e-04
Identities = 51/198 (25%), Positives = 83/198 (41%), Gaps = 30/198 (15%)
Query: 15 LSTIGHVDHGKTTLTAAITKYYSEEKKEYGDIDSAPEEKLRGITIATAHVSYETDKRFYS 74
++ IG + GK++L AI EE+ DI G T + + +E D R Y
Sbjct: 181 IAIIGRPNVGKSSLINAILG---EERVIVSDIA--------GTTRDSIDIEFERDGRKYV 229
Query: 75 HIDCPGH------ADYVKNMITGATQ-----ADGAILVCAAEDGPKPQTREHILLARQIG 123
ID G + V+ T AD +LV A +G Q L + G
Sbjct: 230 LIDTAGIRRKGKITESVEKYSVARTLKAIERADVVLLVIDATEGISEQDLRIAGLIEEAG 289
Query: 124 ISSIVVYMNKVDAVDDDEL-LDISEYEIRDLLKEHKYSDDTPIIRGSALCALQGTNKELG 182
++V +NK D V++DE ++ + ++R L ++ PI+ SAL QG +K
Sbjct: 290 RGIVIV-VNKWDLVEEDEATMEEFKKKLRRKLPFLDFA---PIVFISALTG-QGLDKLF- 343
Query: 183 EDSIHALMKAVDTHIPTP 200
++I + + I T
Sbjct: 344 -EAIKEIYECATRRISTS 360
Score = 27.5 bits (61), Expect = 6.8
Identities = 14/55 (25%), Positives = 25/55 (45%), Gaps = 3/55 (5%)
Query: 94 QADGAILVCAAEDGPKPQTREHILLARQIGISSIVVYMNKVDAVDDDELLDISEY 148
+AD + V +G P E + R+ I+V +NK+D + +E E+
Sbjct: 83 EADVILFVVDGREGITPADEEIAKILRRSKKPVILV-VNKIDNLKAEE--LAYEF 134
>gnl|CDD|58096 cd04089, eRF3_II, eRF3_II: domain II of the eukaryotic class II
release factor (eRF3). In eukaryotes, translation
termination is mediated by two interacting release
factors, eRF1 and eRF3, which act as class I and II
factors, respectively. eRF1 functions as an omnipotent
release factor, decoding all three stop codons and
triggering the release of the nascent peptide catalyzed
by the ribsome. eRF3 is a GTPase, which enhances the
termination efficiency by stimulating the eRF1 activity
in a GTP-dependent manner. Sequence comparison of class
II release factors with elongation factors shows that
eRF3 is more similar to eEF1alpha whereas prokaryote RF3
is more similar to EF-G, implying that their precise
function may differ. Only eukaryote RF3s are found in
this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a
translation termination factor which is divided into
three regions N, M and a C-terminal eEF1a-like region
essential for translation termination. Sup35NM is a
non-pathogenic prion-like protein with the property of
aggregating into polymer-like fibrils..
Length = 82
Score = 39.3 bits (92), Expect = 0.002
Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 3/72 (4%)
Query: 221 RGTVVTGCIKRGRIKAGSDVEIIGMGGKKLKVKCTDVEMFRKKLDEAIAGDNVGLLLRGV 280
GTVV G ++ G IK G + ++ K +V+ + ++ A G+NV L L+G+
Sbjct: 13 MGTVVLGKVESGTIKKGDKLLVMP---NKTQVEVLSIYNEDVEVRYARPGENVRLRLKGI 69
Query: 281 NRADVPRGRVVC 292
D+ G V+C
Sbjct: 70 EEEDISPGFVLC 81
>gnl|CDD|133258 cd00882, Ras_like_GTPase, Ras-like GTPase superfamily. The Ras-like
superfamily of small GTPases consists of several
families with an extremely high degree of structural and
functional similarity. The Ras superfamily is divided
into at least four families in eukaryotes: the Ras, Rho,
Rab, and Sar1/Arf families. This superfamily also
includes proteins like the GTP translation factors,
Era-like GTPases, and G-alpha chain of the
heterotrimeric G proteins. Members of the Ras
superfamily regulate a wide variety of cellular
functions: the Ras family regulates gene expression, the
Rho family regulates cytoskeletal reorganization and
gene expression, the Rab and Sar1/Arf families regulate
vesicle trafficking, and the Ran family regulates
nucleocytoplasmic transport and microtubule
organization. The GTP translation factor family regulate
initiation, elongation, termination, and release in
translation, and the Era-like GTPase family regulates
cell division, sporulation, and DNA replication. Members
of the Ras superfamily are identified by the GTP binding
site, which is made up of five characteristic sequence
motifs, and the switch I and switch II regions.
Length = 157
Score = 38.6 bits (90), Expect = 0.003
Identities = 32/159 (20%), Positives = 51/159 (32%), Gaps = 20/159 (12%)
Query: 17 TIGHVDHGKTTLTAAITKYYSEEKKEYGDIDSAPEEKLRGITIATAHVSYETDKRFYSHI 76
+G GKT+L + G E + I + + + K
Sbjct: 1 VVGDSGVGKTSLLNRLL----------GGEFVPEEYETTIIDFYSKTIEVDGKKVKLQIW 50
Query: 77 DCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISS----IVVYMN 132
D G + ADG ILV D + + LL I I++ N
Sbjct: 51 DTAGQERFRSLRRLYYRGADGIILVYDVTDRESFENVKEWLLLILINKEGENIPIILVGN 110
Query: 133 KVDAVDDDELLDISEYEIRDLLKEHKYSDDTPIIRGSAL 171
K+D ++ +SE E+ + L + P SA
Sbjct: 111 KIDLPEERV---VSEEELAEQLAKEL---GVPYFETSAK 143
>gnl|CDD|58085 cd03694, GTPBP_II, Domain II of the GP-1 family of GTPase. This
group includes proteins similar to GTPBP1 and GTPBP2.
GTPB1 is structurally, related to elongation factor 1
alpha, a key component of protein biosynthesis
machinery. Immunohistochemical analyses on mouse tissues
revealed that GTPBP1 is expressed in some neurons and
smooth muscle cells of various organs as well as
macrophages. Immunofluorescence analyses revealed that
GTPBP1 is localized exclusively in cytoplasm and shows a
diffuse granular network forming a gradient from the
nucleus to the periphery of the cells in smooth muscle
cell lines and macrophages. No significant difference
was observed in the immune response to protein antigen
between mutant mice and wild-type mice, suggesting
normal function of antigen-presenting cells of the
mutant mice. The absence of an eminent phenotype in
GTPBP1-deficient mice may be due to functional
compensation by GTPBP2, which is similar to GTPBP1 in
structure and tissue distribution..
Length = 87
Score = 38.2 bits (89), Expect = 0.004
Identities = 20/85 (23%), Positives = 37/85 (43%), Gaps = 1/85 (1%)
Query: 208 FLMHIEGSCGIEGRGTVVTGCIKRGRIKAGSDVEIIGMG-GKKLKVKCTDVEMFRKKLDE 266
I+ + G GTVV G + +G I+ G + + G V + R +
Sbjct: 1 AEFQIDEIYSVPGVGTVVGGTVSKGVIRLGDTLLLGPDQDGSFRPVTVKSIHRNRSPVRV 60
Query: 267 AIAGDNVGLLLRGVNRADVPRGRVV 291
AG + L L+ ++R+ + +G V+
Sbjct: 61 VRAGQSASLALKKIDRSLLRKGMVL 85
>gnl|CDD|58089 cd03698, eRF3_II_like, eRF3_II_like: domain similar to domain II of
the eukaryotic class II release factor (eRF3). In
eukaryotes, translation termination is mediated by two
interacting release factors, eRF1 and eRF3, which act as
class I and II factors, respectively. eRF1 functions as
an omnipotent release factor, decoding all three stop
codons and triggering the release of the nascent peptide
catalyzed by the ribsome. eRF3 is a GTPase, which
enhances the termination efficiency by stimulating the
eRF1 activity in a GTP-dependent manner. Sequence
comparison of class II release factors with elongation
factors shows that eRF3 is more similar to eEF1alpha
whereas prokaryote RF3 is more similar to EF-G, implying
that their precise function may differ. Only eukaryote
RF3s are found in this group. Saccharomyces cerevisiae
eRF3 (Sup35p) is a translation termination factor which
is divided into three regions N, M and a C-terminal
eEF1a-like region essential for translation termination.
Sup35NM is a non-pathogenic prion-like protein with
the property of aggregating into polymer-like fibrils.
This group also contains proteins similar to S.
cerevisiae Hbs1, a G protein known to be important for
efficient growth and protein synthesis under conditions
of limiting translation initiation and, to associate
with Dom34. It has been speculated that yeast Hbs1 and
Dom34 proteins may function as part of a complex with a
role in gene expression..
Length = 83
Score = 37.8 bits (88), Expect = 0.005
Identities = 26/86 (30%), Positives = 50/86 (58%), Gaps = 4/86 (4%)
Query: 207 PFLMHIEGSCGIEGRGTVVTGCIKRGRIKAGSDVEIIGMGGKKLKVKCTDVEMFRKKLDE 266
PF + I + GTVV+G ++ G I+ G + ++ + ++VK + + +++D
Sbjct: 1 PFRLPISDKYK-DQGGTVVSGKVESGSIQKGDTL-LVMPSKESVEVK--SIYVDDEEVDY 56
Query: 267 AIAGDNVGLLLRGVNRADVPRGRVVC 292
A+AG+NV L L+G++ D+ G V+C
Sbjct: 57 AVAGENVRLKLKGIDEEDISPGDVLC 82
>gnl|CDD|133365 cd04165, GTPBP1_like, GTPBP1-like. Mammalian GTP binding protein 1
(GTPBP1), GTPBP2, and nematode homologs AGP-1 and CGP-1
are GTPases whose specific functions remain unknown. In
mouse, GTPBP1 is expressed in macrophages, in smooth
muscle cells of various tissues and in some neurons of
the cerebral cortex; GTPBP2 tissue distribution appears
to overlap that of GTPBP1. In human leukemia and
macrophage cell lines, expression of both GTPBP1 and
GTPBP2 is enhanced by interferon-gamma (IFN-gamma). The
chromosomal location of both genes has been identified
in humans, with GTPBP1 located in chromosome 22q12-13.1
and GTPBP2 located in chromosome 6p21-12. Human
glioblastoma multiforme (GBM), a highly-malignant
astrocytic glioma and the most common cancer in the
central nervous system, has been linked to chromosomal
deletions and a translocation on chromosome 6. The GBM
translocation results in a fusion of GTPBP2 and PTPRZ1,
a protein involved in oligodendrocyte differentiation,
recovery, and survival. This fusion product may
contribute to the onset of GBM.
Length = 224
Score = 37.2 bits (87), Expect = 0.008
Identities = 40/162 (24%), Positives = 65/162 (40%), Gaps = 47/162 (29%)
Query: 18 IGHVDHGKTTLTAAITKYYSEEKKEYGDIDSA-----------PEEKLRGIT--IATAHV 64
+G+VD GK+TL +T+ G++D+ E G T ++ +
Sbjct: 5 VGNVDAGKSTLLGVLTQ---------GELDNGRGKARLNLFRHKHEVESGRTSSVSNEIL 55
Query: 65 SYETDKRF----YSH------------------IDCPGHADYVKNMITGAT--QADGAIL 100
+++D +H ID GH Y+K + G T D A+L
Sbjct: 56 GFDSDGEVVNYPDNHLSESDIEICEKSSKLVTFIDLAGHERYLKTTLFGLTGYAPDYAML 115
Query: 101 VCAAEDGPKPQTREHILLARQIGISSIVVYMNKVDAVDDDEL 142
V AA G T+EH+ LA + I + V + K+D + L
Sbjct: 116 VVAANAGIIGMTKEHLGLALALNI-PVFVVVTKIDLAPANIL 156
>gnl|CDD|32410 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 37.2 bits (86), Expect = 0.008
Identities = 42/174 (24%), Positives = 59/174 (33%), Gaps = 16/174 (9%)
Query: 18 IGHVDHGKTTLTAAITKYYSEEKKEYGDIDSAPEEKLRGITIATAHVSYETDKRFYSHI- 76
IG V GKTT A++ D S + R T+A S E D+ H+
Sbjct: 16 IGPVGAGKTTFVRALS--DKPLVITEADASSVSGKGKRPTTVAMDFGSIELDEDTGVHLF 73
Query: 77 DCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISSIVVYMNKVDA 136
PG + + A GAI++ + E I +VV +NK D
Sbjct: 74 GTPGQERFKFMWEILSRGAVGAIVLVDSSRPITFHAEEIIDFLTSRNPIPVVVAINKQDL 133
Query: 137 VDDDELLDISEYEIRDLLKEHKYSDDTPIIRGSALCALQGTNKELGEDSIHALM 190
D I E +LL P+I A T E D + L+
Sbjct: 134 FDALPPEKIREALKLELL-------SVPVIEIDA------TEGEGARDQLDVLL 174
>gnl|CDD|58082 cd03691, BipA_TypA_II, BipA_TypA_II: domain II of BipA (also called
TypA) having homology to domain II of the elongation
factors (EFs) EF-G and EF-Tu. BipA is a highly
conserved protein with global regulatory properties in
Escherichia coli. BipA is phosphorylated on a tyrosine
residue under some cellular conditions. Mutants show
altered regulation of some pathways. BipA functions as a
translation factor that is required specifically for the
expression of the transcriptional modulator Fis. BipA
binds to ribosomes at a site that coincides with that of
EF-G and has a GTPase activity that is sensitive to high
GDP:GTP ratios and, is stimulated by 70S ribosomes
programmed with mRNA and aminoacylated tRNAs. The growth
rate-dependent induction of BipA allows the efficient
expression of Fis, thereby modulating a range of
downstream processes, including DNA metabolism and type
III secretion..
Length = 86
Score = 36.6 bits (85), Expect = 0.012
Identities = 21/58 (36%), Positives = 30/58 (51%), Gaps = 4/58 (6%)
Query: 222 GTVVTGCIKRGRIKAGSDVEIIGMGGKKLKVKCTDVEMF----RKKLDEAIAGDNVGL 275
G + G I RG +K G V ++ GK K K T + F R +++EA AGD V +
Sbjct: 15 GRIAIGRIFRGTVKVGQQVAVVKRDGKIEKAKITKLFGFEGLKRVEVEEAEAGDIVAI 72
>gnl|CDD|58075 cd04093, HBS1_C, HBS1_C: this family represents the C-terminal
domain of Hsp70 subfamily B suppressor 1 (HBS1) which is
homologous to the domain III of EF-1alpha. This group
contains proteins similar to yeast Hbs1, a G protein
known to be important for efficient growth and protein
synthesis under conditions of limiting translation
initiation and, to associate with Dom34. It has been
speculated that yeast Hbs1 and Dom34 proteins may
function as part of a complex with a role in gene
expression..
Length = 107
Score = 35.9 bits (83), Expect = 0.018
Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 13/55 (23%)
Query: 342 LSPGSQAVMPGDRVDLEVELIYPIAMEPNQT------FSMREGGKTVGAGLILEI 390
L+ G A++ E+EL PI +E + +R G+T+ AGL+ EI
Sbjct: 60 LTKGQTAIV-------EIELERPIPLELFKDNKELGRVVLRRDGETIAAGLVTEI 107
>gnl|CDD|58086 cd03695, CysN_NodQ_II, CysN_NodQ_II: This subfamily represents the
domain II of the large subunit of ATP sulfurylase
(ATPS): CysN or the N-terminal portion of NodQ, found
mainly in proteobacteria and homologous to the domain II
of EF-Tu. Escherichia coli ATPS consists of CysN and a
smaller subunit CysD and CysN. ATPS produces
adenosine-5'-phosphosulfate (APS) from ATP and sulfate,
coupled with GTP hydrolysis. In the subsequent reaction
APS is phosphorylated by an APS kinase (CysC), to
produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS) for
use in amino acid (aa) biosynthesis. The Rhizobiaceae
group (alpha-proteobacteria) appears to carry out the
same chemistry for the sufation of a nodulation factor.
In Rhizobium meliloti, a the hererodimeric complex
comprised of NodP and NodQ appears to possess both ATPS
and APS kinase activities. The N and C termini of NodQ
correspond to CysN and CysC, respectively. Other
eubacteria, Archaea, and eukaryotes use a different ATP
sulfurylase, which shows no aa sequence similarity to
CysN or NodQ. CysN and the N-terminal portion of NodQ
show similarity to GTPases involved in translation, in
particular, EF-Tu and EF-1alpha..
Length = 81
Score = 34.7 bits (80), Expect = 0.048
Identities = 27/69 (39%), Positives = 38/69 (55%), Gaps = 5/69 (7%)
Query: 225 VTGCIKRGRIKAGSDVEIIGMGGKKLKVKCTDVEMFRKKLDEAIAGDNVGLLLRGVNRAD 284
G I G I+ G +V ++ GK +VK +E F +LDEA AG++V L L + D
Sbjct: 18 YAGTIASGSIRVGDEV-VVLPSGKTSRVK--SIETFDGELDEAGAGESVTLTLE--DEID 72
Query: 285 VPRGRVVCA 293
V RG V+ A
Sbjct: 73 VSRGDVIVA 81
>gnl|CDD|30567 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 33.3 bits (76), Expect = 0.13
Identities = 28/124 (22%), Positives = 44/124 (35%), Gaps = 18/124 (14%)
Query: 66 YETDKRFYSHIDCPG---------HADYVKNMI----TGATQADGAILVCAAEDGPKPQT 112
+E D +D PG + K +I G +L+ A PK
Sbjct: 66 FEVDDELR-LVDLPGYGYAKVPKEVKEKWKKLIEEYLEKRANLKGVVLLIDARHPPKDLD 124
Query: 113 REHILLARQIGISSIVVYMNKVDAVDDDELLDISEYEIRDLLKEHKYSDDTPIIRGSALC 172
RE I ++GI IVV + K D + E ++ + LK K D + +
Sbjct: 125 REMIEFLLELGIPVIVV-LTKADKLKKSERNK-QLNKVAEELK--KPPPDDQWVVLFSSL 180
Query: 173 ALQG 176
+G
Sbjct: 181 KKKG 184
>gnl|CDD|133295 cd01895, EngA2, EngA2 subfamily. This CD represents the second
GTPase domain of EngA and its orthologs, which are
composed of two adjacent GTPase domains. Since the
sequences of the two domains are more similar to each
other than to other GTPases, it is likely that an
ancient gene duplication, rather than a fusion of
evolutionarily distinct GTPases, gave rise to this
family. Although the exact function of these proteins
has not been elucidated, studies have revealed that the
E. coli EngA homolog, Der, and Neisseria gonorrhoeae
EngA are essential for cell viability. A recent report
suggests that E. coli Der functions in ribosome assembly
and stability.
Length = 174
Score = 32.4 bits (75), Expect = 0.21
Identities = 26/101 (25%), Positives = 44/101 (43%), Gaps = 15/101 (14%)
Query: 95 ADGAILVCAAEDGPKPQTREHIL-LARQIGISSIVVYMNKVDAVDDDELLDISEYEIRDL 153
AD +LV A +G Q I L + G + ++V +NK D V+ D + +++
Sbjct: 85 ADVVLLVIDATEGITEQD-LRIAGLILEEGKALVIV-VNKWDLVEKDS--KTMKEFKKEI 140
Query: 154 LKEHKYSDDTPIIRGSALCALQGTNKELGEDSIHALMKAVD 194
++ + D PI+ SAL G + L A+D
Sbjct: 141 RRKLPFLDYAPIVFISALT---GQG-------VDKLFDAID 171
>gnl|CDD|133363 cd04163, Era, Era subfamily. Era (E. coli Ras-like protein) is a
multifunctional GTPase found in all bacteria except some
eubacteria. It binds to the 16S ribosomal RNA (rRNA) of
the 30S subunit and appears to play a role in the
assembly of the 30S subunit, possibly by chaperoning the
16S rRNA. It also contacts several assembly elements of
the 30S subunit. Era couples cell growth with
cytokinesis and plays a role in cell division and energy
metabolism. Homologs have also been found in
eukaryotes. Era contains two domains: the N-terminal
GTPase domain and a C-terminal domain KH domain that is
critical for RNA binding. Both domains are important
for Era function. Era is functionally able to
compensate for deletion of RbfA, a cold-shock adaptation
protein that is required for efficient processing of the
16S rRNA.
Length = 168
Score = 31.3 bits (72), Expect = 0.44
Identities = 24/110 (21%), Positives = 43/110 (39%), Gaps = 18/110 (16%)
Query: 85 VKNMITGATQADGAILVCAAEDGPKPQTREHILLARQI---GISSIVVYMNKVDAVDD-D 140
VK + D +L D +P + + I+V +NK+D V D +
Sbjct: 73 VKAAWSALKDVD-LVLFVV--DASEPIGEGDEFILELLKKSKTPVILV-LNKIDLVKDKE 128
Query: 141 ELLDISEYEIRDLLKEHKYSDDTPIIRGSALCALQGTNKELGEDSIHALM 190
+LL + E L + +++ PI AL+G N + + I +
Sbjct: 129 DLLPLLEK----LKELGPFAEIFPI------SALKGENVDELLEEIVKYL 168
>gnl|CDD|73167 cd00655, RNAP_Rpb7_N_like, RNAP_Rpb7_N_like: This conserved domain
represents the N-terminal ribonucleoprotein (RNP) domain
of the Rpb7 subunit of eukaryotic RNA polymerase (RNAP)
II and its homologs, Rpa43 of eukaryotic RNAP I, Rpc25
of eukaryotic RNAP III, and RpoE (subunit E) of archaeal
RNAP. These proteins have, in addition to their
N-terminal RNP domain, a C-terminal
oligonucleotide-binding (OB) domain. Each of these
subunits heterodimerizes with another RNAP subunit (Rpb7
to Rpb4, Rpc25 to Rpc17, RpoE to RpoF, and Rpa43 to
Rpa14). The heterodimer is thought to tether the RNAP to
a given promoter via its interactions with a
promoter-bound transcription factor.The heterodimer is
also thought to bind and position nascent RNA as it
exits the polymerase complex..
Length = 80
Score = 31.0 bits (70), Expect = 0.58
Identities = 16/55 (29%), Positives = 24/55 (43%), Gaps = 3/55 (5%)
Query: 258 EMFRKKLDEAIAGD---NVGLLLRGVNRADVPRGRVVCAPGSIQEYSRFRASVYI 309
+ + L E GD VG++L + D+P G + GS FRA V+
Sbjct: 23 GVKKCLLQEKGEGDRTPVVGIILAIKDTKDIPEGAIRPGDGSAYVNVSFRAVVFK 77
>gnl|CDD|58071 cd03705, EF1_alpha_III, Domain III of EF-1. Eukaryotic elongation
factor 1 (EF-1) is responsible for the GTP-dependent
binding of aminoacyl-tRNAs to ribosomes. EF-1 is
composed of four subunits: the alpha chain, which binds
GTP and aminoacyl-tRNAs, the gamma chain that probably
plays a role in anchoring the complex to other cellular
components and the beta and delta (or beta') chains.
This family is the alpha subunit, and represents the
counterpart of bacterial EF-Tu for the archaea (aEF-1
alpha) and eukaryotes (eEF-1 alpha)..
Length = 104
Score = 30.5 bits (69), Expect = 0.75
Identities = 23/108 (21%), Positives = 37/108 (34%), Gaps = 24/108 (22%)
Query: 299 EYSRFRASVYILTASEGGRTTGFMDNYRPQFFMDTADVTGRI-------------ILSPG 345
F A V +L G G Y P TA V R L
Sbjct: 2 VAESFTAQVIVL-NHPGQIKPG----YTPVLDCHTAHVACRFAEILSKIDPRTGKKLEEN 56
Query: 346 SQAVMPGDRVDLEVELIYPIAMEPNQT------FSMREGGKTVGAGLI 387
+ + GD +++ P+ +E F++R+ G+TV G++
Sbjct: 57 PKFLKSGDAAIVKIVPQKPLVVETFSEYPPLGRFAVRDMGQTVAVGIV 104
>gnl|CDD|133282 cd01882, BMS1, Bms1. Bms1 is an essential, evolutionarily
conserved, nucleolar protein. Its depletion interferes
with processing of the 35S pre-rRNA at sites A0, A1, and
A2, and the formation of 40S subunits. Bms1, the
putative endonuclease Rc11, and the essential U3 small
nucleolar RNA form a stable subcomplex that is believed
to control an early step in the formation of the 40S
subumit. The C-terminal domain of Bms1 contains a
GTPase-activating protein (GAP) that functions
intramolecularly. It is believed that Rc11 activates
Bms1 by acting as a guanine-nucleotide exchange factor
(GEF) to promote GDP/GTP exchange, and that activated
(GTP-bound) Bms1 delivers Rc11 to the preribosomes.
Length = 225
Score = 30.3 bits (69), Expect = 0.89
Identities = 27/85 (31%), Positives = 39/85 (45%), Gaps = 20/85 (23%)
Query: 24 GKTTLTAAITKYYSEEKKEYGDIDSAPEEKLRG-ITIATAHVSYETDKRFYSHIDCPGHA 82
GKTTL ++ K Y+ K+ DI +G IT+ T KR + I+CP
Sbjct: 51 GKTTLIKSLVKNYT--KQNISDI--------KGPITVVTG------KKRRLTFIECP--- 91
Query: 83 DYVKNMITGATQADGAILVCAAEDG 107
+ + MI A AD +L+ A G
Sbjct: 92 NDINAMIDIAKVADLVLLLIDASFG 116
>gnl|CDD|30869 COG0523, COG0523, Putative GTPases (G3E family) [General function
prediction only].
Length = 323
Score = 29.9 bits (67), Expect = 1.4
Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 2/58 (3%)
Query: 96 DGAILVCAAEDGPKPQTREHILLARQIGISSIVVYMNKVDAVDDDELLDISEYEIRDL 153
DG + V A + L Q+ + ++V +NK D VD +E L+ E +R L
Sbjct: 118 DGVVTVVDAAHFLEGLDAIAELAEDQLAFADVIV-LNKTDLVDAEE-LEALEARLRKL 173
>gnl|CDD|58079 cd03688, eIF2_gamma_II, eIF2_gamma_II: this subfamily represents
the domain II of the gamma subunit of eukaryotic
translation initiation factor 2 (eIF2-gamma) found in
Eukaryota and Archaea. eIF2 is a G protein that delivers
the methionyl initiator tRNA to the small ribosomal
subunit and releases it upon GTP hydrolysis after the
recognition of the initiation codon. eIF2 is composed
three subunits, alpha, beta and gamma. Subunit gamma
shows strongest conservation, and it confers both tRNA
binding and GTP/GDP binding..
Length = 113
Score = 29.7 bits (67), Expect = 1.5
Identities = 30/116 (25%), Positives = 48/116 (41%), Gaps = 26/116 (22%)
Query: 203 SLDAPFLMHIEGSCGI--------EGRGTVVTGCIKRGRIKAGSDVEII-GMGGKKL-KV 252
+P M + S + + +G V G + +G +K G ++EI G+ K K+
Sbjct: 1 DFTSPPRMIVIRSFDVNKPGTEVDDLKGGVAGGSLLQGVLKVGDEIEIRPGIVVKDEGKI 60
Query: 253 KC-------TDVEMFRKKLDEAIAGDNVGLLLRGVN------RADVPRGRVVCAPG 295
KC ++ L EA+ G GL+ G +AD G+VV PG
Sbjct: 61 KCRPIFTKIVSLKAENNDLQEAVPG---GLIGVGTKLDPTLTKADRLVGQVVGEPG 113
>gnl|CDD|133279 cd01878, HflX, HflX subfamily. A distinct conserved domain with a
glycine-rich segment N-terminal of the GTPase domain
characterizes the HflX subfamily. The E. coli HflX has
been implicated in the control of the lambda cII
repressor proteolysis, but the actual biological
functions of these GTPases remain unclear. HflX is
widespread, but not universally represented in all three
superkingdoms.
Length = 204
Score = 29.7 bits (68), Expect = 1.6
Identities = 24/114 (21%), Positives = 43/114 (37%), Gaps = 35/114 (30%)
Query: 92 ATQADGAILVCAAEDGPKPQTREHI-----LLARQIGISS---IVVYMNKVDAVDDDELL 143
+AD + V D P E I +L +++G I+V NK+D +DD+EL
Sbjct: 118 VAEADLLLHVV---DASDPDYEEQIETVEKVL-KELGAEDIPMILVL-NKIDLLDDEELE 172
Query: 144 DISEYEIRDLLKEHKYSDDTPIIRGSALCALQGTNKELGEDSIHALMKAVDTHI 197
+ E D + + A G + L++A++ +
Sbjct: 173 ERLEAGRPDAV---------------FISAKTGEG-------LDELLEAIEELL 204
>gnl|CDD|176240 cd08279, Zn_ADH_class_III, Class III alcohol dehydrogenase.
Glutathione-dependent formaldehyde dehydrogenases (FDHs,
Class III ADH) are members of the zinc-dependent/medium
chain alcohol dehydrogenase family. FDH converts
formaldehyde and NAD(P) to formate and NAD(P)H. The
initial step in this process the spontaneous formation
of a S-(hydroxymethyl)glutathione adduct from
formaldehyde and glutathione, followed by FDH-mediated
oxidation (and detoxification) of the adduct to
S-formylglutathione. NAD(P)(H)-dependent oxidoreductases
are the major enzymes in the interconversion of alcohols
and aldehydes or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. Class III ADH are also known as
glutathione-dependent formaldehyde dehydrogenase (FDH),
which convert aldehydes to corresponding carboxylic acid
and alcohol. ADH is a member of the medium chain
alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of an
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
Length = 363
Score = 29.4 bits (67), Expect = 2.0
Identities = 12/36 (33%), Positives = 16/36 (44%), Gaps = 9/36 (25%)
Query: 215 SCGIEGRGTVVTGC---IKRGRIKAGSDVEIIGMGG 247
CG V TG + R++ G V +IG GG
Sbjct: 164 GCG------VTTGVGAVVNTARVRPGDTVAVIGCGG 193
>gnl|CDD|145217 pfam01926, MMR_HSR1, GTPase of unknown function.
Length = 106
Score = 28.4 bits (64), Expect = 3.7
Identities = 28/118 (23%), Positives = 42/118 (35%), Gaps = 20/118 (16%)
Query: 24 GKTTLTAAITKYYSEEKKEYGDIDSAPEEKLRGITIATAHVSYETDKRFYSHIDCPG--- 80
GK+TL A+T A G T E D + +D PG
Sbjct: 1 GKSTLINALTG-----------KKRAIVSDYPGTTRDPNEGRVELDGKQIILVDTPGIIE 49
Query: 81 HADYVKNMITGAT-----QADGAILVCAAEDGPKPQTREHILLARQIGISSIVVYMNK 133
A + + T +AD + V A +G + E + L ++G I+V NK
Sbjct: 50 GASKGEGELGNRTLEAIEEADLILHVVDASEGLTEEDLEILDLLLELGKPVILVL-NK 106
>gnl|CDD|29076 cd01445, TST_Repeats, Thiosulfate sulfurtransferases (TST) contain
2 copies of the Rhodanese Homology Domain. Only the
second repeat contains the catalytically active Cys
residue. The role of the 1st repeat is uncertain, but
believed to be involved in protein interaction. This CD
aligns the 1st and 2nd repeats..
Length = 138
Score = 28.2 bits (62), Expect = 3.7
Identities = 11/60 (18%), Positives = 23/60 (38%)
Query: 107 GPKPQTREHILLARQIGISSIVVYMNKVDAVDDDELLDISEYEIRDLLKEHKYSDDTPII 166
+P+ L + I +S + +D +E ++ SE E + + D +I
Sbjct: 40 ETQPEPDAVGLDSGHIPGASFFDFEECLDEAGFEESMEPSEAEFAAMFEAKGIDLDKHLI 99
>gnl|CDD|34614 COG5009, MrcA, Membrane carboxypeptidase/penicillin-binding
protein [Cell envelope biogenesis, outer membrane].
Length = 797
Score = 28.3 bits (63), Expect = 3.9
Identities = 14/40 (35%), Positives = 20/40 (50%), Gaps = 7/40 (17%)
Query: 36 YSEEKKEYGDIDSAPEEKLRGITIATAHVSYETDKRFYSH 75
Y EE++ ID P+ + A ++ E DKRFY H
Sbjct: 62 YGEERRIPVPIDDIPDR------LINAFLAAE-DKRFYEH 94
>gnl|CDD|73299 cd02036, MinD, Bacterial cell division requires the formation of a
septum at mid-cell. The site is determined by the min
operon products MinC, MinD and MinE. MinC is a
nonspecific inhibitor of the septum protein FtsZ. MinE
is the supressor of MinC. MinD plays a pivotal role,
selecting the mid-cell over other sites through the
activation and regulation of MinC and MinE. MinD is a
membrane-associated ATPase, related to nitrogenase iron
protein. More distantly related proteins include
flagellar biosynthesis proteins and ParA chromosome
partitioning proteins. MinD is a monomer..
Length = 179
Score = 27.8 bits (62), Expect = 4.8
Identities = 33/134 (24%), Positives = 50/134 (37%), Gaps = 15/134 (11%)
Query: 24 GKTTLTAAITKYYSEEKKEY----GDIDSAPEEKLRGI---TIATAHVSYETDKRFYSHI 76
GKTT TA + ++ + D+ + + G+ + T H D Y I
Sbjct: 12 GKTTTTANLGTALAQLGYKVVLIDADLGLRNLDLILGLENRVVYTLHDVLAGD---YILI 68
Query: 77 DCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISSIVVYMNKVD- 135
D P + + IT AD A+LV E L +GI + V +N+V
Sbjct: 69 DSPAGIE--RGFITAIAPADEALLVTTPEISSLRDADRVKGLLEALGIKVVGVIVNRVRP 126
Query: 136 --AVDDDELLDISE 147
D + DI E
Sbjct: 127 DMVEGGDMVEDIEE 140
>gnl|CDD|144490 pfam00912, Transgly, Transglycosylase. The penicillin-binding
proteins are bifunctional proteins consisting of
transglycosylase and transpeptidase in the N- and
C-terminus respectively. The transglycosylase domain
catalyses the polymerisation of murein glycan chains.
Length = 174
Score = 27.6 bits (62), Expect = 6.5
Identities = 14/40 (35%), Positives = 20/40 (50%), Gaps = 7/40 (17%)
Query: 36 YSEEKKEYGDIDSAPEEKLRGITIATAHVSYETDKRFYSH 75
+ EE + Y +D P + A V+ E D+RFYSH
Sbjct: 8 FGEENRVYVPLDEIPP------HLINAVVAIE-DRRFYSH 40
>gnl|CDD|133297 cd01897, NOG, NOG1 is a nucleolar GTP-binding protein present in
eukaryotes ranging from trypanosomes to humans. NOG1 is
functionally linked to ribosome biogenesis and found in
association with the nuclear pore complexes and
identified in many preribosomal complexes. Thus,
defects in NOG1 can lead to defects in 60S biogenesis.
The S. cerevisiae NOG1 gene is essential for cell
viability, and mutations in the predicted G motifs
abrogate function. It is a member of the ODN family of
GTP-binding proteins that also includes the bacterial
Obg and DRG proteins.
Length = 168
Score = 27.5 bits (62), Expect = 6.8
Identities = 10/34 (29%), Positives = 20/34 (58%)
Query: 127 IVVYMNKVDAVDDDELLDISEYEIRDLLKEHKYS 160
++V +NK+D + ++L +I E E + + K S
Sbjct: 116 VIVVLNKIDLLTFEDLSEIEEEEELEGEEVLKIS 149
>gnl|CDD|146149 pfam03361, Herpes_IE2_3, Herpes virus intermediate/early protein
2/3. These viral sequences are similar to UL117 protein
of human and chimpanzee cytomegalovirus, and to
intermediate/early proteins 2 and 3 of certain herpes
viruses. UL117 is thought to be a glycoprotein that is
expressed at early and late times after infection. This
region is close to the C-terminus of the protein and may
be a transmembrane region.
Length = 162
Score = 27.3 bits (61), Expect = 6.9
Identities = 14/39 (35%), Positives = 18/39 (46%), Gaps = 4/39 (10%)
Query: 75 HIDCPGHADYVKNMITGATQAD--GAILVCA--AEDGPK 109
H CP +D +I AT D GA +C A+ PK
Sbjct: 99 HDLCPRSSDVRTMIIQAATPKDFLGAAKLCLPLAQKFPK 137
>gnl|CDD|147030 pfam04670, Gtr1_RagA, Gtr1/RagA G protein conserved region. GTR1
was first identified in S. cerevisiae as a suppressor of
a mutation in RCC1. Biochemical analysis revealed that
Gtr1 is in fact a G protein of the Ras family. The
RagA/B proteins are the human homologues of Gtr1.
Included in this family is the human Rag C, a novel
protein that has been shown to interact with RagA/B.
Length = 230
Score = 27.2 bits (61), Expect = 7.4
Identities = 28/134 (20%), Positives = 52/134 (38%), Gaps = 29/134 (21%)
Query: 50 PEEKLR-GITIATAHVSYETDKRFYSHI-----DCPGHADYVKNMITGATQAD------G 97
P + LR G TI RF ++ DCPG D+++N Q + G
Sbjct: 25 PRDTLRLGATIDVEQSHV----RFLGNLTLNLWDCPGQDDFMEN--YLTRQKEHIFSNVG 78
Query: 98 AILV---CAAEDGPKPQTR--EHILLARQI--GISSIVVYMNKVDAVDDDELLDISEY-- 148
++ + + + + I Q + V ++K+D + +DE +I E
Sbjct: 79 VLIYVFDVESREYEEDLATLVKIIEALYQYSPNA-KVFVLIHKMDLLSEDERKEIFEDRK 137
Query: 149 -EIRDLLKEHKYSD 161
EI + +++ D
Sbjct: 138 EEIIEEIEDFGIED 151
>gnl|CDD|31527 COG1336, COG1336, Uncharacterized protein predicted to be involved
in DNA repair (RAMP superfamily) [DNA replication,
recombination, and repair].
Length = 298
Score = 27.2 bits (60), Expect = 8.1
Identities = 33/178 (18%), Positives = 56/178 (31%), Gaps = 32/178 (17%)
Query: 216 CGIEGRGTVVTGCIK----RGRIKAGSDVEIIGMGGKKLKVKCTDVEM--FRKKLDEAIA 269
IEG+ K + D+ + + G+ K D + + I
Sbjct: 139 NDIEGKALSYPDEGKVYLEEITLNVLEDLTLGDLLGELSKTVFEDDNLPKEFNEQRLVIV 198
Query: 270 GDNVGLLLRGVNRADVPRGRVVCAPGSIQEYSRFRASVYILTASEGGRTTGFMDNYRPQF 329
DNV + ++ V R R+ T EGG + + Y P+
Sbjct: 199 SDNVFSDIVNLSTEIVTRIRINRETK---------------TVEEGGL---WYEEYIPE- 239
Query: 330 FMDTADVTGRIILSPGSQAVMPGDRVDLEVELIYPIAMEPNQTFSMREGGKTVGAGLI 387
T + + + V+ D EV + N + G +TVG GL+
Sbjct: 240 --GTLFYSLINVFLIYCEEVLDDDEKVREV-----LKRLSNLRYLQIGGKETVGKGLV 290
>gnl|CDD|146100 pfam03294, Pox_Rap94, RNA polymerase-associated transcription
specificity factor, Rap94.
Length = 796
Score = 27.0 bits (60), Expect = 8.2
Identities = 11/33 (33%), Positives = 17/33 (51%)
Query: 128 VVYMNKVDAVDDDELLDISEYEIRDLLKEHKYS 160
Y N + ++ LLD +Y I +L +H YS
Sbjct: 243 KTYKNNFSEIINNSLLDWGKYIIPNLKNKHLYS 275
>gnl|CDD|73297 cd02034, CooC, The accessory protein CooC, which contains a
nucleotide-binding domain (P-loop) near the N-terminus,
participates in the maturation of the nickel center of
carbon monoxide dehydrogenase (CODH). CODH from
Rhodospirillum rubrum catalyzes the reversible
oxidation of CO to CO2. CODH contains a
nickel-iron-sulfur cluster (C-center) and an
iron-sulfur cluster (B-center). CO oxidation occurs at
the C-center. Three accessory proteins encoded by
cooCTJ genes are involved in nickel incorporation into
a nickel site. CooC functions as a nickel insertase
that mobilizes nickel to apoCODH using energy released
from ATP hydrolysis. CooC is a homodimer and has NTPase
activities. Mutation at the P-loop abolishs its
function..
Length = 116
Score = 27.1 bits (60), Expect = 9.5
Identities = 11/29 (37%), Positives = 19/29 (65%)
Query: 24 GKTTLTAAITKYYSEEKKEYGDIDSAPEE 52
GKTT+ A + +Y +E+ K ID+ P++
Sbjct: 11 GKTTIAALLARYLAEKGKPVLAIDADPDD 39
>gnl|CDD|30822 COG0474, MgtA, Cation transport ATPase [Inorganic ion transport and
metabolism].
Length = 917
Score = 26.9 bits (59), Expect = 9.8
Identities = 16/73 (21%), Positives = 30/73 (41%), Gaps = 19/73 (26%)
Query: 105 EDGPKPQTREHILLARQIGISSIVVYMNKVD-------------------AVDDDELLDI 145
ED P+ +E I R+ GI ++ + V+ +D EL +
Sbjct: 545 EDPPREDVKEAIEELREAGIKVWMITGDHVETAIAIAKECGIEAEAESALVIDGAELDAL 604
Query: 146 SEYEIRDLLKEHK 158
S+ E+ +L++E
Sbjct: 605 SDEELAELVEELS 617
>gnl|CDD|176182 cd05279, Zn_ADH1, Liver alcohol dehydrogenase and related
zinc-dependent alcohol dehydrogenases.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. There are 7 vertebrate ADH 7
classes, 6 of which have been identified in humans.
Class III, glutathione-dependent formaldehyde
dehydrogenase, has been identified as the primordial
form and exists in diverse species, including plants,
micro-organisms, vertebrates, and invertebrates. Class
I, typified by liver dehydrogenase, is an evolving
form. Gene duplication and functional specialization of
ADH into ADH classes and subclasses created numerous
forms in vertebrates. For example, the A, B and C
(formerly alpha, beta, gamma) human class I subunits
have high overall structural similarity, but differ in
the substrate binding pocket and therefore in substrate
specificity. In human ADH catalysis, the zinc ion helps
coordinate the alcohol, followed by deprotonation of a
histidine (His-51), the ribose of NAD, a serine
(Ser-48), then the alcohol, which allows the transfer of
a hydride to NAD+, creating NADH and a zinc-bound
aldehyde or ketone. In yeast and some bacteria, the
active site zinc binds an aldehyde, polarizing it, and
leading to the reverse reaction. ADH is a member of the
medium chain alcohol dehydrogenase family (MDR), which
has a NAD(P)(H)-binding domain in a Rossmann fold of an
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES.
These proteins typically form dimers (typically higher
plants, mammals) or tetramers (yeast, bacteria), and
have 2 tightly bound zinc atoms per subunit, a catalytic
zinc at the active site and a structural zinc in a lobe
of the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding domains
at the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
Length = 365
Score = 27.0 bits (60), Expect = 10.0
Identities = 10/37 (27%), Positives = 15/37 (40%), Gaps = 3/37 (8%)
Query: 216 CGIEGRGTVVTGCIKRGRIKAGSDVEIIGMGGKKLKV 252
CG T + ++ GS + G+GG L V
Sbjct: 166 CGFS---TGYGAAVNTAKVTPGSTCAVFGLGGVGLSV 199
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.318 0.137 0.393
Gapped
Lambda K H
0.267 0.0787 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 4,681,549
Number of extensions: 251688
Number of successful extensions: 909
Number of sequences better than 10.0: 1
Number of HSP's gapped: 787
Number of HSP's successfully gapped: 106
Length of query: 392
Length of database: 6,263,737
Length adjustment: 96
Effective length of query: 296
Effective length of database: 4,189,273
Effective search space: 1240024808
Effective search space used: 1240024808
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: 58 (26.0 bits)