Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_011428690.1 RHE_RS28430 trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase
Query= reanno::azobra:AZOBR_RS23695
(1235 letters)
>NCBI__GCF_000092045.1:WP_011428690.1
Length = 1235
Score = 1628 bits (4216), Expect = 0.0
Identities = 839/1227 (68%), Positives = 963/1227 (78%), Gaps = 10/1227 (0%)
Query: 12 PGEAAPFADFAPPIRPATELRAAITAAYRRPEPECLPFLFEQASLPPGVITAAAATARKL 71
P APFA FAPP+RP +ELR AITAAYRRPE ECLP L A + +TAR L
Sbjct: 14 PAGGAPFAAFAPPVRPQSELRRAITAAYRRPETECLPPLVAAARVSEAKRYDIRSTARTL 73
Query: 72 ITALRAKPRGRGVEGLIHEYSLSSQEGMALMCLAEALLRIPDHATRDALIRDKIAGGDWQ 131
I ALRAK +G GVEGL+ EYSLSSQEG+ALMCLAEALLRIPD TRDALIRDKIA G+W
Sbjct: 74 IEALRAKHKGTGVEGLVQEYSLSSQEGVALMCLAEALLRIPDTDTRDALIRDKIAEGNWT 133
Query: 132 AHLGKGGSMFVNAATWGLLITGKLTSAGGEQALSSALTRLIARGGEPLIRRGVDFAMRMM 191
+H+G G SMFVNAATWGL++TGKLTS +++LS+ALTRLIAR GEP+IRRGVD AMRMM
Sbjct: 134 SHIGGGKSMFVNAATWGLVVTGKLTSTVNDRSLSAALTRLIARAGEPVIRRGVDMAMRMM 193
Query: 192 GEQFVTGQTIQEALTNARTMEAEGFRYSYDMLGEAALTAEDAARYYADYVNAIHAIGTAS 251
GEQFVTG+TI+EAL AR +EA GFRYSYDMLGEAA TA DA RY+ DY AIHAIG AS
Sbjct: 194 GEQFVTGETIEEALKRARPLEARGFRYSYDMLGEAATTAADAERYFKDYEKAIHAIGKAS 253
Query: 252 AGRGVYEGPGISIKLSAIHPRYSRAQADRVMDELLPRVKALALLAKGYDIGLNIDAEEAD 311
GRG+Y+GPGISIKLSA+HPRYSR+QA RVM ELLP+VKALA+LAKGYDIGLNIDAEEAD
Sbjct: 254 NGRGIYDGPGISIKLSALHPRYSRSQAGRVMGELLPKVKALAVLAKGYDIGLNIDAEEAD 313
Query: 312 RLELSLDLMESLCFDPDLAGWNGIGFVVQAYGKRCPYVIDFLIDLARRSGHRLMIRLVKG 371
RLELSLDL+E LCF P+LAGWNG+GFVVQAYGKRCP+V+D++IDLARRSG R+M+RLVKG
Sbjct: 314 RLELSLDLLEELCFAPELAGWNGLGFVVQAYGKRCPFVLDYIIDLARRSGRRMMVRLVKG 373
Query: 372 AYWDSEIKRAQLDGLPDFPVYTRKVYTDVSYVACARKLLAAPEAVFPQFATHNAQTLATI 431
AYWD+EIKRAQLDGL D+PVYTRK+YTDV+Y+ACARKLLAA +AVFPQFATHNAQTLATI
Sbjct: 374 AYWDAEIKRAQLDGLDDYPVYTRKIYTDVAYIACARKLLAAADAVFPQFATHNAQTLATI 433
Query: 432 YEMAGSDFQVGKYEFQCLHGMGEPLYKEVVG--PLKRPCRIYAPVGTHETLLAYLVRRLL 489
Y +AG DF VGKYEFQCLHGMGEPLY EVVG L RPCRIYAPVGTHETLLAYLVRRLL
Sbjct: 434 YHLAGPDFGVGKYEFQCLHGMGEPLYDEVVGKEKLDRPCRIYAPVGTHETLLAYLVRRLL 493
Query: 490 ENGANSSFVNRIADPAVPVDELVADPVAVARAIAPTGAPHALIALPRNLYAPERANSAGI 549
ENGANSSFV+RI+DP V V+ L+ADP A+ GAPH IA P+ LY RANS+G+
Sbjct: 494 ENGANSSFVHRISDPNVSVEALIADPAETVAAMPVVGAPHVQIAAPKALYGSARANSSGL 553
Query: 550 DLSDETELARLSAALSASAEMTWTAAPLLADGERAGQAQPVRNPADRRDVVGSVTEASEA 609
DLS E L+ L+ L+++A W A P+LADG G + V NPAD RDVVG+VTE
Sbjct: 554 DLSSEATLSDLAQTLASTAATPWHALPILADGSTDGVTREVLNPADHRDVVGTVTELKVE 613
Query: 610 LVAEAFGHAVAAASAWAATPPEERAASLFRAADTMQERMPTLLGLIVREAGKSLPNAIAE 669
A A A WAA PP ERAA L RAAD MQ R+ L+G+I+REAGKS NA+ E
Sbjct: 614 EAARVVAMAAEYAPQWAAVPPAERAACLDRAADIMQARIKVLMGIIMREAGKSAANAVGE 673
Query: 670 VREAIDFLRYYGAQVRDRFDNATHRPLGPVVCISPWNFPLAIFSGQIAAALAAGNPVLAK 729
VREA+DFLRYY Q R +H PLGP+VCISPWNFPLAIF+GQ+AAAL AGNPVLAK
Sbjct: 674 VREAVDFLRYYADQARKTL-GPSHLPLGPIVCISPWNFPLAIFTGQVAAALVAGNPVLAK 732
Query: 730 PAEETPLIAAEAVRILHAAGIPAGALQLLPGAGEVGAALVGHEAVRGVMFTGSTEVARLI 789
PA TP+IA+E+V+ILH AG+P GALQ +PG+G +GA +VG + GVMFTGSTEVAR+I
Sbjct: 733 PAGVTPIIASESVKILHEAGVPVGALQFVPGSGRLGAGMVGAQQTAGVMFTGSTEVARMI 792
Query: 790 QRQLAGRLLPDGAPIPLIAETGGQNAMIVDSSALAEQVVGDVIASAFDSAGQRCSALRIL 849
Q QLA RL G PIPLIAETGGQN MIVDSSALAEQVV DV+ SAFDSAGQRCSALR+L
Sbjct: 793 QAQLAERLSATGKPIPLIAETGGQNGMIVDSSALAEQVVADVVTSAFDSAGQRCSALRVL 852
Query: 850 CLQEDVADRTLAMLKGAMRELRIGNPDRLAVDVGPVISEEARATIAAHIEAMRAKGRNVE 909
CLQ+DVADRTLAMLKGA REL IG DRL++DVGPVI++ A+A I HIEAMR GR VE
Sbjct: 853 CLQDDVADRTLAMLKGAFRELTIGRTDRLSIDVGPVINDGAKAEIDQHIEAMRGAGRKVE 912
Query: 910 FLPLPAETADGTFIAPTVIEIGGIHELEREVFGPVLHVVRFHRDDLDALVDSINATGYGL 969
LPLP A GTF+ PT+IEI + +L +EVFGPVLHVVRF R+ LD L+D INA+GYGL
Sbjct: 913 QLPLPESAAKGTFVPPTIIEIKSLSDLTKEVFGPVLHVVRFKRNGLDRLIDDINASGYGL 972
Query: 970 TFGLHTRIDATIERVTGRIGAGNVYVNRNTIGAVVGVQPFGGHGLSGTGPKAGGPLYLSR 1029
TFGLHTR+D TI VT RI AGN+YVNRN IGAVVGVQPFGG GLSGTGPKAGGPLY+ R
Sbjct: 973 TFGLHTRLDETIAHVTSRIKAGNLYVNRNIIGAVVGVQPFGGRGLSGTGPKAGGPLYIGR 1032
Query: 1030 LLSRRPKGWLEFRGPDAARA--AGLAYGEWLRAKGFTAEASRCAGYVARSAIGGGAELNG 1087
L+ R P + D+ A Y WL KG T E GY +RSA+G EL G
Sbjct: 1033 LVQRAPVPPQQ----DSVHTDLALRDYIVWLDKKGLTDEGEAARGYASRSALGLERELTG 1088
Query: 1088 PVGERNLYELHGRGRVLLLPQTRTGLLLQLGAVLATGNSAAVDAPPDLAELLRGLPPALA 1147
PVGERNLY LH RGR+LL+PQT TGL Q+ A LATGN AVDA P +L GLP A+A
Sbjct: 1089 PVGERNLYALHPRGRILLVPQTETGLYRQIAAALATGNHLAVDAGPLSKSVLAGLPAAVA 1148
Query: 1148 ARVRTTADWRDVGPLAAVLVEGDRERVTAINRRVADLPGPILLVQAATAEALAAGRGEGY 1207
+R+ T+DW GP + LVEGDR+RV A+N+++A LPGP+LLVQAAT E L + E Y
Sbjct: 1149 SRLSWTSDWEKDGPFSGALVEGDRDRVLAVNKKIAALPGPLLLVQAATTEELTSD-PEAY 1207
Query: 1208 DLDLLLNERSVSVNTAAAGGNASLVAM 1234
L+ LL E S S+NTAAAGGNASL+A+
Sbjct: 1208 CLNWLLEEVSTSINTAAAGGNASLMAI 1234
Lambda K H
0.319 0.136 0.396
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 3780
Number of extensions: 168
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 1235
Length of database: 1235
Length adjustment: 48
Effective length of query: 1187
Effective length of database: 1187
Effective search space: 1408969
Effective search space used: 1408969
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 59 (27.3 bits)
Align candidate WP_011428690.1 RHE_RS28430 (trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase)
to HMM TIGR01238 (delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88))
# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file: ../tmp/path.carbon/TIGR01238.hmm
# target sequence database: /tmp/gapView.3248135.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR01238 [M=500]
Accession: TIGR01238
Description: D1pyr5carbox3: delta-1-pyrroline-5-carboxylate dehydrogenase
Scores for complete sequences (score includes all domains):
--- full sequence --- --- best 1 domain --- -#dom-
E-value score bias E-value score bias exp N Sequence Description
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
1.8e-215 702.1 1.6 2.8e-215 701.5 1.6 1.3 1 NCBI__GCF_000092045.1:WP_011428690.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000092045.1:WP_011428690.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 701.5 1.6 2.8e-215 2.8e-215 2 497 .. 542 1035 .. 541 1038 .. 0.98
Alignments for each domain:
== domain 1 score: 701.5 bits; conditional E-value: 2.8e-215
TIGR01238 2 lygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvsead 72
lyg++r ns G+dl+ e +l +l + l ++aa ++a+pi+ + +g ++ v npad++d+vG+v+e +
NCBI__GCF_000092045.1:WP_011428690.1 542 LYGSARANSSGLDLSSEATLSDLAQTLASTAATPWHALPIL-ADGSTDGVTREVLNPADHRDVVGTVTELK 611
8****************************************.6667899999******************* PP
TIGR01238 73 aaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdflr 143
+e+ + v a + +++w a++++eraa+l+r+ad+++ ++ l+++++reaGk+ na+ evreavdflr
NCBI__GCF_000092045.1:WP_011428690.1 612 VEEAARVVAMAAEYAPQWAAVPPAERAACLDRAADIMQARIKVLMGIIMREAGKSAANAVGEVREAVDFLR 682
*********************************************************************** PP
TIGR01238 144 yyakqvedvldeesakalGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaaravellqeaG 214
yya+q++++l+ + +lG++vcispwnfplaiftGq+aaal+aGn v+akpa t++ia+++v++l+eaG
NCBI__GCF_000092045.1:WP_011428690.1 683 YYADQARKTLGPS-HLPLGPIVCISPWNFPLAIFTGQVAAALVAGNPVLAKPAGVTPIIASESVKILHEAG 752
**********987.9******************************************************** PP
TIGR01238 215 vpagviqllpGrGedvGaaltsderiaGviftGstevarlinkalakredap...vpliaetGGqnamivd 282
vp g++q++pG G +Ga + ++ aGv+ftGstevar+i+ +la+r a +pliaetGGqn mivd
NCBI__GCF_000092045.1:WP_011428690.1 753 VPVGALQFVPGSGR-LGAGMVGAQQTAGVMFTGSTEVARMIQAQLAERLSATgkpIPLIAETGGQNGMIVD 822
*************9.*********************************9876666**************** PP
TIGR01238 283 stalaeqvvadvlasafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidaea 353
s+alaeqvvadv++safdsaGqrcsalrvlc+q+dvadr+l ++kGa el +g+ rl dvGpvi++ a
NCBI__GCF_000092045.1:WP_011428690.1 823 SSALAEQVVADVVTSAFDSAGQRCSALRVLCLQDDVADRTLAMLKGAFRELTIGRTDRLSIDVGPVINDGA 893
*********************************************************************** PP
TIGR01238 354 kqnllahiekmkakakkvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkvv 424
k ++ +hie+m++ ++kv q+ l + + kgtfv+pt++e+++l++l kevfGpvlhvvr+k++ ld+++
NCBI__GCF_000092045.1:WP_011428690.1 894 KAEIDQHIEAMRGAGRKVEQLPLPE--SAAKGTFVPPTIIEIKSLSDLTKEVFGPVLHVVRFKRNGLDRLI 962
***********************99..789***************************************** PP
TIGR01238 425 dkinakGygltlGvhsrieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrl 495
d ina+Gyglt+G+h+r +et++++++r+k+Gn+yvnrn++GavvGvqpfGG+GlsGtGpkaGGply+ rl
NCBI__GCF_000092045.1:WP_011428690.1 963 DDINASGYGLTFGLHTRLDETIAHVTSRIKAGNLYVNRNIIGAVVGVQPFGGRGLSGTGPKAGGPLYIGRL 1033
**********************************************************************9 PP
TIGR01238 496 tr 497
++
NCBI__GCF_000092045.1:WP_011428690.1 1034 VQ 1035
97 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (500 nodes)
Target sequences: 1 (1235 residues searched)
Passed MSV filter: 1 (1); expected 0.0 (0.02)
Passed bias filter: 1 (1); expected 0.0 (0.02)
Passed Vit filter: 1 (1); expected 0.0 (0.001)
Passed Fwd filter: 1 (1); expected 0.0 (1e-05)
Initial search space (Z): 1 [actual number of targets]
Domain search space (domZ): 1 [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 44.27
//
[ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory