Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_092995715.1 BLP65_RS09020 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA
Query= reanno::SB2B:6938573
(1058 letters)
>NCBI__GCF_900102855.1:WP_092995715.1
Length = 1045
Score = 994 bits (2569), Expect = 0.0
Identities = 532/1034 (51%), Positives = 692/1034 (66%), Gaps = 9/1034 (0%)
Query: 26 QNYIVDEEAYLKELIALVPSSDEEIARITSRAHDLVAKVRQYEKKGLMVGIDAFLQQYSL 85
++++ DE +++L+ S E RI +RA LV VR+ + L +DAFL +Y L
Sbjct: 20 ESHLADEARCIEQLLDAASFSPEVSQRIEARAAALVRTVRKSRRPQLP--LDAFLGEYGL 77
Query: 86 ETQEGIILMCLAEALLRIPDAETADALIADKLSGAKWDEHMSKSDSVLVNASTWGLMLTG 145
+++EG++LMCLAE LLRIPD TAD LI DKL A WD H+ +S S LVNASTWGL+LTG
Sbjct: 78 DSEEGVLLMCLAEGLLRIPDPATADRLIRDKLVPAHWDAHIGRSPSPLVNASTWGLLLTG 137
Query: 146 KIVQLDKNL-DGTPSNLLSRLVNRLGEPVIRQAMYAAMKIMGKQFVLGRTIEEGLKNAAE 204
++V L ++ + +P +LSR++ R EP++R A+ AM ++ +QFV+GR+I+E L +AE
Sbjct: 138 RLVALSRDGGEPSPGRVLSRMLARSSEPMLRGALNGAMHLLARQFVMGRSIDEALHRSAE 197
Query: 205 KRKLGYTHSYDMLGEAALTMKDADKYYRDYANAIQALGTAKFDESEAPRPTISIKLSALH 264
Y +SYDMLGEAALT DA Y YANAI A+G E A RP ISIKLSALH
Sbjct: 198 GDAARYRYSYDMLGEAALTRDDAANYRDAYANAIVAVGGTTSGELLA-RPGISIKLSALH 256
Query: 265 PRYEVANEDRVMTELYATLIKLIEQARSLNVGIQIDAEEVDRLELSLKLFKKLYQSDAAK 324
PRYE A R + EL L +L A V + IDAEE RLELSL++F++
Sbjct: 257 PRYEYAQRCRTVPELAGVLAELAALAHEHGVPLTIDAEEAHRLELSLEVFQRTLADPRLV 316
Query: 325 GWGLLGIVVQAYSKRALPVLMWLTRLAKEQGDEIPLRLVKGAYWDSELKWAQQAGEAGYP 384
G LG+ VQAY KRA VL WL+ LA+ IP+RLVKGAYWD E+K AQQ G GYP
Sbjct: 317 GSESLGLAVQAYQKRAPAVLEWLSTLARTLRHRIPVRLVKGAYWDYEIKQAQQLGLPGYP 376
Query: 385 LFTRKAATDVSYLACARYLLSEATRGVIYPQFASHNAQTVAAITAMVGDRKFEFQRLHGM 444
++TRKA +DV+YLACAR+L + +YPQFA+HNA TVAAI + R FEFQRLHGM
Sbjct: 377 VYTRKAHSDVAYLACARHLFASDR---LYPQFATHNAHTVAAILYLADGRPFEFQRLHGM 433
Query: 445 GQELYDTVLAEAAVPTVRIYAPIGAHKDLLPYLVRRLLENGANTSFVHKLVDPKTPIESL 504
G+ LY+ ++ + V R+YAP+G+H++LLPYLVRRLLENGANTSFVH++ DP P+E L
Sbjct: 434 GEALYNDLVRDG-VAACRVYAPVGSHQELLPYLVRRLLENGANTSFVHRIADPDIPVERL 492
Query: 505 VTHPLKTLQGYKTLANNKIVKPADIFGAERKNSKGLNMNIISESEPFFAALEKFKDTQWS 564
P + + T N I P ++GAER+NS+GL ++ + +AAL W+
Sbjct: 493 AADPAQRIHTRGTSPNPAIPLPDALYGAERRNSRGLALDNCRDQTALYAALHGQLQHDWN 552
Query: 565 AGPLVNGETLSGEVRDVVSPYNTTLKVGQVAFANEATIEQAIAGADKAFASWCRTPVETR 624
A P++ GE +SG VR V SP++ +VGQV A+ +A+ A +W TPV R
Sbjct: 553 AAPMIGGEMISGRVRPVTSPHDRQCRVGQVWEADAQIARRAMESARSGARAWSATPVAER 612
Query: 625 ANALQKLADLLEENREELIALCTREAGKSIQDGIDEVREAVDFCRYYAVQAKKMMSKPEL 684
+ AL++ ADL+E N LIALC RE G+++ D + +VREAVDF RYYA A+ ++ P
Sbjct: 613 SEALRRAADLMESNYPTLIALCIREGGRTLPDALADVREAVDFLRYYATLAEHDLA-PRT 671
Query: 685 LPGPTGELNELFLQGRGVFVCISPWNFPLAIFLGQVAAALATGNTVIAKPAEQTCLIGFR 744
LPGPTGE N L +GRGV CISPWNFP+AIF GQ+AAAL GN V+AKPA QT L+G +
Sbjct: 672 LPGPTGEENRLLYEGRGVIACISPWNFPVAIFTGQIAAALVAGNAVVAKPAHQTPLVGMQ 731
Query: 745 AVQLAHEAGIPKDVLQFLPGTGAVVGAKLTSDERIGGVCFTGSTTTAKVINRALAGRDGA 804
+L H+AG+P VL +LPG A V L S + GV FTGST +A+ I R LA RDG
Sbjct: 732 ICRLLHQAGVPPAVLHYLPGPSAAVAPTLLSHPALAGVLFTGSTASARHIQRTLAARDGP 791
Query: 805 IIPLIAETGGQNAMVVDSTSQPEQVVNDVVSSAFTSAGQRCSALRVLYLQEDIAERVLDV 864
++PLIAETGG NAMVVDS++ PEQVV DV+ SAF SAGQRCSALR+L LQE+ AERVL +
Sbjct: 792 LLPLIAETGGVNAMVVDSSALPEQVVVDVLRSAFNSAGQRCSALRLLCLQEECAERVLGL 851
Query: 865 LKGAMDELTLGNPGSVKTDVGPVIDAAAKANLNAHIDHIKQVGRLIHQLSLPEGTENGHF 924
L GA+ EL +G+P TD+GPVID AA+ L+ HI +++ RL+ +LP G +
Sbjct: 852 LSGALAELHIGDPLEPDTDIGPVIDEAARDTLDRHIRRMEKQQRLVACAALPPAAAKGCY 911
Query: 925 VAPTAVEIDSIKVLTKENFGPILHVVRYKAAGLQKVIDDINSTGFGLTLGIHSRNEGHAL 984
VAP E+D VL +E FGPILHVVRY+ L+ ++D IN++G GLT GIHSR +
Sbjct: 912 VAPCIFELDDAGVLREEVFGPILHVVRYRGGDLEALLDTINASGHGLTFGIHSRVDATVR 971
Query: 985 EVADKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTGPKAGGPHYLTRFVTEKTRTNNITA 1044
VA+++ GNVYINR+ IGA VGVQPFGG+GLSGTGPKAGGP YL V EK+ N A
Sbjct: 972 RVAERIGAGNVYINRDIIGATVGVQPFGGRGLSGTGPKAGGPDYLRPLVQEKSIATNTAA 1031
Query: 1045 IGGNATLLSLGDAD 1058
+GGN LL+ D +
Sbjct: 1032 VGGNTGLLAGSDEE 1045
Lambda K H
0.317 0.134 0.380
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: 2531
Number of extensions: 105
Number of successful extensions: 6
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: 1058
Length of database: 1045
Length adjustment: 45
Effective length of query: 1013
Effective length of database: 1000
Effective search space: 1013000
Effective search space used: 1013000
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 (26.9 bits)
Align candidate WP_092995715.1 BLP65_RS09020 (bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA)
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.24453.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
1.3e-200 653.1 0.0 1.6e-200 652.8 0.0 1.1 1 lcl|NCBI__GCF_900102855.1:WP_092995715.1 BLP65_RS09020 bifunctional proli
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900102855.1:WP_092995715.1 BLP65_RS09020 bifunctional proline dehydrogenase/L-glutamate gamma-semialde
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 652.8 0.0 1.6e-200 1.6e-200 2 498 .. 517 1022 .. 516 1024 .. 0.98
Alignments for each domain:
== domain 1 score: 652.8 bits; conditional E-value: 1.6e-200
TIGR01238 2 lygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqv 68
lyg r+ns G+ l+n + l + l+ +++++++aap++g++ +g ++pv++p dr+ vGqv
lcl|NCBI__GCF_900102855.1:WP_092995715.1 517 LYGAERRNSRGLALDNCRDQTALYAALHGQLQHDWNAAPMIGGE-MISGRVRPVTSPHDRQCRVGQV 582
89***************************************765.56899***************** PP
TIGR01238 69 seadaaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaev 135
eada+ +++a++sa + + wsat+ +er+ l+r+adl+es+ p+l+al++re G+tl +a+a+v
lcl|NCBI__GCF_900102855.1:WP_092995715.1 583 WEADAQIARRAMESARSGARAWSATPVAERSEALRRAADLMESNYPTLIALCIREGGRTLPDALADV 649
******************************************************************* PP
TIGR01238 136 reavdflryyakqvedvldeesaka............lGavvcispwnfplaiftGqiaaalaaGnt 190
reavdflryya +e++l + +G++ cispwnfp+aiftGqiaaal+aGn+
lcl|NCBI__GCF_900102855.1:WP_092995715.1 650 REAVDFLRYYATLAEHDLAPRTLPGptgeenrllyegRGVIACISPWNFPVAIFTGQIAAALVAGNA 716
******************999877689999************************************* PP
TIGR01238 191 viakpaeqtsliaaravellqeaGvpagviqllpGrGedvGaaltsderiaGviftGstevarlink 257
v+akpa qt+l+ ++ ll++aGvp++v+ lpG + v +l s++++aGv+ftGst+ ar i++
lcl|NCBI__GCF_900102855.1:WP_092995715.1 717 VVAKPAHQTPLVGMQICRLLHQAGVPPAVLHYLPGPSAAVAPTLLSHPALAGVLFTGSTASARHIQR 783
******************************************************************* PP
TIGR01238 258 alakredapvpliaetGGqnamivdstalaeqvvadvlasafdsaGqrcsalrvlcvqedvadrvlt 324
+la r+ + pliaetGG nam+vds+al+eqvv+dvl+saf+saGqrcsalr+lc+qe+ a+rvl
lcl|NCBI__GCF_900102855.1:WP_092995715.1 784 TLAARDGPLLPLIAETGGVNAMVVDSSALPEQVVVDVLRSAFNSAGQRCSALRLLCLQEECAERVLG 850
******************************************************************* PP
TIGR01238 325 likGamdelkvgkpirlttdvGpvidaeakqnllahiekmkakakkvaqvkleddvesekgtfvapt 391
l+ Ga+ el++g p + td+Gpvid+ a++ l +hi++m+++++ va + l ++ kg +vap
lcl|NCBI__GCF_900102855.1:WP_092995715.1 851 LLSGALAELHIGDPLEPDTDIGPVIDEAARDTLDRHIRRMEKQQRLVACAALPP--AAAKGCYVAPC 915
************************************************999988..899******** PP
TIGR01238 392 lfelddldelkkevfGpvlhvvrykadeldkvvdkinakGygltlGvhsrieetvrqiekrakvGnv 458
+feldd l++evfGp+lhvvry+ +l+ ++d ina+G+glt+G+hsr++ tvr++ +r+ +Gnv
lcl|NCBI__GCF_900102855.1:WP_092995715.1 916 IFELDDAGVLREEVFGPILHVVRYRGGDLEALLDTINASGHGLTFGIHSRVDATVRRVAERIGAGNV 982
******************************************************************* PP
TIGR01238 459 yvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrltrv 498
y+nr+++Ga vGvqpfGG+GlsGtGpkaGGp yl l++
lcl|NCBI__GCF_900102855.1:WP_092995715.1 983 YINRDIIGATVGVQPFGGRGLSGTGPKAGGPDYLRPLVQE 1022
**********************************999875 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (500 nodes)
Target sequences: 1 (1045 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 17.94
//
[ok]
This GapMind analysis is from Sep 24 2021. 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