Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate GFF427 PS417_02175 transcriptional regulator
Query= reanno::pseudo3_N2E3:AO353_12810
(1317 letters)
>FitnessBrowser__WCS417:GFF427
Length = 1317
Score = 2471 bits (6404), Expect = 0.0
Identities = 1253/1317 (95%), Positives = 1284/1317 (97%)
Query: 1 MATTTLGVKLDDPTRERLKAAATSIDRTPHWLIKQAIFNYLEKLEGGATLTELSGLTRSE 60
MATTTLGVKLDDPTRERLKAAATSIDRTPHWLIKQAIFNYLEKLEGGATLTEL+GL+ +
Sbjct: 1 MATTTLGVKLDDPTRERLKAAATSIDRTPHWLIKQAIFNYLEKLEGGATLTELNGLSSKD 60
Query: 61 ADEGAEVHVDHAHQCFLEFAESILPQSVLRASITAAYRRPEPEVVPMLIEQARLPAPMAE 120
AD+ EV DHAHQCFLEFAESILPQSVLRASITAAYRRPEPEVVPMLIEQARLP PMAE
Sbjct: 61 ADDAGEVQTDHAHQCFLEFAESILPQSVLRASITAAYRRPEPEVVPMLIEQARLPTPMAE 120
Query: 121 ATNKLAASIAEKLRNQKSAGGRAGIVQGLLQEFSLSSQEGVALMCLAEALLRIPDKGTRD 180
ATNKLAASIAEKLRNQKSAGGRAGIVQGLLQEFSLSSQEGVALMCLAEALLRIPDKGTRD
Sbjct: 121 ATNKLAASIAEKLRNQKSAGGRAGIVQGLLQEFSLSSQEGVALMCLAEALLRIPDKGTRD 180
Query: 181 ALIRDKISTGNWQPHLGNSPSLFVNAATWGLLLTGKLVATHNEAGLTSSLSRIIGKSGEP 240
ALIRDKISTGNWQPHLGNSPSLFVNAATWGLLLTGKLVATHNEAGLTSSLSRIIGKSGEP
Sbjct: 181 ALIRDKISTGNWQPHLGNSPSLFVNAATWGLLLTGKLVATHNEAGLTSSLSRIIGKSGEP 240
Query: 241 MIRKGVDMAMRLMGEQFVTGETIAEALANASKFEAKGFRYSYDMLGEAALTEHDAQKYLA 300
MIRKGVDMAMRLMGEQFVTGETIAEALANASKFEAKGFRYSYDMLGEAALTEHDAQKYLA
Sbjct: 241 MIRKGVDMAMRLMGEQFVTGETIAEALANASKFEAKGFRYSYDMLGEAALTEHDAQKYLA 300
Query: 301 SYEQAIHSIGKASHGRGIYEGPGISIKLSALHPRYSRAQYERVMDELYPRLLSLTLLAKQ 360
SYEQAIHSIGKASHGRGIYEGPGISIKLSALHPRYSRAQYERVMDELYPRLLSLTLLAKQ
Sbjct: 301 SYEQAIHSIGKASHGRGIYEGPGISIKLSALHPRYSRAQYERVMDELYPRLLSLTLLAKQ 360
Query: 361 YDIGLNIDAEEADRLELSLDLLERLCFEPQLTGWNGIGFVIQAYQKRCPYVIDYVIDLAR 420
YDIGLNIDAEEADRLELSLDLLERLCFEPQLTGWNGIGFVIQAYQKRCPYVIDYVIDLAR
Sbjct: 361 YDIGLNIDAEEADRLELSLDLLERLCFEPQLTGWNGIGFVIQAYQKRCPYVIDYVIDLAR 420
Query: 421 RSRHRLMIRLVKGAYWDSEIKRAQVEGLEGYPVYTRKVYTDVSYIACARKLLSVPEVIYP 480
RSRHRLMIRLVKGAYWDSEIKRAQVEGLEGYPVYTRKVYTDVSYIACARKLLSVPEVIYP
Sbjct: 421 RSRHRLMIRLVKGAYWDSEIKRAQVEGLEGYPVYTRKVYTDVSYIACARKLLSVPEVIYP 480
Query: 481 QFATHNAHTLSAIYHIAGQNYYPGQYEFQCLHGMGEPLYEQVVGKVSEGKLNRPCRVYAP 540
QFATHNAHTLSAIYHIAGQNYYPGQYEFQCLHGMGEPLYEQVVGKVS+GKLNRPCRVYAP
Sbjct: 481 QFATHNAHTLSAIYHIAGQNYYPGQYEFQCLHGMGEPLYEQVVGKVSDGKLNRPCRVYAP 540
Query: 541 VGTHETLLAYLVRRLLENGANTSFVNRIADQSISIQELVADPVSSIEQMATLEGGFGLPH 600
VGTHETLLAYLVRRLLENGANTSFVNRIADQSISIQELVADPV+SIEQMATLEGGFGLPH
Sbjct: 541 VGTHETLLAYLVRRLLENGANTSFVNRIADQSISIQELVADPVASIEQMATLEGGFGLPH 600
Query: 601 PRIPLPRDLYGSERANSSGIDLANEHRLASLSCALLATAHNNWKAAPMLGCAASAETPVP 660
PRIPLPRDLYGS+RANS+GIDLANEHRLASLSCALLATAHNNWKAAPMLGCA+S + P
Sbjct: 601 PRIPLPRDLYGSDRANSAGIDLANEHRLASLSCALLATAHNNWKAAPMLGCASSEQAAAP 660
Query: 661 VLNPSDLRDVVGHVQEATVTDADNAIQCALNAAPIWQATPPAERAAILERAADLMESEIQ 720
VLNPSDLRDVVGHVQEATV D DNAIQCA++A PIWQATPPAERAAILERAADLME EIQ
Sbjct: 661 VLNPSDLRDVVGHVQEATVEDVDNAIQCAISAGPIWQATPPAERAAILERAADLMEGEIQ 720
Query: 721 PLMGLLAREAGKTFANAIAEVREAVDFLRYYAVQARNDFTNDAHRPLGPVVCISPWNFPL 780
PLMGLLAREAGKTFANAIAEVREAVDFLRYYAVQARNDFTNDAHRPLGPVVCISPWNFPL
Sbjct: 721 PLMGLLAREAGKTFANAIAEVREAVDFLRYYAVQARNDFTNDAHRPLGPVVCISPWNFPL 780
Query: 781 AIFSGQVAAALAAGNPVLAKPAEQTPLVAAQAVRILLEAGIPEGVLQLLPGRGETVGARL 840
AIFSGQVAAALAAGNPVLAKPAEQTPLVAAQAVRILLEAGIPEGVLQLLPG+GETVGARL
Sbjct: 781 AIFSGQVAAALAAGNPVLAKPAEQTPLVAAQAVRILLEAGIPEGVLQLLPGQGETVGARL 840
Query: 841 VGDDRVKGVMFTGSTEVARLLQRNVAGRLDAQGRPIPLIAETGGQNAMIVDSSALTEQVV 900
VGDDRVKGVMFTGSTEVARLLQRNVAGRLDAQGRPIPLIAETGGQNAMIVDSSALTEQVV
Sbjct: 841 VGDDRVKGVMFTGSTEVARLLQRNVAGRLDAQGRPIPLIAETGGQNAMIVDSSALTEQVV 900
Query: 901 IDVVSSAFDSAGQRCSALRVLCLQEDSADRVIEMLKGAMAECRLGNPERLSVDIGPVIDA 960
IDVVSSAFDSAGQRCSALRVLCLQEDSADRVIEMLKGAMAECRLGNPERLSVDIGPVIDA
Sbjct: 901 IDVVSSAFDSAGQRCSALRVLCLQEDSADRVIEMLKGAMAECRLGNPERLSVDIGPVIDA 960
Query: 961 EAKAGIEKHIQAMRDKGRNVYQVAIADMEECKRGTFVMPTLIELESFDELQREIFGPVLH 1020
EAKAGIEKHIQAMRDKGRNVYQVAIAD EE KRGTFVMPTLIEL+SFDELQREIFGPVLH
Sbjct: 961 EAKAGIEKHIQAMRDKGRNVYQVAIADGEEIKRGTFVMPTLIELDSFDELQREIFGPVLH 1020
Query: 1021 VVRYKRKDIDQLIGQINASGYGLTLGVHTRIDETIAKVIDNVNAGNVYVNRNIVGAVVGV 1080
VVRYKRK+IDQLIGQINASGYGLTLGVHTRIDETIAKVIDNVNAGNVYVNRNIVGAVVGV
Sbjct: 1021 VVRYKRKEIDQLIGQINASGYGLTLGVHTRIDETIAKVIDNVNAGNVYVNRNIVGAVVGV 1080
Query: 1081 QPFGGEGLSGTGPKAGGPLYLYRLLSTRPTDAIEQSFARGDTLSAPDVRLRDAMSKPLTA 1140
QPFGGEGLSGTGPKAGGPLYLYRLLSTRPTDAIEQSF RGD L+APDVRLRDAMS+PLTA
Sbjct: 1081 QPFGGEGLSGTGPKAGGPLYLYRLLSTRPTDAIEQSFVRGDALAAPDVRLRDAMSQPLTA 1140
Query: 1141 LKTWADSHKLTELSALCAQFATQSQSGITRTLNGPTGERNSYAILPREHVLCLAEVESDL 1200
LKTWAD +K ++LSALC+QFA QSQSGITR L GPTGERNSYAILPREHVLCLA+VE DL
Sbjct: 1141 LKTWADGNKFSDLSALCSQFAAQSQSGITRQLAGPTGERNSYAILPREHVLCLADVEGDL 1200
Query: 1201 LSQLAAVLAVGGSAVWPEGELSKALLARLPKDVQARIKLVADWNKDEVVFDAVLHHGHSD 1260
L+QLAAVLAVGGSAVWPE +L+KAL RLPK++QA+IK VADW KDEVVFDAVLHHG SD
Sbjct: 1201 LTQLAAVLAVGGSAVWPETDLTKALFPRLPKEIQAKIKRVADWTKDEVVFDAVLHHGDSD 1260
Query: 1261 QLRAVCQQVAKRAGAIIGVQGLSQGETNIALERLVIERALSVNTAAAGGNASLMTIG 1317
QLRAVCQQVA+R GAI+GVQGLSQGET +ALERLVIERALSVNTAAAGGNASLMTIG
Sbjct: 1261 QLRAVCQQVAQRGGAIVGVQGLSQGETAVALERLVIERALSVNTAAAGGNASLMTIG 1317
Lambda K H
0.318 0.134 0.386
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: 4529
Number of extensions: 147
Number of successful extensions: 1
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: 1317
Length of database: 1317
Length adjustment: 48
Effective length of query: 1269
Effective length of database: 1269
Effective search space: 1610361
Effective search space used: 1610361
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: 59 (27.3 bits)
Align candidate GFF427 PS417_02175 (transcriptional regulator)
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.15874.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
7.9e-248 808.8 1.4 1.2e-247 808.2 1.4 1.3 1 lcl|FitnessBrowser__WCS417:GFF427 PS417_02175 transcriptional regu
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF427 PS417_02175 transcriptional regulator
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 808.2 1.4 1.2e-247 1.2e-247 1 499 [. 608 1108 .. 608 1109 .. 0.99
Alignments for each domain:
== domain 1 score: 808.2 bits; conditional E-value: 1.2e-247
TIGR01238 1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvseadaa 74
dlyg+ r ns+G+dlane++l+sl+ ll++a+++++aap++ + a +e+ a pv np d +d+vG+v+ea +
lcl|FitnessBrowser__WCS417:GFF427 608 DLYGSDRANSAGIDLANEHRLASLSCALLATAHNNWKAAPML-GCASSEQAAAPVLNPSDLRDVVGHVQEATVE 680
89****************************************.77889999*********************** PP
TIGR01238 75 evqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdflryyakq 148
+v++a+++a++a ++w+at+++eraailer+adl+e ++ l++ll reaGkt+ naiaevreavdflryya q
lcl|FitnessBrowser__WCS417:GFF427 681 DVDNAIQCAISAGPIWQATPPAERAAILERAADLMEGEIQPLMGLLAREAGKTFANAIAEVREAVDFLRYYAVQ 754
************************************************************************** PP
TIGR01238 149 vedvldeesakalGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaaravellqeaGvpagviql 222
+++++ ++++++lG+vvcispwnfplaif Gq+aaalaaGn v+akpaeqt+l+aa+av +l+eaG+p gv+ql
lcl|FitnessBrowser__WCS417:GFF427 755 ARNDFTNDAHRPLGPVVCISPWNFPLAIFSGQVAAALAAGNPVLAKPAEQTPLVAAQAVRILLEAGIPEGVLQL 828
************************************************************************** PP
TIGR01238 223 lpGrGedvGaaltsderiaGviftGstevarlinkalakredap...vpliaetGGqnamivdstalaeqvvad 293
lpG+Ge+vGa l d+r++Gv+ftGstevarl+++++a r da+ +pliaetGGqnamivds+al+eqvv+d
lcl|FitnessBrowser__WCS417:GFF427 829 LPGQGETVGARLVGDDRVKGVMFTGSTEVARLLQRNVAGRLDAQgrpIPLIAETGGQNAMIVDSSALTEQVVID 902
******************************************99988*************************** PP
TIGR01238 294 vlasafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidaeakqnllahiekmkak 367
v++safdsaGqrcsalrvlc+qed adrv++++kGam e+++g+p+rl d+Gpvidaeak +++hi++m++k
lcl|FitnessBrowser__WCS417:GFF427 903 VVSSAFDSAGQRCSALRVLCLQEDSADRVIEMLKGAMAECRLGNPERLSVDIGPVIDAEAKAGIEKHIQAMRDK 976
************************************************************************** PP
TIGR01238 368 akkvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkvvdkinakGygltlGvhsr 441
+++v+qv +d e+++gtfv ptl+eld++del++e+fGpvlhvvryk++e+d+++ +ina+GygltlGvh+r
lcl|FitnessBrowser__WCS417:GFF427 977 GRNVYQVAIADGEEIKRGTFVMPTLIELDSFDELQREIFGPVLHVVRYKRKEIDQLIGQINASGYGLTLGVHTR 1050
************************************************************************** PP
TIGR01238 442 ieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrltrvr 499
i+et++++ +++++Gnvyvnrn+vGavvGvqpfGGeGlsGtGpkaGGplylyrl+++r
lcl|FitnessBrowser__WCS417:GFF427 1051 IDETIAKVIDNVNAGNVYVNRNIVGAVVGVQPFGGEGLSGTGPKAGGPLYLYRLLSTR 1108
******************************************************9876 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (500 nodes)
Target sequences: 1 (1317 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: 24.99
//
[ok]
This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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