Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate PP_4947 PP_4947 proline dehydrogenase/1-pyrroline-5-carboxylate dehydrogenase
Query= reanno::pseudo3_N2E3:AO353_12810
(1317 letters)
>FitnessBrowser__Putida:PP_4947
Length = 1317
Score = 2313 bits (5995), Expect = 0.0
Identities = 1165/1317 (88%), Positives = 1235/1317 (93%)
Query: 1 MATTTLGVKLDDPTRERLKAAATSIDRTPHWLIKQAIFNYLEKLEGGATLTELSGLTRSE 60
MATTTLGVKLDDPTRERLKAAA SIDRTPHWLIKQAIFNYLEKLEGGATLTEL+G +
Sbjct: 1 MATTTLGVKLDDPTRERLKAAAQSIDRTPHWLIKQAIFNYLEKLEGGATLTELNGHASNP 60
Query: 61 ADEGAEVHVDHAHQCFLEFAESILPQSVLRASITAAYRRPEPEVVPMLIEQARLPAPMAE 120
AD+ EV DH+HQCFLEFAESILPQSVLR++ITAAYRRPE EVVPML+EQARL AP+A+
Sbjct: 61 ADDAGEVQADHSHQCFLEFAESILPQSVLRSAITAAYRRPEQEVVPMLLEQARLSAPLAD 120
Query: 121 ATNKLAASIAEKLRNQKSAGGRAGIVQGLLQEFSLSSQEGVALMCLAEALLRIPDKGTRD 180
ATNKLAASIAEKLRNQKS GGRAGIVQGLLQEFSLSSQEGVALMCLAEALLRIPDKGTRD
Sbjct: 121 ATNKLAASIAEKLRNQKSVGGRAGIVQGLLQEFSLSSQEGVALMCLAEALLRIPDKGTRD 180
Query: 181 ALIRDKISTGNWQPHLGNSPSLFVNAATWGLLLTGKLVATHNEAGLTSSLSRIIGKSGEP 240
ALIRDKISTGNWQPHLGNSPSLFVNAATWGLLLTGKLV+THNE GLTSSL+RIIGKSGEP
Sbjct: 181 ALIRDKISTGNWQPHLGNSPSLFVNAATWGLLLTGKLVSTHNETGLTSSLTRIIGKSGEP 240
Query: 241 MIRKGVDMAMRLMGEQFVTGETIAEALANASKFEAKGFRYSYDMLGEAALTEHDAQKYLA 300
MIRKGVDMAMRLMGEQFVTGETIAEALANAS+FEAKGFRYSYDMLGEAALTEHDAQKYLA
Sbjct: 241 MIRKGVDMAMRLMGEQFVTGETIAEALANASRFEAKGFRYSYDMLGEAALTEHDAQKYLA 300
Query: 301 SYEQAIHSIGKASHGRGIYEGPGISIKLSALHPRYSRAQYERVMDELYPRLLSLTLLAKQ 360
SYEQAIHSIGKASHGRGIYEGPGISIKLSALHPRYSRAQYERVM+ELYPRLLSLTLLAKQ
Sbjct: 301 SYEQAIHSIGKASHGRGIYEGPGISIKLSALHPRYSRAQYERVMEELYPRLLSLTLLAKQ 360
Query: 361 YDIGLNIDAEEADRLELSLDLLERLCFEPQLTGWNGIGFVIQAYQKRCPYVIDYVIDLAR 420
YDIGLNIDAEEADRLELSLDLLERLCFEP L GWNGIGFVIQAYQKRCPYVIDYVIDLA+
Sbjct: 361 YDIGLNIDAEEADRLELSLDLLERLCFEPSLAGWNGIGFVIQAYQKRCPYVIDYVIDLAK 420
Query: 421 RSRHRLMIRLVKGAYWDSEIKRAQVEGLEGYPVYTRKVYTDVSYIACARKLLSVPEVIYP 480
RSRHRLMIRLVKGAYWDSEIKRAQVEGLEGYPVYTRKVYTDVSY+ACARKLL+VPE IYP
Sbjct: 421 RSRHRLMIRLVKGAYWDSEIKRAQVEGLEGYPVYTRKVYTDVSYVACARKLLAVPEAIYP 480
Query: 481 QFATHNAHTLSAIYHIAGQNYYPGQYEFQCLHGMGEPLYEQVVGKVSEGKLNRPCRVYAP 540
QFATHNAHTLSAIYHIAGQNYYPGQYEFQCLHGMGEPLYEQVVGK+++GKLNRPCRVYAP
Sbjct: 481 QFATHNAHTLSAIYHIAGQNYYPGQYEFQCLHGMGEPLYEQVVGKIADGKLNRPCRVYAP 540
Query: 541 VGTHETLLAYLVRRLLENGANTSFVNRIADQSISIQELVADPVSSIEQMATLEGGFGLPH 600
VGTHETLLAYLVRRLLENGANTSFVNRIAD SISIQELVADPV+SIE+M T EG GLPH
Sbjct: 541 VGTHETLLAYLVRRLLENGANTSFVNRIADHSISIQELVADPVASIERMGTQEGSIGLPH 600
Query: 601 PRIPLPRDLYGSERANSSGIDLANEHRLASLSCALLATAHNNWKAAPMLGCAASAETPVP 660
PRIPLPRDLYG+ERANS+GID+ANEHRLASLSCA+LATAHN+WKAAP+L CAAS P
Sbjct: 601 PRIPLPRDLYGTERANSAGIDMANEHRLASLSCAMLATAHNDWKAAPLLACAASESAAAP 660
Query: 661 VLNPSDLRDVVGHVQEATVTDADNAIQCALNAAPIWQATPPAERAAILERAADLMESEIQ 720
VLNP+D RDVVGHVQEATV D DNAIQCALNAAPIWQATPPAERAAILER ADLME+EIQ
Sbjct: 661 VLNPADHRDVVGHVQEATVADVDNAIQCALNAAPIWQATPPAERAAILERTADLMEAEIQ 720
Query: 721 PLMGLLAREAGKTFANAIAEVREAVDFLRYYAVQARNDFTNDAHRPLGPVVCISPWNFPL 780
PLMGLL REAGKTFANAIAEVREAVDFLRYYAVQARNDF+NDAHRPLGPVVCISPWNFPL
Sbjct: 721 PLMGLLIREAGKTFANAIAEVREAVDFLRYYAVQARNDFSNDAHRPLGPVVCISPWNFPL 780
Query: 781 AIFSGQVAAALAAGNPVLAKPAEQTPLVAAQAVRILLEAGIPEGVLQLLPGRGETVGARL 840
AIF+GQVAAALAAGNPVLAKPAEQTPL+AAQAVR+LLEAGIPEGVLQLLPGRGETVGA L
Sbjct: 781 AIFTGQVAAALAAGNPVLAKPAEQTPLIAAQAVRLLLEAGIPEGVLQLLPGRGETVGAGL 840
Query: 841 VGDDRVKGVMFTGSTEVARLLQRNVAGRLDAQGRPIPLIAETGGQNAMIVDSSALTEQVV 900
VGD+RVKGVMFTGSTEVARLLQRNVAGRLD QGRPIPLIAETGGQNAMIVDSSALTEQVV
Sbjct: 841 VGDERVKGVMFTGSTEVARLLQRNVAGRLDNQGRPIPLIAETGGQNAMIVDSSALTEQVV 900
Query: 901 IDVVSSAFDSAGQRCSALRVLCLQEDSADRVIEMLKGAMAECRLGNPERLSVDIGPVIDA 960
IDVVSSAFDSAGQRCSALRVLCLQEDSADRVIEMLKGAMAE RLG P+RL+VDIGPVIDA
Sbjct: 901 IDVVSSAFDSAGQRCSALRVLCLQEDSADRVIEMLKGAMAESRLGCPDRLAVDIGPVIDA 960
Query: 961 EAKAGIEKHIQAMRDKGRNVYQVAIADMEECKRGTFVMPTLIELESFDELQREIFGPVLH 1020
EAKAGIEKHIQ MR+KGR VYQVAIAD E KRGTFVMPTLIEL+SFDEL+REIFGPVLH
Sbjct: 961 EAKAGIEKHIQGMREKGRPVYQVAIADAAEIKRGTFVMPTLIELDSFDELKREIFGPVLH 1020
Query: 1021 VVRYKRKDIDQLIGQINASGYGLTLGVHTRIDETIAKVIDNVNAGNVYVNRNIVGAVVGV 1080
VVRY R+++DQLI QIN SGYGLTLGVHTRIDETIAKV++ NAGN+YVNRNIVGAVVGV
Sbjct: 1021 VVRYNRRNLDQLIEQINNSGYGLTLGVHTRIDETIAKVVETANAGNMYVNRNIVGAVVGV 1080
Query: 1081 QPFGGEGLSGTGPKAGGPLYLYRLLSTRPTDAIEQSFARGDTLSAPDVRLRDAMSKPLTA 1140
QPFGGEGLSGTGPKAGGPLYLYRLLSTRP DAI + F + D PD L + + KPL
Sbjct: 1081 QPFGGEGLSGTGPKAGGPLYLYRLLSTRPADAIGRHFQQQDGEGTPDRTLHEQLVKPLHG 1140
Query: 1141 LKTWADSHKLTELSALCAQFATQSQSGITRTLNGPTGERNSYAILPREHVLCLAEVESDL 1200
LK WA++++L +L+ALC+QFA+QSQSGI R L GPTGERNSY ILPREHVLCLA+ E+DL
Sbjct: 1141 LKAWAENNQLADLAALCSQFASQSQSGIARLLPGPTGERNSYTILPREHVLCLADNETDL 1200
Query: 1201 LSQLAAVLAVGGSAVWPEGELSKALLARLPKDVQARIKLVADWNKDEVVFDAVLHHGHSD 1260
L+Q AAVLAVG SAVW +GE KAL ARLP+++QA++KLVADWNKDEV FDAV+HHG SD
Sbjct: 1201 LAQFAAVLAVGSSAVWVDGEPGKALRARLPRELQAKVKLVADWNKDEVAFDAVIHHGDSD 1260
Query: 1261 QLRAVCQQVAKRAGAIIGVQGLSQGETNIALERLVIERALSVNTAAAGGNASLMTIG 1317
QLR VCQQVAKRAGAI+GV GLS G+ IALERLVIERA+SVNTAAAGGNASLMTIG
Sbjct: 1261 QLRGVCQQVAKRAGAIVGVHGLSSGDHQIALERLVIERAVSVNTAAAGGNASLMTIG 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: 4440
Number of extensions: 155
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 PP_4947 PP_4947 (proline dehydrogenase/1-pyrroline-5-carboxylate 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.10170.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
8.3e-250 815.3 1.6 1.2e-249 814.9 1.6 1.2 1 lcl|FitnessBrowser__Putida:PP_4947 PP_4947 proline dehydrogenase/1-
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_4947 PP_4947 proline dehydrogenase/1-pyrroline-5-carboxylate dehydrogenase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 814.9 1.6 1.2e-249 1.2e-249 1 499 [. 608 1108 .. 608 1109 .. 0.99
Alignments for each domain:
== domain 1 score: 814.9 bits; conditional E-value: 1.2e-249
TIGR01238 1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvseada 73
dlyg r ns+G+d+ane++l+sl+ +l++a+++++aap++ a +e a pv npad++d+vG+v+ea
lcl|FitnessBrowser__Putida:PP_4947 608 DLYGTERANSAGIDMANEHRLASLSCAMLATAHNDWKAAPLL-ACAASESAAAPVLNPADHRDVVGHVQEATV 679
89****************************************.677889999********************* PP
TIGR01238 74 aevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdflryya 146
a+v++a+++a++a+++w+at+++eraailer adl+e ++ l++ll+reaGkt+ naiaevreavdflryya
lcl|FitnessBrowser__Putida:PP_4947 680 ADVDNAIQCALNAAPIWQATPPAERAAILERTADLMEAEIQPLMGLLIREAGKTFANAIAEVREAVDFLRYYA 752
************************************************************************* PP
TIGR01238 147 kqvedvldeesakalGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaaravellqeaGvpagv 219
q++++++++++++lG+vvcispwnfplaiftGq+aaalaaGn v+akpaeqt+liaa+av ll+eaG+p gv
lcl|FitnessBrowser__Putida:PP_4947 753 VQARNDFSNDAHRPLGPVVCISPWNFPLAIFTGQVAAALAAGNPVLAKPAEQTPLIAAQAVRLLLEAGIPEGV 825
************************************************************************* PP
TIGR01238 220 iqllpGrGedvGaaltsderiaGviftGstevarlinkalakredap...vpliaetGGqnamivdstalaeq 289
+qllpGrGe+vGa l der++Gv+ftGstevarl+++++a r d++ +pliaetGGqnamivds+al+eq
lcl|FitnessBrowser__Putida:PP_4947 826 LQLLPGRGETVGAGLVGDERVKGVMFTGSTEVARLLQRNVAGRLDNQgrpIPLIAETGGQNAMIVDSSALTEQ 898
**********************************************9999*********************** PP
TIGR01238 290 vvadvlasafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidaeakqnllahie 362
vv+dv++safdsaGqrcsalrvlc+qed adrv++++kGam e ++g p rl d+Gpvidaeak +++hi+
lcl|FitnessBrowser__Putida:PP_4947 899 VVIDVVSSAFDSAGQRCSALRVLCLQEDSADRVIEMLKGAMAESRLGCPDRLAVDIGPVIDAEAKAGIEKHIQ 971
************************************************************************* PP
TIGR01238 363 kmkakakkvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkvvdkinakGyglt 435
m++k++ v+qv +d e+++gtfv ptl+eld++delk+e+fGpvlhvvry++++ld+++++in++Gyglt
lcl|FitnessBrowser__Putida:PP_4947 972 GMREKGRPVYQVAIADAAEIKRGTFVMPTLIELDSFDELKREIFGPVLHVVRYNRRNLDQLIEQINNSGYGLT 1044
************************************************************************* PP
TIGR01238 436 lGvhsrieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrltrvr 499
lGvh+ri+et++++ + a++Gn+yvnrn+vGavvGvqpfGGeGlsGtGpkaGGplylyrl+++r
lcl|FitnessBrowser__Putida:PP_4947 1045 LGVHTRIDETIAKVVETANAGNMYVNRNIVGAVVGVQPFGGEGLSGTGPKAGGPLYLYRLLSTR 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 16.42
//
[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