Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_028999944.1 H537_RS0124445 trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase
Query= reanno::acidovorax_3H11:Ac3H11_2850
(1261 letters)
>NCBI__GCF_000430725.1:WP_028999944.1
Length = 1248
Score = 1696 bits (4392), Expect = 0.0
Identities = 886/1258 (70%), Positives = 997/1258 (79%), Gaps = 20/1258 (1%)
Query: 6 APFADFAPRTPLANPLRAAITAAITAATRHPEPEALAPLLAQARLPADQAAAAEQLALRI 65
APFA+F P + LR AIT A R PE EAL L ARLPA A+ LA RI
Sbjct: 9 APFAEFLHPAPYSAELRQAITEA----WRKPEVEALPMLAEMARLPAPLKEQAQALAARI 64
Query: 66 AKALRERKASAGRAGIVQGLLQEFSLSSQEGVALMCLAEALLRIPDKATRDALIRDKISH 125
A LR+RK SAGRAG+VQGLLQE++LSSQEGVALMCLAEALLRIPD+ TRDALIRDKI+
Sbjct: 65 ATTLRDRKPSAGRAGLVQGLLQEYALSSQEGVALMCLAEALLRIPDRETRDALIRDKIAR 124
Query: 126 GQWDAHLGKSPSLFVNAATWGLLITGKLVATHSEGSLGNSLSRLIGKGGEPLIRKGVDMA 185
GQW HLG+SPSLFVNAATWGLLITG+L ATHSE L ++L R++ GGEPLIRK VDMA
Sbjct: 125 GQWHTHLGRSPSLFVNAATWGLLITGRLTATHSESGLSSALGRMLAVGGEPLIRKSVDMA 184
Query: 186 MRMMGEQFVTGETIDEALRNARTMEAEGFRYSYDMLGEAALTSEDAKRYYSSYEQAIHAI 245
MR+MGEQFVTGETID+AL NAR EAEGFRYSYDMLGEAALT++DA+RY +SYE+AIHAI
Sbjct: 185 MRVMGEQFVTGETIDQALANARVREAEGFRYSYDMLGEAALTAQDAQRYLASYERAIHAI 244
Query: 246 GKASAGRGIYEGPGISIKLSALHPRYSRAQFGRVMDELYPLVLRLTALAKQYDIGLNIDA 305
GKASAGRGIYEGPGISIKLSALHPRYSRAQ RV+DELYP++LRL LAK+YDIGLNIDA
Sbjct: 245 GKASAGRGIYEGPGISIKLSALHPRYSRAQLDRVLDELYPVLLRLALLAKRYDIGLNIDA 304
Query: 306 EETDRLELSLDLLERLCHEPTLAGWNGIGFVIQAYQKRCPFVIDCVVDLARRTQRRLMVR 365
EE DRLE+SLDLLERLC EP L GWNGIGFVIQAYQKRCP+VID +VDLARR++RRLM+R
Sbjct: 305 EEADRLEISLDLLERLCFEPALKGWNGIGFVIQAYQKRCPYVIDFIVDLARRSERRLMIR 364
Query: 366 LVKGAYWDSEIKRAQVDGLKDYPVYTRKVHTDISYIACAKKLLAAPEAVYPQFATHNAET 425
LVKGAYWDSEIKRAQ+DG DYPVYTRK +TDI+YIACA+KLLAAP+ VYPQFATHNA T
Sbjct: 365 LVKGAYWDSEIKRAQLDGQLDYPVYTRKPYTDIAYIACARKLLAAPQQVYPQFATHNAHT 424
Query: 426 VATIYQLAG-SNYYAGQYEFQCLHGMGEPLYEQVVGAITAGKLGREIGKGGLGRPCRIYA 484
+A IY LA + + GQYEFQCLHGMGEPLYEQVVG G G LGRPCR+YA
Sbjct: 425 LAAIYHLADPARWQPGQYEFQCLHGMGEPLYEQVVGT----------GAGKLGRPCRVYA 474
Query: 485 PVGTHETLLAYLVRRLLENGANTSFVNRIADETIALDELVKSPVQVVDQQAATEGTAGLP 544
PVGTHETLLAYLVRRLLENGANTSFVNRIAD TI++ ELV+ PV V D+ A EG GLP
Sbjct: 475 PVGTHETLLAYLVRRLLENGANTSFVNRIADATISITELVRDPVDVADELARKEGRFGLP 534
Query: 545 HPRIPLPAALYGAHRSNSRGLDLSNENTLTELAATLQATASHAWTAAPLLAADVPAGTTQ 604
HP IP P LYG R NSRG+DLSNE+ L +L A L+ +A AW+A PLLAA AG +
Sbjct: 535 HPAIPAPRDLYGPARPNSRGIDLSNEHELAKLQAALRQSAGEAWSAEPLLAAGPVAGERE 594
Query: 605 PVRNPADHNDVVGQVQEATTADVDQALVHAQAAATSWAATPPAERAAALLRTADLLEERI 664
VRNPADH DVVG VQ A+ VD A HA AAA WAATPPA RA L R AD LEE +
Sbjct: 595 AVRNPADHGDVVGFVQNASAEHVDLAFSHAAAAAGRWAATPPAARADMLDRAADRLEEDM 654
Query: 665 QPLMGLLMREAGKSASNAVAEVREAVDFLRYYAAQVQSTFDNATHIPLGPVACISPWNFP 724
LMGLL+REAGK+A+NA+AEVREAVDFLRYYA QV+ F+ TH+P+GPV CISPWNFP
Sbjct: 655 PRLMGLLIREAGKTAANAIAEVREAVDFLRYYARQVREDFEPDTHVPVGPVVCISPWNFP 714
Query: 725 LAIFMGQVAAALAAGNPVLAKPAEQTPLIAAEAVRLLWQAGVPRAAVQLLPGQGETVGAR 784
LAIFMGQV+AALAAGNPVLAKPAEQTPLIAAEAVR+LW AGVPR +Q LPG GE VGAR
Sbjct: 715 LAIFMGQVSAALAAGNPVLAKPAEQTPLIAAEAVRVLWAAGVPRDVLQFLPGAGEVVGAR 774
Query: 785 LIGDARVMGVMFTGSTEVARILQRTVAGRLDAAGRPIPLIAETGGQNAMIVDSSALVEQV 844
L+GDARV GV+FTGSTEVARILQR VAGRLDA GRPIPLIAETGGQNAMIVDSSAL EQV
Sbjct: 775 LVGDARVRGVLFTGSTEVARILQRAVAGRLDADGRPIPLIAETGGQNAMIVDSSALAEQV 834
Query: 845 VGDAVSSAFDSAGQRCSALRVLCVQEEAADRVVEMLQGAMGELRVGNPGELRVDVGPVID 904
V D ++SAFDSAGQRCSALRVLCVQE+ ADR++EML GAM E R+G+P L VDVGPVID
Sbjct: 835 VTDVLASAFDSAGQRCSALRVLCVQEDVADRLIEMLLGAMAEWRIGSPDRLAVDVGPVID 894
Query: 905 AEAQAGIAQHIEKFKAQGHRVFQHPNHVSAISAPGTFVPPTLIELNHIGELQREVFGPVL 964
AEA AG+ +H+E +A G RV Q + + GTF+ PT+IEL+ + ELQREVFGPVL
Sbjct: 895 AEALAGLQRHVEGMRASGRRVHQLGACDAGVLGRGTFMLPTVIELDQLSELQREVFGPVL 954
Query: 965 HLVRYARSDLDQLLDQINATGYGLTQGVHTRIDETIARVVNRAHAGNVYVNRNMVGAVVG 1024
H++RY R DLD LL Q+NATGYGLT G+HTRIDETI+RV+ +HAGNVYVNRN+VGAVVG
Sbjct: 955 HVLRYQREDLDALLAQVNATGYGLTMGLHTRIDETISRVLKASHAGNVYVNRNIVGAVVG 1014
Query: 1025 VQPFGGEGLSGTGPKAGGPLYLLRLLSQRPADALARTFAEADRTSPHDTERRERHLAP-L 1083
VQPFGGEGLSGTGPKAGGPLYL RLLS+RPAD + R F E D T D + P L
Sbjct: 1015 VQPFGGEGLSGTGPKAGGPLYLYRLLSRRPADVMTRLF-EPDATL--DLGPFAGQMPPAL 1071
Query: 1084 ATLQQWAHNQGNLALAGHCQRFAQETQSGTSRTLPGPTGERNVYTLAPRARVLCLAHSVD 1143
L WA Q LA C RF Q ++SG S+TLPGPTGE+NVY LA R VLCLA S D
Sbjct: 1072 RALHDWAQQQHQTQLAQVCHRFWQRSRSGASQTLPGPTGEKNVYALAAREAVLCLAGSDD 1131
Query: 1144 DLLVQTAAVLASGGTALWPHAHAGLRAKLPTHVQAQVMLQDNTLSDGSVALDAVLHHGDA 1203
D LVQ AAVLA GG +WP L KLP VQA V++ + S V+ DA L HG A
Sbjct: 1132 DRLVQLAAVLAVGGRCVWPVECEALMRKLPAAVQASVVIARDWASP-EVSFDAALFHGAA 1190
Query: 1204 PSLQAVCTTLARRPGPIVGVTALQPGAADIPLERLLIERALSVNTAAAGGNASLMTIG 1261
P LQA+ LA RPGPIVG+ LQPG D+PLERL++E+A S+NTAAAGGNASLMTIG
Sbjct: 1191 PELQAIRQRLAERPGPIVGIERLQPGETDVPLERLVVEKATSINTAAAGGNASLMTIG 1248
Lambda K H
0.318 0.133 0.387
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: 3901
Number of extensions: 171
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: 1261
Length of database: 1248
Length adjustment: 48
Effective length of query: 1213
Effective length of database: 1200
Effective search space: 1455600
Effective search space used: 1455600
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 WP_028999944.1 H537_RS0124445 (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.4105264.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
2.6e-229 747.7 0.3 3.8e-229 747.2 0.3 1.2 1 NCBI__GCF_000430725.1:WP_028999944.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000430725.1:WP_028999944.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 747.2 0.3 3.8e-229 3.8e-229 1 498 [. 543 1042 .. 543 1044 .. 0.99
Alignments for each domain:
== domain 1 score: 747.2 bits; conditional E-value: 3.8e-229
TIGR01238 1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvsea 71
dlyg +r ns G+dl+ne+el++l++ l+++a + + a p+++ ++ ge + v+npad+ d+vG v++a
NCBI__GCF_000430725.1:WP_028999944.1 543 DLYGPARPNSRGIDLSNEHELAKLQAALRQSAGEAWSAEPLLAAGPV-AGEREAVRNPADHGDVVGFVQNA 612
89****************************************76666.5899******************* PP
TIGR01238 72 daaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdfl 142
+a++v+ a + a aa+ w at+++ ra +l+r+ad le++mp l++ll+reaGkt naiaevreavdfl
NCBI__GCF_000430725.1:WP_028999944.1 613 SAEHVDLAFSHAAAAAGRWAATPPAARADMLDRAADRLEEDMPRLMGLLIREAGKTAANAIAEVREAVDFL 683
*********************************************************************** PP
TIGR01238 143 ryyakqvedvldeesakalGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaaravellqea 213
ryya+qv+++++ +++ ++G+vvcispwnfplaif+Gq++aalaaGn v+akpaeqt+liaa+av +l a
NCBI__GCF_000430725.1:WP_028999944.1 684 RYYARQVREDFEPDTHVPVGPVVCISPWNFPLAIFMGQVSAALAAGNPVLAKPAEQTPLIAAEAVRVLWAA 754
*********************************************************************** PP
TIGR01238 214 GvpagviqllpGrGedvGaaltsderiaGviftGstevarlinkalakredap...vpliaetGGqnamiv 281
Gvp v+q+lpG+Ge vGa l d+r++Gv+ftGstevar +++a+a r da+ +pliaetGGqnamiv
NCBI__GCF_000430725.1:WP_028999944.1 755 GVPRDVLQFLPGAGEVVGARLVGDARVRGVLFTGSTEVARILQRAVAGRLDADgrpIPLIAETGGQNAMIV 825
***************************************************97777*************** PP
TIGR01238 282 dstalaeqvvadvlasafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidae 352
ds+alaeqvv+dvlasafdsaGqrcsalrvlcvqedvadr+++++ Gam e ++g p rl dvGpvidae
NCBI__GCF_000430725.1:WP_028999944.1 826 DSSALAEQVVTDVLASAFDSAGQRCSALRVLCVQEDVADRLIEMLLGAMAEWRIGSPDRLAVDVGPVIDAE 896
*********************************************************************** PP
TIGR01238 353 akqnllahiekmkakakkvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkv 423
a l++h+e m+a +++v+q+ d +gtf+ pt++eld+l+el++evfGpvlhv+ry++++ld +
NCBI__GCF_000430725.1:WP_028999944.1 897 ALAGLQRHVEGMRASGRRVHQLGACDAGVLGRGTFMLPTVIELDQLSELQREVFGPVLHVLRYQREDLDAL 967
************************99999****************************************** PP
TIGR01238 424 vdkinakGygltlGvhsrieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyr 494
+ ++na+Gyglt+G+h+ri+et+ ++ k ++Gnvyvnrn+vGavvGvqpfGGeGlsGtGpkaGGplylyr
NCBI__GCF_000430725.1:WP_028999944.1 968 LAQVNATGYGLTMGLHTRIDETISRVLKASHAGNVYVNRNIVGAVVGVQPFGGEGLSGTGPKAGGPLYLYR 1038
*********************************************************************** PP
TIGR01238 495 ltrv 498
l++
NCBI__GCF_000430725.1:WP_028999944.1 1039 LLSR 1042
*986 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (500 nodes)
Target sequences: 1 (1248 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 55.59
//
[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