Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_011384888.1 AMB_RS12610 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA
Query= reanno::HerbieS:HSERO_RS00905
(1230 letters)
>NCBI__GCF_000009985.1:WP_011384888.1
Length = 1039
Score = 926 bits (2394), Expect = 0.0
Identities = 534/1028 (51%), Positives = 668/1028 (64%), Gaps = 41/1028 (3%)
Query: 21 LPTPSPLRAAITAAYRRDEREAVQWLLQQVQEEQPWKDATQQLARKLVQQVREKRTRSSG 80
LP P P R AI A E + V L + E + A LV R R R+ G
Sbjct: 7 LPAPDPERQAIHRAAGTSEADLVSGLSAGIPLEDEARRRIVNRAVNLVDGARRNR-RTLG 65
Query: 81 VDALMHEFSLSSEEGVALMCLAEALLRIPDRQTADRLIADKISKGDWRKHLGESPSLFVN 140
+D L++E+ LS+ EGV LMCLAEALLRIPD T D LI DKI+ DW HLG SPS+FVN
Sbjct: 66 LDGLLNEYRLSTREGVVLMCLAEALLRIPDDHTVDLLIKDKIASADWDGHLGHSPSVFVN 125
Query: 141 AATWGLLITGKLVSTSSESGLTQAITRLIGKGGEPLIRKGVDLAMRMLGNQFVTGQTIEE 200
A+TW L++ +L+ + + R+ G+ GE ++R+ + AM ++G QFV G+TI E
Sbjct: 126 ASTWALVLGDRLLHLEEDG--RAVLGRMAGRLGEAVVRRALRHAMGLMGRQFVLGRTIAE 183
Query: 201 ALDNSRENEKRGYRYSYDMLGEAALTMHDADAYYQSYESAIHAIGRASNGRGIKDGPGIS 260
ALDN+R E RGYR+S+DMLGEAA A Y ++Y AI A+GR + G G GPG+S
Sbjct: 184 ALDNARAWEARGYRHSFDMLGEAARCEQAAQDYLRAYAGAIEALGRHAKGAGPIAGPGLS 243
Query: 261 VKLSALHPRYSRAQHARVMSELLPRLKQLLLLAKQYDIGLNIDAEEADRLELSLDMMEVL 320
VKLSALHPR+ AQ RV+ EL+PRL+ L A+ IGL IDAEEADRL++SLD+ME
Sbjct: 244 VKLSALHPRFEMAQRQRVLGELVPRLRDLCHRARDAGIGLTIDAEEADRLDISLDVMEAA 303
Query: 321 VADPDLAGFDGLGFVVQGYQKRCPFVIDYLVDLARRNGRRLMIRLVKGAYWDSEIKRAQV 380
+ADP L G+DG G VQ YQKR VI + LA R +RLMIRLVKGAYWD E+KRAQ
Sbjct: 304 LADPALDGWDGFGMAVQAYQKRARPVIAWAGALAARRQQRLMIRLVKGAYWDGEVKRAQE 363
Query: 381 DGLEGYPVYTRKVHTDLSYLTCAQKLLAATDVIYPQFATHNAHTLAAIYHWARQHQIDNY 440
GL G+PV+T K TD+SYL CA LLA D+ YPQFATHNAHT AA+ ++
Sbjct: 364 RGLGGFPVFTTKEATDVSYLACAADLLARPDLFYPQFATHNAHTAAAVMEMT--GGAGDW 421
Query: 441 EFQCLHGMGETLYDQVVGPDNLGKACRVYAPVGSHQTLLAYLVRRLLENGANSSFVNQIV 500
EFQ LHGMGE LY Q+V P+ CR YAPVGSHQ LL YLVRRLLENGANSSFV+++
Sbjct: 422 EFQRLHGMGEALYAQLV-PE---FPCRTYAPVGSHQELLPYLVRRLLENGANSSFVSRLA 477
Query: 501 DEAVPLDRLVGDPIETVRAQGGLPHPAIAVPHRLYGEERKNSAGIDLSNEDRLQQLGQLF 560
DE +P + DP+ A G + +A P L+G R+NS G+DLS+ L QL
Sbjct: 478 DEEIPAHVVAADPL---AALGRITPQLVAEPSALFGPSRRNSGGLDLSSPAVLAQLDLAL 534
Query: 561 ISMADRQWQAAPLLAADTAAQSAQAAQLVRNPADLREVVGQVSEATVADVDTALRAATDY 620
++A + ++AP++ D + QAA+ V +PAD R VVG+V +A+ ADV+ AL +A
Sbjct: 535 AAVATPE-RSAPIV--DGRERENQAAKPVLDPADHRRVVGEVVDASPADVEAALASARAA 591
Query: 621 APQWQSTPATERAAMLERAADLLEEHIAELMALAVREAGKSLPNAIAEVREAVDFLRYYA 680
P W RA++LERAAD LE A MALA+REAGK++P+A++EVREAVDFLR+YA
Sbjct: 592 FPAWDDLGGEARASILERAADRLEADRARFMALAIREAGKTIPDALSEVREAVDFLRFYA 651
Query: 681 --IASRHDGNVLAWGPV--------------VCISPWNFPLAIFIGEVSAALAAGNVVLA 724
+R V GPV CISPWNFPLAIF+G+V+AALAAGN V+A
Sbjct: 652 AEARARFSQPVRLPGPVGESNELMLGGRGVFACISPWNFPLAIFVGQVAAALAAGNAVVA 711
Query: 725 KPAEQTALIAHRAVQLLHEAGIPRAALQLLPGRGETVGAALTSDVRVKGVIFTGSTEVAQ 784
KPA QT L+A AV+LLH+AG+P AL L+PG G +G ALT + V + FTGST A+
Sbjct: 712 KPAPQTPLMAAAAVRLLHQAGVPPQALHLVPG-GPAIGEALTVNPLVDAIAFTGSTATAR 770
Query: 785 LINRTLAQRQHDDGDGSGEHGEVPLIAETGGQNALIVDSSALAEQVVQDVLSSAFDSAGQ 844
INR A DG PLIAETGG NA+IVDSSAL EQVV D L SAF SAGQ
Sbjct: 771 HINRLRAAM---DGP------LAPLIAETGGLNAMIVDSSALPEQVVADCLESAFRSAGQ 821
Query: 845 RCSALRILCLQEDIADRTLAMLKGAMAELRVGRPDRLSIDIGPVIDAEARQNLLDHIERM 904
RCSALR+ +Q + R +L GAMAEL +G P LS D+GPVID +R+ LL H R+
Sbjct: 822 RCSALRVAFIQREAWTRIQPLLAGAMAELSLGDPALLSTDVGPVIDEASRRRLLAHGGRL 881
Query: 905 RASARAVHQLPLGEECQHGTFVAPTVIEIDDLAQLQREVFGPVLHVLRYRRDALPQLIDA 964
R + R + Q +C+ GTF AP ++D+L LQ EVFGP+LHV+ + L Q++D
Sbjct: 882 RHAGRMIGQSACPPDCRVGTFFAPMAHQLDNLDLLQSEVFGPILHVIPWEAGRLEQVLDC 941
Query: 965 INATGYGLTLGVHSRIDETIEFVAQRAHVGNIYVNRNIVGAVVGVQPFGGEGKSGTGPKA 1024
+ AT YGLTLG+HSRID TI V RA +GNIYVNR ++GAVVG QPFGG G SGTG KA
Sbjct: 942 VAATSYGLTLGIHSRIDATIAQVIARARIGNIYVNRTMIGAVVGSQPFGGLGLSGTGAKA 1001
Query: 1025 GGPLYLKR 1032
GGP L R
Sbjct: 1002 GGPNTLIR 1009
Score = 38.9 bits (89), Expect = 2e-06
Identities = 63/234 (26%), Positives = 86/234 (36%), Gaps = 51/234 (21%)
Query: 999 NRNIVGAVVGVQPFGGEGKSGTGPKA-------GGPLYLKRLQRNAQLHEE--------L 1043
+R +VG VV P E + A GG L+R A E
Sbjct: 566 HRRVVGEVVDASPADVEAALASARAAFPAWDDLGGEARASILERAADRLEADRARFMALA 625
Query: 1044 TRAQPADVPNALLD--SLLDWARTHGHERLAANGQRYHRDSLLQRSLVLPGPTGERNTLG 1101
R +P+AL + +D+ R + E A Q LPGP GE N L
Sbjct: 626 IREAGKTIPDALSEVREAVDFLRFYAAEARARFSQPVR----------LPGPVGESNELM 675
Query: 1102 FAPRGLVLCAAG---SVGTLLNQLAAAFATGN---------TALVDERSAAIL-PSGLP- 1147
RG+ C + + + Q+AAA A GN T L+ + +L +G+P
Sbjct: 676 LGGRGVFACISPWNFPLAIFVGQVAAALAAGNAVVAKPAPQTPLMAAAAVRLLHQAGVPP 735
Query: 1148 -----APVRAAIRRASQLDAEPLQAALV---DSHQAAHWRARLAAREGALVPLI 1193
P AI A L PL A+ + A H AA +G L PLI
Sbjct: 736 QALHLVPGGPAIGEA--LTVNPLVDAIAFTGSTATARHINRLRAAMDGPLAPLI 787
Score = 27.3 bits (59), Expect = 0.007
Identities = 13/24 (54%), Positives = 16/24 (66%)
Query: 1203 LWRLLAERALCINTTAAGGNASLM 1226
L R ER L +NT AAGG+ +LM
Sbjct: 1007 LIRYGVERCLSVNTAAAGGDVALM 1030
Lambda K H
0.319 0.134 0.389
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: 3106
Number of extensions: 164
Number of successful extensions: 12
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 1230
Length of database: 1039
Length adjustment: 46
Effective length of query: 1184
Effective length of database: 993
Effective search space: 1175712
Effective search space used: 1175712
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: 58 (26.9 bits)
Align candidate WP_011384888.1 AMB_RS12610 (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.28597.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
3.2e-184 599.0 0.1 4.9e-184 598.4 0.1 1.2 1 lcl|NCBI__GCF_000009985.1:WP_011384888.1 AMB_RS12610 bifunctional proline
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011384888.1 AMB_RS12610 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehy
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 598.4 0.1 4.9e-184 4.9e-184 2 495 .. 508 1010 .. 507 1014 .. 0.98
Alignments for each domain:
== domain 1 score: 598.4 bits; conditional E-value: 4.9e-184
TIGR01238 2 lygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqv 68
l+g +r+ns G+dl+ +l++l+ l ++a+ + ++apiv+++ ++++ a+pv +pad++ +vG+v
lcl|NCBI__GCF_000009985.1:WP_011384888.1 508 LFGPSRRNSGGLDLSSPAVLAQLDLALAAVATPE-RSAPIVDGRERENQAAKPVLDPADHRRVVGEV 573
899**********************998887766.789***************************** PP
TIGR01238 69 seadaaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaev 135
a+ a+v++a+ sa aaf+ w + + ra+iler+ad le + ++al++reaGkt+ +a++ev
lcl|NCBI__GCF_000009985.1:WP_011384888.1 574 VDASPADVEAALASARAAFPAWDDLGGEARASILERAADRLEADRARFMALAIREAGKTIPDALSEV 640
******************************************************************* PP
TIGR01238 136 reavdflryyakqvedvldeesaka.............lGavvcispwnfplaiftGqiaaalaaGn 189
reavdflr+ya +++ +++ + +G++ cispwnfplaif+Gq+aaalaaGn
lcl|NCBI__GCF_000009985.1:WP_011384888.1 641 REAVDFLRFYAAEARARFSQPVRLPgpvgesnelmlggRGVFACISPWNFPLAIFVGQVAAALAAGN 707
********************9666699**************************************** PP
TIGR01238 190 tviakpaeqtsliaaravellqeaGvpagviqllpGrGedvGaaltsderiaGviftGstevarlin 256
+v+akpa qt+l+aa av ll++aGvp+ ++ l+pG + +G alt ++ + ++ftGst++ar in
lcl|NCBI__GCF_000009985.1:WP_011384888.1 708 AVVAKPAPQTPLMAAAAVRLLHQAGVPPQALHLVPGGPA-IGEALTVNPLVDAIAFTGSTATARHIN 773
************************************666.*************************** PP
TIGR01238 257 kalakredapvpliaetGGqnamivdstalaeqvvadvlasafdsaGqrcsalrvlcvqedvadrvl 323
+ a + + +pliaetGG namivds+al+eqvvad l+saf saGqrcsalrv ++q++ r+
lcl|NCBI__GCF_000009985.1:WP_011384888.1 774 RLRAAMDGPLAPLIAETGGLNAMIVDSSALPEQVVADCLESAFRSAGQRCSALRVAFIQREAWTRIQ 840
**99999999********************************************************* PP
TIGR01238 324 tlikGamdelkvgkpirlttdvGpvidaeakqnllahiekmkakakkvaqvkleddvesekgtfvap 390
l+ Gam el +g p +l tdvGpvid+ ++++llah ++++ ++ + q +++ gtf ap
lcl|NCBI__GCF_000009985.1:WP_011384888.1 841 PLLAGAMAELSLGDPALLSTDVGPVIDEASRRRLLAHGGRLRHAGRMIGQSACPP--DCRVGTFFAP 905
**************************************************99988..9********* PP
TIGR01238 391 tlfelddldelkkevfGpvlhvvrykadeldkvvdkinakGygltlGvhsrieetvrqiekrakvGn 457
++ +ld+ld l+ evfGp+lhv+ ++a +l++v+d + a+ ygltlG+hsri+ t++q+ ra++Gn
lcl|NCBI__GCF_000009985.1:WP_011384888.1 906 MAHQLDNLDLLQSEVFGPILHVIPWEAGRLEQVLDCVAATSYGLTLGIHSRIDATIAQVIARARIGN 972
******************************************************************* PP
TIGR01238 458 vyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrl 495
+yvnr ++GavvG qpfGG GlsGtG kaGGp l r+
lcl|NCBI__GCF_000009985.1:WP_011384888.1 973 IYVNRTMIGAVVGSQPFGGLGLSGTGAKAGGPNTLIRY 1010
********************************999886 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (500 nodes)
Target sequences: 1 (1039 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: 00:00:00.02
# Mc/sec: 21.89
//
[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