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.16854.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 22.50 // [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:
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