Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate Ac3H11_2850 Transcriptional repressor of PutA and PutP / Proline dehydrogenase (EC 1.5.99.8) (Proline oxidase) / Delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.1.12)
Query= reanno::acidovorax_3H11:Ac3H11_2850 (1261 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2850 Length = 1261 Score = 2471 bits (6405), Expect = 0.0 Identities = 1261/1261 (100%), Positives = 1261/1261 (100%) Query: 1 MTLPTAPFADFAPRTPLANPLRAAITAAITAATRHPEPEALAPLLAQARLPADQAAAAEQ 60 MTLPTAPFADFAPRTPLANPLRAAITAAITAATRHPEPEALAPLLAQARLPADQAAAAEQ Sbjct: 1 MTLPTAPFADFAPRTPLANPLRAAITAAITAATRHPEPEALAPLLAQARLPADQAAAAEQ 60 Query: 61 LALRIAKALRERKASAGRAGIVQGLLQEFSLSSQEGVALMCLAEALLRIPDKATRDALIR 120 LALRIAKALRERKASAGRAGIVQGLLQEFSLSSQEGVALMCLAEALLRIPDKATRDALIR Sbjct: 61 LALRIAKALRERKASAGRAGIVQGLLQEFSLSSQEGVALMCLAEALLRIPDKATRDALIR 120 Query: 121 DKISHGQWDAHLGKSPSLFVNAATWGLLITGKLVATHSEGSLGNSLSRLIGKGGEPLIRK 180 DKISHGQWDAHLGKSPSLFVNAATWGLLITGKLVATHSEGSLGNSLSRLIGKGGEPLIRK Sbjct: 121 DKISHGQWDAHLGKSPSLFVNAATWGLLITGKLVATHSEGSLGNSLSRLIGKGGEPLIRK 180 Query: 181 GVDMAMRMMGEQFVTGETIDEALRNARTMEAEGFRYSYDMLGEAALTSEDAKRYYSSYEQ 240 GVDMAMRMMGEQFVTGETIDEALRNARTMEAEGFRYSYDMLGEAALTSEDAKRYYSSYEQ Sbjct: 181 GVDMAMRMMGEQFVTGETIDEALRNARTMEAEGFRYSYDMLGEAALTSEDAKRYYSSYEQ 240 Query: 241 AIHAIGKASAGRGIYEGPGISIKLSALHPRYSRAQFGRVMDELYPLVLRLTALAKQYDIG 300 AIHAIGKASAGRGIYEGPGISIKLSALHPRYSRAQFGRVMDELYPLVLRLTALAKQYDIG Sbjct: 241 AIHAIGKASAGRGIYEGPGISIKLSALHPRYSRAQFGRVMDELYPLVLRLTALAKQYDIG 300 Query: 301 LNIDAEETDRLELSLDLLERLCHEPTLAGWNGIGFVIQAYQKRCPFVIDCVVDLARRTQR 360 LNIDAEETDRLELSLDLLERLCHEPTLAGWNGIGFVIQAYQKRCPFVIDCVVDLARRTQR Sbjct: 301 LNIDAEETDRLELSLDLLERLCHEPTLAGWNGIGFVIQAYQKRCPFVIDCVVDLARRTQR 360 Query: 361 RLMVRLVKGAYWDSEIKRAQVDGLKDYPVYTRKVHTDISYIACAKKLLAAPEAVYPQFAT 420 RLMVRLVKGAYWDSEIKRAQVDGLKDYPVYTRKVHTDISYIACAKKLLAAPEAVYPQFAT Sbjct: 361 RLMVRLVKGAYWDSEIKRAQVDGLKDYPVYTRKVHTDISYIACAKKLLAAPEAVYPQFAT 420 Query: 421 HNAETVATIYQLAGSNYYAGQYEFQCLHGMGEPLYEQVVGAITAGKLGREIGKGGLGRPC 480 HNAETVATIYQLAGSNYYAGQYEFQCLHGMGEPLYEQVVGAITAGKLGREIGKGGLGRPC Sbjct: 421 HNAETVATIYQLAGSNYYAGQYEFQCLHGMGEPLYEQVVGAITAGKLGREIGKGGLGRPC 480 Query: 481 RIYAPVGTHETLLAYLVRRLLENGANTSFVNRIADETIALDELVKSPVQVVDQQAATEGT 540 RIYAPVGTHETLLAYLVRRLLENGANTSFVNRIADETIALDELVKSPVQVVDQQAATEGT Sbjct: 481 RIYAPVGTHETLLAYLVRRLLENGANTSFVNRIADETIALDELVKSPVQVVDQQAATEGT 540 Query: 541 AGLPHPRIPLPAALYGAHRSNSRGLDLSNENTLTELAATLQATASHAWTAAPLLAADVPA 600 AGLPHPRIPLPAALYGAHRSNSRGLDLSNENTLTELAATLQATASHAWTAAPLLAADVPA Sbjct: 541 AGLPHPRIPLPAALYGAHRSNSRGLDLSNENTLTELAATLQATASHAWTAAPLLAADVPA 600 Query: 601 GTTQPVRNPADHNDVVGQVQEATTADVDQALVHAQAAATSWAATPPAERAAALLRTADLL 660 GTTQPVRNPADHNDVVGQVQEATTADVDQALVHAQAAATSWAATPPAERAAALLRTADLL Sbjct: 601 GTTQPVRNPADHNDVVGQVQEATTADVDQALVHAQAAATSWAATPPAERAAALLRTADLL 660 Query: 661 EERIQPLMGLLMREAGKSASNAVAEVREAVDFLRYYAAQVQSTFDNATHIPLGPVACISP 720 EERIQPLMGLLMREAGKSASNAVAEVREAVDFLRYYAAQVQSTFDNATHIPLGPVACISP Sbjct: 661 EERIQPLMGLLMREAGKSASNAVAEVREAVDFLRYYAAQVQSTFDNATHIPLGPVACISP 720 Query: 721 WNFPLAIFMGQVAAALAAGNPVLAKPAEQTPLIAAEAVRLLWQAGVPRAAVQLLPGQGET 780 WNFPLAIFMGQVAAALAAGNPVLAKPAEQTPLIAAEAVRLLWQAGVPRAAVQLLPGQGET Sbjct: 721 WNFPLAIFMGQVAAALAAGNPVLAKPAEQTPLIAAEAVRLLWQAGVPRAAVQLLPGQGET 780 Query: 781 VGARLIGDARVMGVMFTGSTEVARILQRTVAGRLDAAGRPIPLIAETGGQNAMIVDSSAL 840 VGARLIGDARVMGVMFTGSTEVARILQRTVAGRLDAAGRPIPLIAETGGQNAMIVDSSAL Sbjct: 781 VGARLIGDARVMGVMFTGSTEVARILQRTVAGRLDAAGRPIPLIAETGGQNAMIVDSSAL 840 Query: 841 VEQVVGDAVSSAFDSAGQRCSALRVLCVQEEAADRVVEMLQGAMGELRVGNPGELRVDVG 900 VEQVVGDAVSSAFDSAGQRCSALRVLCVQEEAADRVVEMLQGAMGELRVGNPGELRVDVG Sbjct: 841 VEQVVGDAVSSAFDSAGQRCSALRVLCVQEEAADRVVEMLQGAMGELRVGNPGELRVDVG 900 Query: 901 PVIDAEAQAGIAQHIEKFKAQGHRVFQHPNHVSAISAPGTFVPPTLIELNHIGELQREVF 960 PVIDAEAQAGIAQHIEKFKAQGHRVFQHPNHVSAISAPGTFVPPTLIELNHIGELQREVF Sbjct: 901 PVIDAEAQAGIAQHIEKFKAQGHRVFQHPNHVSAISAPGTFVPPTLIELNHIGELQREVF 960 Query: 961 GPVLHLVRYARSDLDQLLDQINATGYGLTQGVHTRIDETIARVVNRAHAGNVYVNRNMVG 1020 GPVLHLVRYARSDLDQLLDQINATGYGLTQGVHTRIDETIARVVNRAHAGNVYVNRNMVG Sbjct: 961 GPVLHLVRYARSDLDQLLDQINATGYGLTQGVHTRIDETIARVVNRAHAGNVYVNRNMVG 1020 Query: 1021 AVVGVQPFGGEGLSGTGPKAGGPLYLLRLLSQRPADALARTFAEADRTSPHDTERRERHL 1080 AVVGVQPFGGEGLSGTGPKAGGPLYLLRLLSQRPADALARTFAEADRTSPHDTERRERHL Sbjct: 1021 AVVGVQPFGGEGLSGTGPKAGGPLYLLRLLSQRPADALARTFAEADRTSPHDTERRERHL 1080 Query: 1081 APLATLQQWAHNQGNLALAGHCQRFAQETQSGTSRTLPGPTGERNVYTLAPRARVLCLAH 1140 APLATLQQWAHNQGNLALAGHCQRFAQETQSGTSRTLPGPTGERNVYTLAPRARVLCLAH Sbjct: 1081 APLATLQQWAHNQGNLALAGHCQRFAQETQSGTSRTLPGPTGERNVYTLAPRARVLCLAH 1140 Query: 1141 SVDDLLVQTAAVLASGGTALWPHAHAGLRAKLPTHVQAQVMLQDNTLSDGSVALDAVLHH 1200 SVDDLLVQTAAVLASGGTALWPHAHAGLRAKLPTHVQAQVMLQDNTLSDGSVALDAVLHH Sbjct: 1141 SVDDLLVQTAAVLASGGTALWPHAHAGLRAKLPTHVQAQVMLQDNTLSDGSVALDAVLHH 1200 Query: 1201 GDAPSLQAVCTTLARRPGPIVGVTALQPGAADIPLERLLIERALSVNTAAAGGNASLMTI 1260 GDAPSLQAVCTTLARRPGPIVGVTALQPGAADIPLERLLIERALSVNTAAAGGNASLMTI Sbjct: 1201 GDAPSLQAVCTTLARRPGPIVGVTALQPGAADIPLERLLIERALSVNTAAAGGNASLMTI 1260 Query: 1261 G 1261 G Sbjct: 1261 G 1261 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: 4343 Number of extensions: 160 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: 1261 Length of database: 1261 Length adjustment: 48 Effective length of query: 1213 Effective length of database: 1213 Effective search space: 1471369 Effective search space used: 1471369 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 Ac3H11_2850 (Transcriptional repressor of PutA and PutP / Proline dehydrogenase (EC 1.5.99.8) (Proline oxidase) / Delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.1.12))
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.30664.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.4e-231 752.8 5.5 1e-230 752.4 5.5 1.2 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2850 Transcriptional repressor of Put Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2850 Transcriptional repressor of PutA and PutP / Proline dehydrogenase ( # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 752.4 5.5 1e-230 1e-230 2 499 .. 554 1053 .. 553 1054 .. 0.99 Alignments for each domain: == domain 1 score: 752.4 bits; conditional E-value: 1e-230 TIGR01238 2 lygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadr 61 lyg r+ns G+dl+ne++l +l + l+++a + + aap++ + g +qpv+npad+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2850 554 LYGAHRSNSRGLDLSNENTLTELAATLQATASHAWTAAPLL-AADVPAGTTQPVRNPADH 612 8****************************************.6667889*********** PP TIGR01238 62 kdivGqvseadaaevqeavdsavaafaewsatdakeraailerladlleshmpelvallv 121 +d+vGqv+ea +a+v++a+ a+aa++ w at+++eraa l r adlle+++ l++ll+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2850 613 NDVVGQVQEATTADVDQALVHAQAAATSWAATPPAERAAALLRTADLLEERIQPLMGLLM 672 ************************************************************ PP TIGR01238 122 reaGktlsnaiaevreavdflryyakqvedvldeesakalGavvcispwnfplaiftGqi 181 reaGk+ sna+aevreavdflryya qv+ ++d+ ++ +lG+v cispwnfplaif+Gq+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2850 673 REAGKSASNAVAEVREAVDFLRYYAAQVQSTFDNATHIPLGPVACISPWNFPLAIFMGQV 732 ************************************************************ PP TIGR01238 182 aaalaaGntviakpaeqtsliaaravellqeaGvpagviqllpGrGedvGaaltsderia 241 aaalaaGn v+akpaeqt+liaa+av ll +aGvp +++qllpG+Ge+vGa l d+r+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2850 733 AAALAAGNPVLAKPAEQTPLIAAEAVRLLWQAGVPRAAVQLLPGQGETVGARLIGDARVM 792 ************************************************************ PP TIGR01238 242 GviftGstevarlinkalakredap...vpliaetGGqnamivdstalaeqvvadvlasa 298 Gv+ftGstevar +++++a r da +pliaetGGqnamivds+al eqvv d ++sa lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2850 793 GVMFTGSTEVARILQRTVAGRLDAAgrpIPLIAETGGQNAMIVDSSALVEQVVGDAVSSA 852 ***********************97777******************************** PP TIGR01238 299 fdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidaeakqnll 358 fdsaGqrcsalrvlcvqe+ adrv+++++Gam el+vg+p++l+ dvGpvidaea+ + lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2850 853 FDSAGQRCSALRVLCVQEEAADRVVEMLQGAMGELRVGNPGELRVDVGPVIDAEAQAGIA 912 ************************************************************ PP TIGR01238 359 ahiekmkakakkvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvvrykad 418 +hiek ka++++v+q + + s gtfv+ptl+el+++ el++evfGpvlh+vry ++ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2850 913 QHIEKFKAQGHRVFQHPNHVSAISAPGTFVPPTLIELNHIGELQREVFGPVLHLVRYARS 972 ********************99************************************** PP TIGR01238 419 eldkvvdkinakGygltlGvhsrieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeG 478 +ld+++d+ina+Gyglt Gvh+ri+et++++ +ra++Gnvyvnrn+vGavvGvqpfGGeG lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2850 973 DLDQLLDQINATGYGLTQGVHTRIDETIARVVNRAHAGNVYVNRNMVGAVVGVQPFGGEG 1032 ************************************************************ PP TIGR01238 479 lsGtGpkaGGplylyrltrvr 499 lsGtGpkaGGplyl rl++ r lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2850 1033 LSGTGPKAGGPLYLLRLLSQR 1053 *****************9865 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (500 nodes) Target sequences: 1 (1261 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 18.49 // [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