Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate 6938573 Sama_2676 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase (RefSeq)
Query= reanno::SB2B:6938573 (1058 letters) >FitnessBrowser__SB2B:6938573 Length = 1058 Score = 2068 bits (5357), Expect = 0.0 Identities = 1058/1058 (100%), Positives = 1058/1058 (100%) Query: 1 MFKASEVLAGRYDNANLDELFSLISQNYIVDEEAYLKELIALVPSSDEEIARITSRAHDL 60 MFKASEVLAGRYDNANLDELFSLISQNYIVDEEAYLKELIALVPSSDEEIARITSRAHDL Sbjct: 1 MFKASEVLAGRYDNANLDELFSLISQNYIVDEEAYLKELIALVPSSDEEIARITSRAHDL 60 Query: 61 VAKVRQYEKKGLMVGIDAFLQQYSLETQEGIILMCLAEALLRIPDAETADALIADKLSGA 120 VAKVRQYEKKGLMVGIDAFLQQYSLETQEGIILMCLAEALLRIPDAETADALIADKLSGA Sbjct: 61 VAKVRQYEKKGLMVGIDAFLQQYSLETQEGIILMCLAEALLRIPDAETADALIADKLSGA 120 Query: 121 KWDEHMSKSDSVLVNASTWGLMLTGKIVQLDKNLDGTPSNLLSRLVNRLGEPVIRQAMYA 180 KWDEHMSKSDSVLVNASTWGLMLTGKIVQLDKNLDGTPSNLLSRLVNRLGEPVIRQAMYA Sbjct: 121 KWDEHMSKSDSVLVNASTWGLMLTGKIVQLDKNLDGTPSNLLSRLVNRLGEPVIRQAMYA 180 Query: 181 AMKIMGKQFVLGRTIEEGLKNAAEKRKLGYTHSYDMLGEAALTMKDADKYYRDYANAIQA 240 AMKIMGKQFVLGRTIEEGLKNAAEKRKLGYTHSYDMLGEAALTMKDADKYYRDYANAIQA Sbjct: 181 AMKIMGKQFVLGRTIEEGLKNAAEKRKLGYTHSYDMLGEAALTMKDADKYYRDYANAIQA 240 Query: 241 LGTAKFDESEAPRPTISIKLSALHPRYEVANEDRVMTELYATLIKLIEQARSLNVGIQID 300 LGTAKFDESEAPRPTISIKLSALHPRYEVANEDRVMTELYATLIKLIEQARSLNVGIQID Sbjct: 241 LGTAKFDESEAPRPTISIKLSALHPRYEVANEDRVMTELYATLIKLIEQARSLNVGIQID 300 Query: 301 AEEVDRLELSLKLFKKLYQSDAAKGWGLLGIVVQAYSKRALPVLMWLTRLAKEQGDEIPL 360 AEEVDRLELSLKLFKKLYQSDAAKGWGLLGIVVQAYSKRALPVLMWLTRLAKEQGDEIPL Sbjct: 301 AEEVDRLELSLKLFKKLYQSDAAKGWGLLGIVVQAYSKRALPVLMWLTRLAKEQGDEIPL 360 Query: 361 RLVKGAYWDSELKWAQQAGEAGYPLFTRKAATDVSYLACARYLLSEATRGVIYPQFASHN 420 RLVKGAYWDSELKWAQQAGEAGYPLFTRKAATDVSYLACARYLLSEATRGVIYPQFASHN Sbjct: 361 RLVKGAYWDSELKWAQQAGEAGYPLFTRKAATDVSYLACARYLLSEATRGVIYPQFASHN 420 Query: 421 AQTVAAITAMVGDRKFEFQRLHGMGQELYDTVLAEAAVPTVRIYAPIGAHKDLLPYLVRR 480 AQTVAAITAMVGDRKFEFQRLHGMGQELYDTVLAEAAVPTVRIYAPIGAHKDLLPYLVRR Sbjct: 421 AQTVAAITAMVGDRKFEFQRLHGMGQELYDTVLAEAAVPTVRIYAPIGAHKDLLPYLVRR 480 Query: 481 LLENGANTSFVHKLVDPKTPIESLVTHPLKTLQGYKTLANNKIVKPADIFGAERKNSKGL 540 LLENGANTSFVHKLVDPKTPIESLVTHPLKTLQGYKTLANNKIVKPADIFGAERKNSKGL Sbjct: 481 LLENGANTSFVHKLVDPKTPIESLVTHPLKTLQGYKTLANNKIVKPADIFGAERKNSKGL 540 Query: 541 NMNIISESEPFFAALEKFKDTQWSAGPLVNGETLSGEVRDVVSPYNTTLKVGQVAFANEA 600 NMNIISESEPFFAALEKFKDTQWSAGPLVNGETLSGEVRDVVSPYNTTLKVGQVAFANEA Sbjct: 541 NMNIISESEPFFAALEKFKDTQWSAGPLVNGETLSGEVRDVVSPYNTTLKVGQVAFANEA 600 Query: 601 TIEQAIAGADKAFASWCRTPVETRANALQKLADLLEENREELIALCTREAGKSIQDGIDE 660 TIEQAIAGADKAFASWCRTPVETRANALQKLADLLEENREELIALCTREAGKSIQDGIDE Sbjct: 601 TIEQAIAGADKAFASWCRTPVETRANALQKLADLLEENREELIALCTREAGKSIQDGIDE 660 Query: 661 VREAVDFCRYYAVQAKKMMSKPELLPGPTGELNELFLQGRGVFVCISPWNFPLAIFLGQV 720 VREAVDFCRYYAVQAKKMMSKPELLPGPTGELNELFLQGRGVFVCISPWNFPLAIFLGQV Sbjct: 661 VREAVDFCRYYAVQAKKMMSKPELLPGPTGELNELFLQGRGVFVCISPWNFPLAIFLGQV 720 Query: 721 AAALATGNTVIAKPAEQTCLIGFRAVQLAHEAGIPKDVLQFLPGTGAVVGAKLTSDERIG 780 AAALATGNTVIAKPAEQTCLIGFRAVQLAHEAGIPKDVLQFLPGTGAVVGAKLTSDERIG Sbjct: 721 AAALATGNTVIAKPAEQTCLIGFRAVQLAHEAGIPKDVLQFLPGTGAVVGAKLTSDERIG 780 Query: 781 GVCFTGSTTTAKVINRALAGRDGAIIPLIAETGGQNAMVVDSTSQPEQVVNDVVSSAFTS 840 GVCFTGSTTTAKVINRALAGRDGAIIPLIAETGGQNAMVVDSTSQPEQVVNDVVSSAFTS Sbjct: 781 GVCFTGSTTTAKVINRALAGRDGAIIPLIAETGGQNAMVVDSTSQPEQVVNDVVSSAFTS 840 Query: 841 AGQRCSALRVLYLQEDIAERVLDVLKGAMDELTLGNPGSVKTDVGPVIDAAAKANLNAHI 900 AGQRCSALRVLYLQEDIAERVLDVLKGAMDELTLGNPGSVKTDVGPVIDAAAKANLNAHI Sbjct: 841 AGQRCSALRVLYLQEDIAERVLDVLKGAMDELTLGNPGSVKTDVGPVIDAAAKANLNAHI 900 Query: 901 DHIKQVGRLIHQLSLPEGTENGHFVAPTAVEIDSIKVLTKENFGPILHVVRYKAAGLQKV 960 DHIKQVGRLIHQLSLPEGTENGHFVAPTAVEIDSIKVLTKENFGPILHVVRYKAAGLQKV Sbjct: 901 DHIKQVGRLIHQLSLPEGTENGHFVAPTAVEIDSIKVLTKENFGPILHVVRYKAAGLQKV 960 Query: 961 IDDINSTGFGLTLGIHSRNEGHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTG 1020 IDDINSTGFGLTLGIHSRNEGHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTG Sbjct: 961 IDDINSTGFGLTLGIHSRNEGHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTG 1020 Query: 1021 PKAGGPHYLTRFVTEKTRTNNITAIGGNATLLSLGDAD 1058 PKAGGPHYLTRFVTEKTRTNNITAIGGNATLLSLGDAD Sbjct: 1021 PKAGGPHYLTRFVTEKTRTNNITAIGGNATLLSLGDAD 1058 Lambda K H 0.317 0.134 0.380 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: 3068 Number of extensions: 91 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: 1058 Length of database: 1058 Length adjustment: 45 Effective length of query: 1013 Effective length of database: 1013 Effective search space: 1026169 Effective search space used: 1026169 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: 58 (26.9 bits)
Align candidate 6938573 Sama_2676 (bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase (RefSeq))
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.25957.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.4e-218 711.1 1.2 4.6e-218 710.6 1.2 1.2 1 lcl|FitnessBrowser__SB2B:6938573 Sama_2676 bifunctional proline d Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6938573 Sama_2676 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 710.6 1.2 4.6e-218 4.6e-218 1 497 [. 528 1034 .. 528 1037 .. 0.98 Alignments for each domain: == domain 1 score: 710.6 bits; conditional E-value: 4.6e-218 TIGR01238 1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvseadaae 75 d++g rkns+G+++++ se +++ + l+k + ++ a p+v+++ +ge++ v++p++ +vGqv +a++a+ lcl|FitnessBrowser__SB2B:6938573 528 DIFGAERKNSKGLNMNIISESEPFFAALEKFKDTQWSAGPLVNGE-TLSGEVRDVVSPYNTTLKVGQVAFANEAT 601 89****************************************766.5689************************* PP TIGR01238 76 vqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdflryyakqve 150 +++a+ a +afa w t+ + ra l++ladlle++ el+al+ reaGk++++ i+evreavdf+ryya q++ lcl|FitnessBrowser__SB2B:6938573 602 IEQAIAGADKAFASWCRTPVETRANALQKLADLLEENREELIALCTREAGKSIQDGIDEVREAVDFCRYYAVQAK 676 **************************************************************************9 PP TIGR01238 151 dvldeesaka.............lGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaaravellqe 212 + +++ + +G++vcispwnfplaif+Gq+aaala+Gntviakpaeqt li rav+l +e lcl|FitnessBrowser__SB2B:6938573 677 KMMSKPELLPgptgelnelflqgRGVFVCISPWNFPLAIFLGQVAAALATGNTVIAKPAEQTCLIGFRAVQLAHE 751 999998777799*************************************************************** PP TIGR01238 213 aGvpagviqllpGrGedvGaaltsderiaGviftGstevarlinkalakredapvpliaetGGqnamivdstala 287 aG+p v+q+lpG G+ vGa ltsderi+Gv ftGst +a+ in+ala r+ a +pliaetGGqnam+vdst+ + lcl|FitnessBrowser__SB2B:6938573 752 AGIPKDVLQFLPGTGAVVGAKLTSDERIGGVCFTGSTTTAKVINRALAGRDGAIIPLIAETGGQNAMVVDSTSQP 826 *************************************************************************** PP TIGR01238 288 eqvvadvlasafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidaeakqnllahie 362 eqvv dv++saf saGqrcsalrvl++qed+a+rvl+++kGamdel +g+p+ +tdvGpvida ak nl ahi+ lcl|FitnessBrowser__SB2B:6938573 827 EQVVNDVVSSAFTSAGQRCSALRVLYLQEDIAERVLDVLKGAMDELTLGNPGSVKTDVGPVIDAAAKANLNAHID 901 *************************************************************************** PP TIGR01238 363 kmkakakkvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkvvdkinakGygltlG 437 ++k++++ ++q+ l + +e+g fvapt++e+d+++ l ke fGp+lhvvryka l+kv+d in++G+gltlG lcl|FitnessBrowser__SB2B:6938573 902 HIKQVGRLIHQLSLPE--GTENGHFVAPTAVEIDSIKVLTKENFGPILHVVRYKAAGLQKVIDDINSTGFGLTLG 974 **************99..8999***************************************************** PP TIGR01238 438 vhsrieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrltr 497 +hsr+e+ + ++++vGnvy+nrn++GavvGvqpfGG+GlsGtGpkaGGp+yl r++ lcl|FitnessBrowser__SB2B:6938573 975 IHSRNEGHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTGPKAGGPHYLTRFVT 1034 *********************************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (500 nodes) Target sequences: 1 (1058 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: 19.42 // [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:
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