Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate Echvi_1300 Echvi_1300 delta-1-pyrroline-5-carboxylate dehydrogenase, group 1
Query= BRENDA::P30038 (563 letters) >FitnessBrowser__Cola:Echvi_1300 Length = 543 Score = 513 bits (1321), Expect = e-150 Identities = 258/530 (48%), Positives = 351/530 (66%), Gaps = 3/530 (0%) Query: 34 NEPVLAFTQGSPERDALQKALKDLKGRMEAIPCVVGDEEVWTSDVQYQVSPFNHGHKVAK 93 NEPV + G+P R LQ AL++ + + +P +G EEV T + P +H H + Sbjct: 13 NEPVFDYAPGTPARAKLQAALQEARSKEVDVPMYIGSEEVRTGNKIPLSPPHDHQHLLGH 72 Query: 94 FCYADKSLLNKAIEAALAARKEWDLKPIADRAQIFLKAADMLSGPRRAEILAKTMVGQGK 153 F DKS + +AI AAL A++ W+ RA IFLKAAD+++GP R ++ A TM+GQ K Sbjct: 73 FHEGDKSHVEQAINAALGAKEAWETMEWEQRAAIFLKAADLIAGPYRYKMNAATMLGQSK 132 Query: 154 TVIQAEIDAAAELIDFFRFNAKYAVELEGQQP-ISVPPSTNSTVYRGLEGFVAAISPFNF 212 QAEID+A E++DF RFN KY E+ QQP IS N R LEGFV A++PFNF Sbjct: 133 NAFQAEIDSACEIVDFLRFNVKYMTEIYKQQPPISGDGVWNRLEQRPLEGFVFALTPFNF 192 Query: 213 TAIGGNLAGAPALMGNVVLWKPSDTAMLASYAVYRILREAGLPPNIIQFVPADGPLFGDT 272 TAI GNL APA+MGN V+WKP+ T + + + ++ REAG+P +I V DGP G+ Sbjct: 193 TAIAGNLPTAPAMMGNTVVWKPAYTQIYTANLLMQVFREAGVPDGVINLVYVDGPAAGEV 252 Query: 273 VTSSEHLCGINFTGSVPTFKHLWKQVAQNLDRFHTFPRLAGECGGKNFHFVHRSADVESV 332 + GI+FTGS F+ +WK + N++++ ++PR+ GE GGK+F H+SAD + + Sbjct: 253 IFEHPEFAGIHFTGSTAVFQTIWKTIGNNIEKYKSYPRIVGETGGKDFVIAHKSADAKQL 312 Query: 333 VSGTLRSAFEYGGQKCSACSRLYVPHSLWPQIKGRLLEEHSRIKVGDPAEDFGTFFSAVI 392 +G +R AFE+ GQKCSA SR Y+P +LW +K + E+ + IK+G P EDF F +AVI Sbjct: 313 ATGLVRGAFEFQGQKCSAASRAYIPSNLWEDVKKYMQEDLASIKMGGP-EDFSNFINAVI 371 Query: 393 DAKSFARIKKWLEHARSSPSLTILAGGKCDDSVGYFVEPCIVESKDPQEPIMKEEIFGPV 452 D KSF +I K+++ A+S L ++AGG D S GYFVEP ++ +KDP M EEIFGPV Sbjct: 372 DEKSFDKIAKYIDTAKSD-GLEVVAGGHYDKSKGYFVEPTVLLTKDPMYTTMCEEIFGPV 430 Query: 453 LSVYVYPDDKYKETLQLVDSTTSYGLTGAVFSQDKDVVQEATKVLRNAAGNFYINDKSTG 512 L++YVY +D ++E L+LVD T+ YGLTGA+FS D+ Q AT+ LRNAAGNFYINDK TG Sbjct: 431 LTIYVYQEDHFEEALELVDQTSPYGLTGAIFSHDRYAAQLATQKLRNAAGNFYINDKPTG 490 Query: 513 SIVGQQPFGGARASGTNDKPGGPHYILRWTSPQVIKETHKPLGDWSYAYM 562 ++VGQQPFGGAR SGTNDK G +LRW SP+ IKET D+ Y ++ Sbjct: 491 AVVGQQPFGGARKSGTNDKAGAMINMLRWVSPRTIKETFVTPTDYRYPFL 540 Lambda K H 0.319 0.135 0.411 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: 870 Number of extensions: 37 Number of successful extensions: 4 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: 563 Length of database: 543 Length adjustment: 36 Effective length of query: 527 Effective length of database: 507 Effective search space: 267189 Effective search space used: 267189 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 (21.7 bits) S2: 53 (25.0 bits)
Align candidate Echvi_1300 Echvi_1300 (delta-1-pyrroline-5-carboxylate dehydrogenase, group 1)
to HMM TIGR01236 (pruA: 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/TIGR01236.hmm # target sequence database: /tmp/gapView.4951.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01236 [M=533] Accession: TIGR01236 Description: D1pyr5carbox1: 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-246 804.2 0.2 3e-246 804.1 0.2 1.0 1 lcl|FitnessBrowser__Cola:Echvi_1300 Echvi_1300 delta-1-pyrroline-5-c Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cola:Echvi_1300 Echvi_1300 delta-1-pyrroline-5-carboxylate dehydrogenase, group 1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 804.1 0.2 3e-246 3e-246 1 531 [. 12 539 .. 12 541 .. 0.99 Alignments for each domain: == domain 1 score: 804.1 bits; conditional E-value: 3e-246 TIGR01236 1 knePvkefrpgskerdllrkelkelkskvleiPlviggkevvksnelievvaPadhqaklakltnateedvkka 74 knePv +++pg+++r +l+++l+e++sk +++P+ ig +ev + n +i P+dhq+ l+++++ ++++v++a lcl|FitnessBrowser__Cola:Echvi_1300 12 KNEPVFDYAPGTPARAKLQAALQEARSKEVDVPMYIGSEEVRTGN-KIPLSPPHDHQHLLGHFHEGDKSHVEQA 84 6***************************************66655.7*************************** PP TIGR01236 75 veaaldakkeWselpfadraaiflkaadllsgkyreeilaatmlgqsktvyqaeidavaelidffrfnvkyare 148 ++aal ak+ W+++++++raaiflkaadl++g+yr++++aatmlgqsk+ +qaeid+++e++df+rfnvky +e lcl|FitnessBrowser__Cola:Echvi_1300 85 INAALGAKEAWETMEWEQRAAIFLKAADLIAGPYRYKMNAATMLGQSKNAFQAEIDSACEIVDFLRFNVKYMTE 158 ************************************************************************** PP TIGR01236 149 lleqqPsvsapgelnkveyrpleGfvaaisPfnftaiaanlagaPalmGnvvvWkPsktavlsnyllmkileea 222 +++qqP +s++g++n+ e rpleGfv+a++Pfnftaia+nl++aPa+mGn+vvWkP+ t+++++ llm++++ea lcl|FitnessBrowser__Cola:Echvi_1300 159 IYKQQPPISGDGVWNRLEQRPLEGFVFALTPFNFTAIAGNLPTAPAMMGNTVVWKPAYTQIYTANLLMQVFREA 232 ************************************************************************** PP TIGR01236 223 GlPpgvinfvpadgvkvsdvvladkdlaalhftGstavfkelwkkvasnldkyrnfPrivGetGGkdfvlvhps 296 G+P gvin+v +dg + ++v+ ++++a++hftGstavf+++wk++ +n++ky+++PrivGetGGkdfv++h+s lcl|FitnessBrowser__Cola:Echvi_1300 233 GVPDGVINLVYVDGPAAGEVIFEHPEFAGIHFTGSTAVFQTIWKTIGNNIEKYKSYPRIVGETGGKDFVIAHKS 306 ************************************************************************** PP TIGR01236 297 adveevvaatirgafeyqGqkcsaasrlyvpkslwkelkeellaelkkvkvgdvddlssfmgavideksfakiv 370 ad ++++++++rgafe+qGqkcsaasr+y+p lw+++k+ + ++l+++k+g ++d+s+f+ avideksf+ki lcl|FitnessBrowser__Cola:Echvi_1300 307 ADAKQLATGLVRGAFEFQGQKCSAASRAYIPSNLWEDVKKYMQEDLASIKMGGPEDFSNFINAVIDEKSFDKIA 380 ************************************************************************** PP TIGR01236 371 kviekakkdpeeleilaGGkyddskGyfvePtvveskdPkeklmkeeifGPvltvyvydddkykeilevvdsts 444 k+i++ak+d le++aGG+yd+skGyfvePtv+++kdP +m eeifGPvlt+yvy++d+++e le+vd+ts lcl|FitnessBrowser__Cola:Echvi_1300 381 KYIDTAKSDG--LEVVAGGHYDKSKGYFVEPTVLLTKDPMYTTMCEEIFGPVLTIYVYQEDHFEEALELVDQTS 452 ********88..************************************************************** PP TIGR01236 445 kyaltGavfakdreaieeaekklrfaaGnfyindkstGavvgqqpfGGarlsGtndkaGapkillrfvsarsik 518 y+ltGa+f++dr a + a++klr+aaGnfyindk+tGavvgqqpfGGar sGtndkaGa+ ++lr+vs+r+ik lcl|FitnessBrowser__Cola:Echvi_1300 453 PYGLTGAIFSHDRYAAQLATQKLRNAAGNFYINDKPTGAVVGQQPFGGARKSGTNDKAGAMINMLRWVSPRTIK 526 ************************************************************************** PP TIGR01236 519 etfkeltdfkypy 531 etf+++td++yp+ lcl|FitnessBrowser__Cola:Echvi_1300 527 ETFVTPTDYRYPF 539 ***********97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (533 nodes) Target sequences: 1 (543 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: 00:00:00.03 # Mc/sec: 8.75 // [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