Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate CA265_RS16605 CA265_RS16605 1-pyrroline-5-carboxylate dehydrogenase
Query= BRENDA::P30038 (563 letters) >FitnessBrowser__Pedo557:CA265_RS16605 Length = 544 Score = 525 bits (1352), Expect = e-153 Identities = 255/530 (48%), Positives = 358/530 (67%), Gaps = 2/530 (0%) Query: 34 NEPVLAFTQGSPERDALQKALKDLKGRMEAIPCVVGDEEVWTSDVQYQVSPFNHGHKVAK 93 NEP+ ++ G+ ER L++A+ D + + IP +G +EV T + + V+P +H H +A Sbjct: 13 NEPINSYAPGTKERSLLKEAIADARSKQLDIPMFIGGQEVHTKNKKKVVAPHDHQHVLAT 72 Query: 94 FCYADKSLLNKAIEAALAARKEWDLKPIADRAQIFLKAADMLSGPRRAEILAKTMVGQGK 153 F Y DKS + +AI+AALAA+ +W+ RA IF+KAAD+++ R +I A TM+GQ K Sbjct: 73 FSYGDKSHVKQAIDAALAAKADWEALAWEHRAAIFMKAADLIATKYRYQINAATMLGQSK 132 Query: 154 TVIQAEIDAAAELIDFFRFNAKYAVELEGQQP-ISVPPSTNSTVYRGLEGFVAAISPFNF 212 QAEIDAA EL+DF RFN Y ++ GQQP +S N T R LEGF+ A++PFNF Sbjct: 133 NAYQAEIDAACELVDFLRFNVSYMQDIYGQQPPVSPNGMWNRTEQRPLEGFIFALTPFNF 192 Query: 213 TAIGGNLAGAPALMGNVVLWKPSDTAMLASYAVYRILREAGLPPNIIQFVPADGPLFGDT 272 TAI GNL A+MGNVV+WKP+DT + A+ + +I REAGLP +I + ADGP GD Sbjct: 193 TAIAGNLPACVAMMGNVVVWKPADTQVYAANVIMQIFREAGLPDGVINLIFADGPEVGDV 252 Query: 273 VTSSEHLCGINFTGSVPTFKHLWKQVAQNLDRFHTFPRLAGECGGKNFHFVHRSADVESV 332 V + GI+FTGS F+ +WK + N+ ++ ++PR+ GE GGK+F VH SADV + Sbjct: 253 VFNHADFAGIHFTGSTKVFQEIWKTIGTNIHKYKSYPRIVGETGGKDFILVHPSADVAAS 312 Query: 333 VSGTLRSAFEYGGQKCSACSRLYVPHSLWPQIKGRLLEEHSRIKVGDPAEDFGTFFSAVI 392 + +R AFEY GQKCSA SR Y+P SLWP+IK ++ + + K+G EDF F +AVI Sbjct: 313 ATAIVRGAFEYQGQKCSAASRTYIPKSLWPEIKKLMIRDLASFKMGG-TEDFSNFINAVI 371 Query: 393 DAKSFARIKKWLEHARSSPSLTILAGGKCDDSVGYFVEPCIVESKDPQEPIMKEEIFGPV 452 D +SF ++ K+++ A+ + ++AGG D S GYF+EP I+ DP+ M EE+FGPV Sbjct: 372 DERSFDKLAKYIDQAKKDKGVEVIAGGNYDKSKGYFIEPTILVVDDPKYTTMCEELFGPV 431 Query: 453 LSVYVYPDDKYKETLQLVDSTTSYGLTGAVFSQDKDVVQEATKVLRNAAGNFYINDKSTG 512 LSVYVY D ++ + L+++D+T+ Y LTGA+ SQD+ +++A+ LRN+AGNFYINDK TG Sbjct: 432 LSVYVYEDQEFDQVLEIIDTTSPYALTGAILSQDRYAIEKASYALRNSAGNFYINDKCTG 491 Query: 513 SIVGQQPFGGARASGTNDKPGGPHYILRWTSPQVIKETHKPLGDWSYAYM 562 ++VGQQPFGGAR SGTNDK G +LRW SP+ IKET P D+ Y ++ Sbjct: 492 AVVGQQPFGGARGSGTNDKAGAMINLLRWVSPRTIKETFNPPTDYRYPFL 541 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: 883 Number of extensions: 32 Number of successful extensions: 3 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: 544 Length adjustment: 36 Effective length of query: 527 Effective length of database: 508 Effective search space: 267716 Effective search space used: 267716 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 CA265_RS16605 CA265_RS16605 (1-pyrroline-5-carboxylate dehydrogenase)
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.20827.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-252 825.0 1.5 1.6e-252 824.8 1.5 1.0 1 lcl|FitnessBrowser__Pedo557:CA265_RS16605 CA265_RS16605 1-pyrroline-5-carb Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Pedo557:CA265_RS16605 CA265_RS16605 1-pyrroline-5-carboxylate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 824.8 1.5 1.6e-252 1.6e-252 2 531 .. 13 540 .. 12 542 .. 0.99 Alignments for each domain: == domain 1 score: 824.8 bits; conditional E-value: 1.6e-252 TIGR01236 2 nePvkefrpgskerdllrkelkelkskvleiPlviggkevvksnelievvaPadhqaklakltnatee 69 neP+++++pg+ker ll++++++++sk+l+iP+ igg+ev ++n + +vvaP+dhq++la++ + +++ lcl|FitnessBrowser__Pedo557:CA265_RS16605 13 NEPINSYAPGTKERSLLKEAIADARSKQLDIPMFIGGQEVHTKN-KKKVVAPHDHQHVLATFSYGDKS 79 9**************************************99888.59********************* PP TIGR01236 70 dvkkaveaaldakkeWselpfadraaiflkaadllsgkyreeilaatmlgqsktvyqaeidavaelid 137 +vk+a++aal+ak +W++l +++raaif+kaadl+++kyr++i+aatmlgqsk+ yqaeida++el+d lcl|FitnessBrowser__Pedo557:CA265_RS16605 80 HVKQAIDAALAAKADWEALAWEHRAAIFMKAADLIATKYRYQINAATMLGQSKNAYQAEIDAACELVD 147 ******************************************************************** PP TIGR01236 138 ffrfnvkyarelleqqPsvsapgelnkveyrpleGfvaaisPfnftaiaanlagaPalmGnvvvWkPs 205 f+rfnv y +++++qqP vs +g +n++e rpleGf++a++Pfnftaia+nl+++ a+mGnvvvWkP+ lcl|FitnessBrowser__Pedo557:CA265_RS16605 148 FLRFNVSYMQDIYGQQPPVSPNGMWNRTEQRPLEGFIFALTPFNFTAIAGNLPACVAMMGNVVVWKPA 215 *****************99************************************************* PP TIGR01236 206 ktavlsnyllmkileeaGlPpgvinfvpadgvkvsdvvladkdlaalhftGstavfkelwkkvasnld 273 +t+v+++ ++m+i++eaGlP gvin++ adg +v+dvv + d+a++hftGst+vf+e+wk++ +n++ lcl|FitnessBrowser__Pedo557:CA265_RS16605 216 DTQVYAANVIMQIFREAGLPDGVINLIFADGPEVGDVVFNHADFAGIHFTGSTKVFQEIWKTIGTNIH 283 ******************************************************************** PP TIGR01236 274 kyrnfPrivGetGGkdfvlvhpsadveevvaatirgafeyqGqkcsaasrlyvpkslwkelkeellae 341 ky+++PrivGetGGkdf+lvhpsadv ++a++rgafeyqGqkcsaasr y+pkslw+e+k+ ++++ lcl|FitnessBrowser__Pedo557:CA265_RS16605 284 KYKSYPRIVGETGGKDFILVHPSADVAASATAIVRGAFEYQGQKCSAASRTYIPKSLWPEIKKLMIRD 351 ******************************************************************** PP TIGR01236 342 lkkvkvgdvddlssfmgavideksfakivkviekakkdpeeleilaGGkyddskGyfvePtvveskdP 409 l++ k+g +d+s+f+ avide+sf+k+ k+i++akkd +e++aGG+yd+skGyf+ePt++ +dP lcl|FitnessBrowser__Pedo557:CA265_RS16605 352 LASFKMGGTEDFSNFINAVIDERSFDKLAKYIDQAKKDK-GVEVIAGGNYDKSKGYFIEPTILVVDDP 418 *************************************98.9*************************** PP TIGR01236 410 keklmkeeifGPvltvyvydddkykeilevvdstskyaltGavfakdreaieeaekklrfaaGnfyin 477 k +m ee+fGPvl+vyvy+d++++++le++d+ts yaltGa++++dr aie+a+ +lr++aGnfyin lcl|FitnessBrowser__Pedo557:CA265_RS16605 419 KYTTMCEELFGPVLSVYVYEDQEFDQVLEIIDTTSPYALTGAILSQDRYAIEKASYALRNSAGNFYIN 486 ******************************************************************** PP TIGR01236 478 dkstGavvgqqpfGGarlsGtndkaGapkillrfvsarsiketfkeltdfkypy 531 dk+tGavvgqqpfGGar sGtndkaGa+ +llr+vs+r+iketf+++td++yp+ lcl|FitnessBrowser__Pedo557:CA265_RS16605 487 DKCTGAVVGQQPFGGARGSGTNDKAGAMINLLRWVSPRTIKETFNPPTDYRYPF 540 ****************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (533 nodes) Target sequences: 1 (544 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: 11.50 // [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