Align delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial; EC 1.5.1.12 (characterized)
to candidate WP_025765157.1 X939_RS0120545 L-glutamate gamma-semialdehyde dehydrogenase
Query= CharProtDB::CH_122352 (572 letters) >NCBI__GCF_000566685.1:WP_025765157.1 Length = 543 Score = 508 bits (1308), Expect = e-148 Identities = 272/540 (50%), Positives = 349/540 (64%), Gaps = 8/540 (1%) Query: 30 YKVPRIDNEPNKHYAAGSPDRKALQEALARTQRNAPLSVPLVIAGKEVKSSSSLTQSNPA 89 + VP + NEP K YA G+ +R L+E L + R + +P I G E S + + P Sbjct: 6 FLVPALKNEPIKSYAPGTAERAELKEMLDQA-RKVQIEIPQYIGGGEKYSGKKVRLAPPH 64 Query: 90 SHGPVATYSN-ATAKDVQAAIESALEARKSWASTPFADRASVFLKAADLISTKYRYDVMA 148 H V Y + TA DV+ AI ALEAR WA+ + RA++FLKAADLI+ YR ++ A Sbjct: 65 DHQHVLGYFHEGTAADVKLAITEALEARTKWAAMDWEQRAAIFLKAADLIAGPYRAEINA 124 Query: 149 LTMHGQGKNAWQAEIDSAAELCDFFRFGVKYAEDLYAQQPVHHAPGVWNRVEYRPLEGFV 208 TM GQ KNA+QAEIDSA EL DF R V + +++Y QQP+ + G+WNR+EYRPLEGFV Sbjct: 125 ATMLGQSKNAYQAEIDSACELIDFLRMNVNFMQEIYEQQPIS-SDGIWNRMEYRPLEGFV 183 Query: 209 YAISPFNFTAIGGNLAGAPALMGNVVVWKPSPSAIASNWLVHQILLEAGLPKNVIQFVPG 268 +AI+PFNFTAI GNL APALMGNV +WKP+ + + + ++ ++ EAGLP VI + Sbjct: 184 FAITPFNFTAIAGNLPAAPALMGNVTLWKPAFTQVYAANVIMKVFKEAGLPDGVINMILV 243 Query: 269 EAEEVTKTVLDHPDFAALHFTGSTNVFRNLYGQISTRVAAGKYRSYPRIVGETGGKNFHL 328 + E + V HPDFA +HFTGST VF+ ++ I +A Y+++PRIVGETGGK+F L Sbjct: 244 DGPEAGEVVFKHPDFAGIHFTGSTKVFQTIWKTIGENIAG--YKTFPRIVGETGGKDFVL 301 Query: 329 IHKSADIRNAAVQTVRGAFEYQGQKCSATSRVYVASSIADSFLEQVASEAKSLKVGPPSD 388 HKSA+ + A VRGAFEYQGQKCSA SR Y+ S+I + E + ++ +K+G D Sbjct: 302 AHKSANAKALATGLVRGAFEYQGQKCSAASRAYIPSNIWEEVKEYIHADLAEIKMGGVED 361 Query: 389 FTNFCGPVIHEASFTKLAKVIDEAKNDPELELLAGGSYDSSKGWYIQPTVYRTTNPDHPL 448 F NF VI E +F K+ ID AK E E++AGG+YD S G++I PTV +PD+ Sbjct: 362 FGNFINAVIDEKAFDKIVGYIDAAKASQEAEIIAGGTYDKSVGYFIAPTVILAHSPDYVT 421 Query: 449 LTRELFGPILVVYAYPDATEADFARIAQKIDATGEYGLTGSVFAQDREALAVANDVLRNA 508 L E+FGP+L +Y Y E F Q +D T Y LTG+VFA DR A+ A L NA Sbjct: 422 LCEEIFGPVLTIYVY---DENKFEETVQLVDQTSPYALTGAVFATDRYAIEYATTNLVNA 478 Query: 509 AGNFYINCKSTGAVVGQQPFGGARASGTNDKAGSGNLLSRFVSLRSIKEEFVPTYKVAYP 568 AGNFYIN K TGAVVGQQPFGGARASGTNDKAGS L R+VS R IKE FV YP Sbjct: 479 AGNFYINDKPTGAVVGQQPFGGARASGTNDKAGSILNLLRWVSPRVIKETFVSPISYQYP 538 Lambda K H 0.316 0.130 0.379 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: 865 Number of extensions: 40 Number of successful extensions: 5 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: 572 Length of database: 543 Length adjustment: 36 Effective length of query: 536 Effective length of database: 507 Effective search space: 271752 Effective search space used: 271752 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 (21.6 bits) S2: 53 (25.0 bits)
Align candidate WP_025765157.1 X939_RS0120545 (L-glutamate gamma-semialdehyde 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.3029401.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-241 787.9 1.6 2.7e-241 787.7 1.6 1.0 1 NCBI__GCF_000566685.1:WP_025765157.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000566685.1:WP_025765157.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 787.7 1.6 2.7e-241 2.7e-241 1 531 [. 12 539 .. 12 541 .. 0.99 Alignments for each domain: == domain 1 score: 787.7 bits; conditional E-value: 2.7e-241 TIGR01236 1 knePvkefrpgskerdllrkelkelkskvleiPlviggkevvksnelievvaPadhqaklakltnateedvkk 73 kneP+k+++pg+ er l++ l ++++ ++eiP igg e ++ + +++ P+dhq++l+ +++ t +dvk NCBI__GCF_000566685.1:WP_025765157.1 12 KNEPIKSYAPGTAERAELKEMLDQARKVQIEIPQYIGGGEKYSGK-KVRLAPPHDHQHVLGYFHEGTAADVKL 83 6*************************************9977766.69************************* PP TIGR01236 74 aveaaldakkeWselpfadraaiflkaadllsgkyreeilaatmlgqsktvyqaeidavaelidffrfnvkya 146 a+ al+a+++W+++++++raaiflkaadl++g+yr+ei+aatmlgqsk+ yqaeid+++elidf+r nv++ NCBI__GCF_000566685.1:WP_025765157.1 84 AITEALEARTKWAAMDWEQRAAIFLKAADLIAGPYRAEINAATMLGQSKNAYQAEIDSACELIDFLRMNVNFM 156 ************************************************************************* PP TIGR01236 147 relleqqPsvsapgelnkveyrpleGfvaaisPfnftaiaanlagaPalmGnvvvWkPsktavlsnyllmkil 219 +e++eqqP +s++g +n++eyrpleGfv+ai+Pfnftaia+nl++aPalmGnv++WkP+ t+v+++ ++mk++ NCBI__GCF_000566685.1:WP_025765157.1 157 QEIYEQQP-ISSDGIWNRMEYRPLEGFVFAITPFNFTAIAGNLPAAPALMGNVTLWKPAFTQVYAANVIMKVF 228 ********.8*************************************************************** PP TIGR01236 220 eeaGlPpgvinfvpadgvkvsdvvladkdlaalhftGstavfkelwkkvasnldkyrnfPrivGetGGkdfvl 292 +eaGlP gvin++ +dg + ++vv ++d+a++hftGst+vf+++wk++ +n+ y++fPrivGetGGkdfvl NCBI__GCF_000566685.1:WP_025765157.1 229 KEAGLPDGVINMILVDGPEAGEVVFKHPDFAGIHFTGSTKVFQTIWKTIGENIAGYKTFPRIVGETGGKDFVL 301 ************************************************************************* PP TIGR01236 293 vhpsadveevvaatirgafeyqGqkcsaasrlyvpkslwkelkeellaelkkvkvgdvddlssfmgavideks 365 +h+sa+ + ++++++rgafeyqGqkcsaasr+y+p +w+e+ke + a+l+++k+g v+d+ +f+ avidek+ NCBI__GCF_000566685.1:WP_025765157.1 302 AHKSANAKALATGLVRGAFEYQGQKCSAASRAYIPSNIWEEVKEYIHADLAEIKMGGVEDFGNFINAVIDEKA 374 ************************************************************************* PP TIGR01236 366 fakivkviekakkdpeeleilaGGkyddskGyfvePtvveskdPkeklmkeeifGPvltvyvydddkykeile 438 f+kiv +i+ ak++ e ei+aGG yd+s Gyf+ Ptv++++ P+ ++ eeifGPvlt+yvyd++k++e+++ NCBI__GCF_000566685.1:WP_025765157.1 375 FDKIVGYIDAAKASQ-EAEIIAGGTYDKSVGYFIAPTVILAHSPDYVTLCEEIFGPVLTIYVYDENKFEETVQ 446 *************65.********************************************************* PP TIGR01236 439 vvdstskyaltGavfakdreaieeaekklrfaaGnfyindkstGavvgqqpfGGarlsGtndkaGapkillrf 511 +vd+ts yaltGavfa dr aie+a+ +l +aaGnfyindk+tGavvgqqpfGGar+sGtndkaG+ +llr+ NCBI__GCF_000566685.1:WP_025765157.1 447 LVDQTSPYALTGAVFATDRYAIEYATTNLVNAAGNFYINDKPTGAVVGQQPFGGARASGTNDKAGSILNLLRW 519 ************************************************************************* PP TIGR01236 512 vsarsiketfkeltdfkypy 531 vs+r+iketf+++ ++yp+ NCBI__GCF_000566685.1:WP_025765157.1 520 VSPRVIKETFVSPISYQYPF 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 16.18 // [ok]
This GapMind analysis is from Sep 24 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