Align delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial; EC 1.5.1.12 (characterized)
to candidate WP_008991251.1 I215_RS06920 L-glutamate gamma-semialdehyde dehydrogenase
Query= CharProtDB::CH_122352 (572 letters) >NCBI__GCF_000300875.1:WP_008991251.1 Length = 543 Score = 519 bits (1336), Expect = e-151 Identities = 276/540 (51%), Positives = 353/540 (65%), Gaps = 8/540 (1%) Query: 30 YKVPRIDNEPNKHYAAGSPDRKALQEALARTQRNAPLSVPLVIAGKEVKSSSSLTQSNPA 89 + VP+ NEP K YA GSP+R A+ E + N+ + +P+ I +EV++ ++ S P Sbjct: 6 FHVPKAVNEPVKSYAPGSPERAAVLEQYDQ-YFNSTVDIPMYIGSEEVRTGNTQPLSPPH 64 Query: 90 SHGP-VATYSNATAKDVQAAIESALEARKSWASTPFADRASVFLKAADLISTKYRYDVMA 148 H V Y A V AI + LEAR WA+ + RA+VFLKAA+LI+ YR + A Sbjct: 65 DHQHIVGKYHLADKSLVSKAIANNLEARGKWAALSWEQRAAVFLKAAELIAGPYRAKINA 124 Query: 149 LTMHGQGKNAWQAEIDSAAELCDFFRFGVKYAEDLYAQQPVHHAPGVWNRVEYRPLEGFV 208 TM Q KN QAEIDSA EL DF F +++ ++Y QP + G+WNRVEYRPLEGFV Sbjct: 125 ATMIAQSKNIHQAEIDSACELIDFLNFNIEFMSNIYQDQPKSES-GIWNRVEYRPLEGFV 183 Query: 209 YAISPFNFTAIGGNLAGAPALMGNVVVWKPSPSAIASNWLVHQILLEAGLPKNVIQFVPG 268 YA++PFNFTAI GNL + A+MGNVV+WKPS S I S ++ I EAGLP VI V G Sbjct: 184 YAVTPFNFTAIAGNLPASAAMMGNVVLWKPSDSQIYSAKVIVDIFKEAGLPDGVINVVYG 243 Query: 269 EAEEVTKTVLDHPDFAALHFTGSTNVFRNLYGQISTRVAAGKYRSYPRIVGETGGKNFHL 328 + + +T TVL PDFA +HFTGST+VF++++ I + Y+SYPRIVGETGGK+F + Sbjct: 244 DPQMITDTVLSSPDFAGIHFTGSTSVFKSIWKNIGNNIDI--YKSYPRIVGETGGKDFII 301 Query: 329 IHKSADIRNAAVQTVRGAFEYQGQKCSATSRVYVASSIADSFLEQVASEAKSLKVGPPSD 388 H S++ + A RGAFE+QGQKCSA SRVY+ SIA L+ V + +S K+G P+ Sbjct: 302 AHPSSNPKQVATAISRGAFEFQGQKCSAASRVYLPESIASQVLDFVKQDVESFKIGAPNQ 361 Query: 389 FTNFCGPVIHEASFTKLAKVIDEAKNDPELELLAGGSYDSSKGWYIQPTVYRTTNPDHPL 448 NF VIHE SF KLA ID+AK D + E+ GG+YD SKG++I PTV TT+P + Sbjct: 362 MENFITAVIHEGSFDKLASYIDQAKEDADAEIFVGGTYDKSKGYFIHPTVIVTTDPKYKT 421 Query: 449 LTRELFGPILVVYAYPDATEADFARIAQKIDATGEYGLTGSVFAQDREALAVANDVLRNA 508 +T ELFGP++ VY Y D +A +D T EYGLTG+VF+ DR + A L+N+ Sbjct: 422 MTTELFGPVVTVYVYKD---DQWAETLNLVDTTSEYGLTGAVFSNDRYTIEEATTALQNS 478 Query: 509 AGNFYINCKSTGAVVGQQPFGGARASGTNDKAGSGNLLSRFVSLRSIKEEFVPTYKVAYP 568 AGNFYIN K TGAVVGQQPFGGARASGTNDKAGS L R+VS R IKE FV YP Sbjct: 479 AGNFYINDKPTGAVVGQQPFGGARASGTNDKAGSAQNLLRWVSPRLIKETFVTPVDYRYP 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: 914 Number of extensions: 41 Number of successful extensions: 6 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_008991251.1 I215_RS06920 (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.662525.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.1e-235 767.3 1.6 4.7e-235 767.1 1.6 1.0 1 NCBI__GCF_000300875.1:WP_008991251.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000300875.1:WP_008991251.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 767.1 1.6 4.7e-235 4.7e-235 2 531 .. 13 539 .. 12 541 .. 0.99 Alignments for each domain: == domain 1 score: 767.1 bits; conditional E-value: 4.7e-235 TIGR01236 2 nePvkefrpgskerdllrkelkelkskvleiPlviggkevvksnelievvaPadhqaklakltnateedvkka 74 nePvk+++pgs+er ++ ++ + +++++iP+ ig +ev +++++ P+dhq+ ++k + a++++v+ka NCBI__GCF_000300875.1:WP_008991251.1 13 NEPVKSYAPGSPERAAVLEQYDQYFNSTVDIPMYIGSEEVR-TGNTQPLSPPHDHQHIVGKYHLADKSLVSKA 84 9***************9999******************955.5558*************************** PP TIGR01236 75 veaaldakkeWselpfadraaiflkaadllsgkyreeilaatmlgqsktvyqaeidavaelidffrfnvkyar 147 + + l+a+ +W++l +++raa+flkaa+l++g+yr++i+aatm++qsk+++qaeid+++elidf+ fn+++ + NCBI__GCF_000300875.1:WP_008991251.1 85 IANNLEARGKWAALSWEQRAAVFLKAAELIAGPYRAKINAATMIAQSKNIHQAEIDSACELIDFLNFNIEFMS 157 ************************************************************************* PP TIGR01236 148 elleqqPsvsapgelnkveyrpleGfvaaisPfnftaiaanlagaPalmGnvvvWkPsktavlsnyllmkile 220 ++++ qP +s +g +n+veyrpleGfv+a++Pfnftaia+nl+++ a+mGnvv+WkPs+ +++s+ +++ i++ NCBI__GCF_000300875.1:WP_008991251.1 158 NIYQDQP-KSESGIWNRVEYRPLEGFVYAVTPFNFTAIAGNLPASAAMMGNVVLWKPSDSQIYSAKVIVDIFK 229 *******.79*************************************************************** PP TIGR01236 221 eaGlPpgvinfvpadgvkvsdvvladkdlaalhftGstavfkelwkkvasnldkyrnfPrivGetGGkdfvlv 293 eaGlP gvin+v +d+ +++d+vl+++d+a++hftGst+vfk++wk++ +n+d y+++PrivGetGGkdf+++ NCBI__GCF_000300875.1:WP_008991251.1 230 EAGLPDGVINVVYGDPQMITDTVLSSPDFAGIHFTGSTSVFKSIWKNIGNNIDIYKSYPRIVGETGGKDFIIA 302 ************************************************************************* PP TIGR01236 294 hpsadveevvaatirgafeyqGqkcsaasrlyvpkslwkelkeellaelkkvkvgdvddlssfmgavideksf 366 hps++ ++v++a+ rgafe+qGqkcsaasr+y+p+s+ ++ + ++++ ++ k+g ++++++f++avi+e sf NCBI__GCF_000300875.1:WP_008991251.1 303 HPSSNPKQVATAISRGAFEFQGQKCSAASRVYLPESIASQVLDFVKQDVESFKIGAPNQMENFITAVIHEGSF 375 ************************************************************************* PP TIGR01236 367 akivkviekakkdpeeleilaGGkyddskGyfvePtvveskdPkeklmkeeifGPvltvyvydddkykeilev 439 +k+ ++i++ak+d+ + ei +GG yd+skGyf++Ptv+ + dPk k+m++e+fGPv+tvyvy+dd++ e+l++ NCBI__GCF_000300875.1:WP_008991251.1 376 DKLASYIDQAKEDA-DAEIFVGGTYDKSKGYFIHPTVIVTTDPKYKTMTTELFGPVVTVYVYKDDQWAETLNL 447 ************99.99******************************************************** PP TIGR01236 440 vdstskyaltGavfakdreaieeaekklrfaaGnfyindkstGavvgqqpfGGarlsGtndkaGapkillrfv 512 vd+ts+y+ltGavf++dr +ieea+ +l+++aGnfyindk+tGavvgqqpfGGar+sGtndkaG++++llr+v NCBI__GCF_000300875.1:WP_008991251.1 448 VDTTSEYGLTGAVFSNDRYTIEEATTALQNSAGNFYINDKPTGAVVGQQPFGGARASGTNDKAGSAQNLLRWV 520 ************************************************************************* PP TIGR01236 513 sarsiketfkeltdfkypy 531 s+r iketf+++ d++yp+ NCBI__GCF_000300875.1:WP_008991251.1 521 SPRLIKETFVTPVDYRYPF 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: 18.00 // [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