Align delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial; EC 1.5.1.12 (characterized)
to candidate WP_062062443.1 N456_RS22400 L-glutamate gamma-semialdehyde dehydrogenase
Query= CharProtDB::CH_122352 (572 letters) >NCBI__GCF_001401755.1:WP_062062443.1 Length = 542 Score = 521 bits (1343), Expect = e-152 Identities = 273/540 (50%), Positives = 355/540 (65%), Gaps = 8/540 (1%) Query: 30 YKVPRIDNEPNKHYAAGSPDRKALQEALARTQRNAPLSVPLVIAGKEVKSSSSLTQSNPA 89 ++VP NEP K YA G+P+R+ + A N+ + VPL I G+E+++ + T + P Sbjct: 6 FQVPTAINEPIKSYAPGTPEREEVLATYA-AMYNSTVDVPLYINGEEIRTGDTGTMAPPH 64 Query: 90 SHGPV-ATYSNATAKDVQAAIESALEARKSWASTPFADRASVFLKAADLISTKYRYDVMA 148 H + TY A + +Q AI++ALEARK WA P+ RA+VFL+AA+LI+ YR + A Sbjct: 65 DHQHILGTYHKAEKQHIQKAIDTALEARKKWAQLPWEQRAAVFLRAAELIAGPYRAKINA 124 Query: 149 LTMHGQGKNAWQAEIDSAAELCDFFRFGVKYAEDLYAQQPVHHAPGVWNRVEYRPLEGFV 208 TM Q KN +QAEID+A E DF RF V++ +Y QP WNR+EYRPLEGFV Sbjct: 125 ATMLAQSKNIFQAEIDAACEFIDFLRFNVEFMTQIYEDQP-DSTSDAWNRLEYRPLEGFV 183 Query: 209 YAISPFNFTAIGGNLAGAPALMGNVVVWKPSPSAIASNWLVHQILLEAGLPKNVIQFVPG 268 YAI+PFNFTAI GNL + ALMGN VVWKPS S I S ++ I EAG+P VI V G Sbjct: 184 YAITPFNFTAISGNLPASAALMGNTVVWKPSDSQIYSAKVIVDIFKEAGVPDGVINVVYG 243 Query: 269 EAEEVTKTVLDHPDFAALHFTGSTNVFRNLYGQISTRVAAGKYRSYPRIVGETGGKNFHL 328 + +T TVL PDFA +HFTGST+VF++++ +I T + Y++YPRIVGETGGK+F + Sbjct: 244 DPVMITDTVLASPDFAGIHFTGSTHVFKDIWAKIGTNIH--NYKTYPRIVGETGGKDFII 301 Query: 329 IHKSADIRNAAVQTVRGAFEYQGQKCSATSRVYVASSIADSFLEQVASEAKSLKVGPPSD 388 H SA+ + A RGAFEYQGQKCSA SR Y+ S+ +Q+ + S K+G P D Sbjct: 302 AHPSANAKQVATGISRGAFEYQGQKCSAASRAYIPKSLWADVEKQLLEDTNSFKMGSPED 361 Query: 389 FTNFCGPVIHEASFTKLAKVIDEAKNDPELELLAGGSYDSSKGWYIQPTVYRTTNPDHPL 448 +NF VIHE SF KLAK ID+AKND + E++AGG+YD SKG++I+PT+ T +P + Sbjct: 362 MSNFITAVIHEGSFDKLAKYIDQAKNDTDAEIIAGGNYDKSKGYFIEPTIIVTKDPKYTT 421 Query: 449 LTRELFGPILVVYAYPDATEADFARIAQKIDATGEYGLTGSVFAQDREALAVANDVLRNA 508 + ELFGP++ +Y Y D + ++ +D T EY LTG++F+ DR A A L N Sbjct: 422 MCTELFGPVVTIYVYDDNQWDETLKL---VDQTSEYALTGAIFSTDRYAATEATKALENC 478 Query: 509 AGNFYINCKSTGAVVGQQPFGGARASGTNDKAGSGNLLSRFVSLRSIKEEFVPTYKVAYP 568 AGNFYIN K TGAVVGQQPFGGARASGTNDKAGS L R+VS R IKE FV YP Sbjct: 479 AGNFYINDKCTGAVVGQQPFGGARASGTNDKAGSYLNLLRWVSPRMIKETFVSPANYRYP 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: 862 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: 542 Length adjustment: 36 Effective length of query: 536 Effective length of database: 506 Effective search space: 271216 Effective search space used: 271216 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_062062443.1 N456_RS22400 (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.245464.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.3e-243 792.7 1.4 9.4e-243 792.5 1.4 1.0 1 NCBI__GCF_001401755.1:WP_062062443.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001401755.1:WP_062062443.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 792.5 1.4 9.4e-243 9.4e-243 2 531 .. 13 539 .. 12 541 .. 0.99 Alignments for each domain: == domain 1 score: 792.5 bits; conditional E-value: 9.4e-243 TIGR01236 2 nePvkefrpgskerdllrkelkelkskvleiPlviggkevvksnelievvaPadhqaklakltnateedvkka 74 neP+k+++pg++er+ + ++ + + ++++++Pl i+g+e+ + ++ ++ P+dhq+ l++ ++a++++++ka NCBI__GCF_001401755.1:WP_062062443.1 13 NEPIKSYAPGTPEREEVLATYAAMYNSTVDVPLYINGEEIRTG-DTGTMAPPHDHQHILGTYHKAEKQHIQKA 84 9**************************************6555.57999************************ PP TIGR01236 75 veaaldakkeWselpfadraaiflkaadllsgkyreeilaatmlgqsktvyqaeidavaelidffrfnvkyar 147 +++al+a+k+W++lp+++raa+fl+aa+l++g+yr++i+aatml+qsk+++qaeida++e idf+rfnv++ + NCBI__GCF_001401755.1:WP_062062443.1 85 IDTALEARKKWAQLPWEQRAAVFLRAAELIAGPYRAKINAATMLAQSKNIFQAEIDAACEFIDFLRFNVEFMT 157 ************************************************************************* PP TIGR01236 148 elleqqPsvsapgelnkveyrpleGfvaaisPfnftaiaanlagaPalmGnvvvWkPsktavlsnyllmkile 220 +++e qP s++ +n+ eyrpleGfv+ai+Pfnftai++nl+++ almGn+vvWkPs+ +++s+ +++ i++ NCBI__GCF_001401755.1:WP_062062443.1 158 QIYEDQP-DSTSDAWNRLEYRPLEGFVYAITPFNFTAISGNLPASAALMGNTVVWKPSDSQIYSAKVIVDIFK 229 *******.79*************************************************************** PP TIGR01236 221 eaGlPpgvinfvpadgvkvsdvvladkdlaalhftGstavfkelwkkvasnldkyrnfPrivGetGGkdfvlv 293 eaG+P gvin+v +d+v+++d+vla++d+a++hftGst+vfk++w k+ +n+++y+++PrivGetGGkdf+++ NCBI__GCF_001401755.1:WP_062062443.1 230 EAGVPDGVINVVYGDPVMITDTVLASPDFAGIHFTGSTHVFKDIWAKIGTNIHNYKTYPRIVGETGGKDFIIA 302 ************************************************************************* PP TIGR01236 294 hpsadveevvaatirgafeyqGqkcsaasrlyvpkslwkelkeellaelkkvkvgdvddlssfmgavideksf 366 hpsa+ ++v++++ rgafeyqGqkcsaasr+y+pkslw +++++ll+++++ k+g ++d+s+f++avi+e sf NCBI__GCF_001401755.1:WP_062062443.1 303 HPSANAKQVATGISRGAFEYQGQKCSAASRAYIPKSLWADVEKQLLEDTNSFKMGSPEDMSNFITAVIHEGSF 375 ************************************************************************* PP TIGR01236 367 akivkviekakkdpeeleilaGGkyddskGyfvePtvveskdPkeklmkeeifGPvltvyvydddkykeilev 439 +k+ k+i++ak+d+ + ei+aGG+yd+skGyf+ePt++ +kdPk +m +e+fGPv+t+yvydd++++e+l++ NCBI__GCF_001401755.1:WP_062062443.1 376 DKLAKYIDQAKNDT-DAEIIAGGNYDKSKGYFIEPTIIVTKDPKYTTMCTELFGPVVTIYVYDDNQWDETLKL 447 ************99.99******************************************************** PP TIGR01236 440 vdstskyaltGavfakdreaieeaekklrfaaGnfyindkstGavvgqqpfGGarlsGtndkaGapkillrfv 512 vd+ts+yaltGa+f+ dr a +ea+k+l ++aGnfyindk+tGavvgqqpfGGar+sGtndkaG+ +llr+v NCBI__GCF_001401755.1:WP_062062443.1 448 VDQTSEYALTGAIFSTDRYAATEATKALENCAGNFYINDKCTGAVVGQQPFGGARASGTNDKAGSYLNLLRWV 520 ************************************************************************* PP TIGR01236 513 sarsiketfkeltdfkypy 531 s+r iketf+++++++yp+ NCBI__GCF_001401755.1:WP_062062443.1 521 SPRMIKETFVSPANYRYPF 539 *****************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (533 nodes) Target sequences: 1 (542 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: 17.37 // [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