Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_089299698.1 CHB84_RS01755 1-pyrroline-5-carboxylate dehydrogenase
Query= BRENDA::P30038 (563 letters) >NCBI__GCF_900188115.1:WP_089299698.1 Length = 542 Score = 501 bits (1290), Expect = e-146 Identities = 259/531 (48%), Positives = 330/531 (62%), Gaps = 3/531 (0%) Query: 34 NEPVLAFTQGSPERDALQKALKDLKGRMEAIP-CVVGDEEVWTSDVQYQVSPFNHGHKVA 92 NE V + GS ER++LQ+ L +L +P V G + + + V+P HGH + Sbjct: 12 NESVYTYAPGSAERESLQRTLAELASEKRELPQTVAGAKRMARGEPFNVVAPHEHGHVLG 71 Query: 93 KFCYADKSLLNKAIEAALAARKEWDLKPIADRAQIFLKAADMLSGPRRAEILAKTMVGQG 152 A + A+ AA A W P +RA +FL+AAD++SG R + A TM+GQ Sbjct: 72 SCAQASDQDVADAVRAAKDAAPAWRELPFDERAAVFLRAADLMSGAWRDTLNAATMLGQS 131 Query: 153 KTVIQAEIDAAAELIDFFRFNAKYAVELEGQQPISVPPSTNSTVYRGLEGFVAAISPFNF 212 K+V Q+EIDA EL+DF RFN +A + +QPISVP + N YR LEGFV AI+PFNF Sbjct: 132 KSVHQSEIDAVCELVDFLRFNVHFARRILAEQPISVPGTWNRAEYRSLEGFVTAITPFNF 191 Query: 213 TAIGGNLAGAPALMGNVVLWKPSDTAMLASYAVYRILREAGLPPNIIQFVPADGPLFGDT 272 TAI GNL APALMGN V+WKP+ T LA++ RIL AGLPP +I V DG Sbjct: 192 TAIAGNLPTAPALMGNTVVWKPTPTQQLAAHFTMRILEAAGLPPGVINMVTGDGAAVSRV 251 Query: 273 VTSSEHLCGINFTGSVPTFKHLWKQVAQNLDRFHTFPRLAGECGGKNFHFVHRSADVESV 332 + G++FTGS TFK LW+ +A NLD + ++PR+ GE GGK+F H SA V+ V Sbjct: 252 ALADPDFAGLHFTGSTATFKMLWRTIADNLDTYRSYPRIVGETGGKDFIVAHPSAHVDKV 311 Query: 333 VSGTLRSAFEYGGQKCSACSRLYVPHSLWPQ-IKGRLLEEHSRIKVGDPAEDFGTFFSAV 391 V+G +R AFEY GQKCSA SR YVP SLW ++ +L + I GD DF F AV Sbjct: 312 VTGIVRGAFEYQGQKCSAASRAYVPRSLWDSGLREQLADVAKTISYGD-VRDFSNFGGAV 370 Query: 392 IDAKSFARIKKWLEHARSSPSLTILAGGKCDDSVGYFVEPCIVESKDPQEPIMKEEIFGP 451 ID ++FA+ L P L +L GG CDDSVGYFVEP ++ DP + E FGP Sbjct: 371 IDHRAFAKHHALLSRVDGDPDLEVLVGGSCDDSVGYFVEPTVLTCTDPHHEVFSTEYFGP 430 Query: 452 VLSVYVYPDDKYKETLQLVDSTTSYGLTGAVFSQDKDVVQEATKVLRNAAGNFYINDKST 511 +++VYVY D +Y L LVDST Y LTGAVF+ D+D V EA +VLR AAGNFY+NDK T Sbjct: 431 IVAVYVYDDAEYSSVLHLVDSTAPYALTGAVFADDRDAVAEAHRVLRYAAGNFYVNDKPT 490 Query: 512 GSIVGQQPFGGARASGTNDKPGGPHYILRWTSPQVIKETHKPLGDWSYAYM 562 GS+V QQPFGGARASGTNDK G ++RWTSP+ IKE D +Y +M Sbjct: 491 GSVVNQQPFGGARASGTNDKAGSLFNMVRWTSPRAIKENFDAPTDHTYPHM 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: 823 Number of extensions: 37 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: 542 Length adjustment: 36 Effective length of query: 527 Effective length of database: 506 Effective search space: 266662 Effective search space used: 266662 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 WP_089299698.1 CHB84_RS01755 (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.964.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.8e-247 805.7 0.0 1.1e-246 805.5 0.0 1.0 1 lcl|NCBI__GCF_900188115.1:WP_089299698.1 CHB84_RS01755 1-pyrroline-5-carb Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900188115.1:WP_089299698.1 CHB84_RS01755 1-pyrroline-5-carboxylate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 805.5 0.0 1.1e-246 1.1e-246 1 532 [. 11 541 .. 11 542 .] 0.99 Alignments for each domain: == domain 1 score: 805.5 bits; conditional E-value: 1.1e-246 TIGR01236 1 knePvkefrpgskerdllrkelkelkskvleiPlviggkevvksnelievvaPadhqaklakltnatee 69 +ne v ++pgs er+ l+++l+el+s+++e+P ++g +++ +e ++vvaP++h ++l++ +a+++ lcl|NCBI__GCF_900188115.1:WP_089299698.1 11 RNESVYTYAPGSAERESLQRTLAELASEKRELPQTVAGAKRMARGEPFNVVAPHEHGHVLGSCAQASDQ 79 69******************************************************************* PP TIGR01236 70 dvkkaveaaldakkeWselpfadraaiflkaadllsgkyreeilaatmlgqsktvyqaeidavaelidf 138 dv++av+aa+da W elpf++raa+fl+aadl+sg +r ++aatmlgqsk+v+q+eidav+el+df lcl|NCBI__GCF_900188115.1:WP_089299698.1 80 DVADAVRAAKDAAPAWRELPFDERAAVFLRAADLMSGAWRDTLNAATMLGQSKSVHQSEIDAVCELVDF 148 ********************************************************************* PP TIGR01236 139 frfnvkyarelleqqPsvsapgelnkveyrpleGfvaaisPfnftaiaanlagaPalmGnvvvWkPskt 207 +rfnv++ar +l+ qP +s+pg++n++eyr+leGfv+ai+Pfnftaia+nl++aPalmGn+vvWkP+ t lcl|NCBI__GCF_900188115.1:WP_089299698.1 149 LRFNVHFARRILAEQP-ISVPGTWNRAEYRSLEGFVTAITPFNFTAIAGNLPTAPALMGNTVVWKPTPT 216 ****************.8*************************************************** PP TIGR01236 208 avlsnyllmkileeaGlPpgvinfvpadgvkvsdvvladkdlaalhftGstavfkelwkkvasnldkyr 276 + l+++ +m+ile+aGlPpgvin+v++dg++vs v+lad+d+a+lhftGsta+fk lw+++a nld+yr lcl|NCBI__GCF_900188115.1:WP_089299698.1 217 QQLAAHFTMRILEAAGLPPGVINMVTGDGAAVSRVALADPDFAGLHFTGSTATFKMLWRTIADNLDTYR 285 ********************************************************************* PP TIGR01236 277 nfPrivGetGGkdfvlvhpsadveevvaatirgafeyqGqkcsaasrlyvpkslwke.lkeellaelkk 344 ++PrivGetGGkdf+++hpsa+v++vv++++rgafeyqGqkcsaasr+yvp+slw+ l+e+l + +k lcl|NCBI__GCF_900188115.1:WP_089299698.1 286 SYPRIVGETGGKDFIVAHPSAHVDKVVTGIVRGAFEYQGQKCSAASRAYVPRSLWDSgLREQLADVAKT 354 *******************************************************8659999******* PP TIGR01236 345 vkvgdvddlssfmgavideksfakivkviekakkdpeeleilaGGkyddskGyfvePtvveskdPkekl 413 + +gdv d+s+f gavid+++fak ++ + dp +le+l+GG +dds GyfvePtv+ + dP++++ lcl|NCBI__GCF_900188115.1:WP_089299698.1 355 ISYGDVRDFSNFGGAVIDHRAFAKHHALLSRVDGDP-DLEVLVGGSCDDSVGYFVEPTVLTCTDPHHEV 422 ************************************.******************************** PP TIGR01236 414 mkeeifGPvltvyvydddkykeilevvdstskyaltGavfakdreaieeaekklrfaaGnfyindkstG 482 +++e+fGP+++vyvydd +y +l++vdst+ yaltGavfa+dr+a+ ea+ +lr+aaGnfy+ndk+tG lcl|NCBI__GCF_900188115.1:WP_089299698.1 423 FSTEYFGPIVAVYVYDDAEYSSVLHLVDSTAPYALTGAVFADDRDAVAEAHRVLRYAAGNFYVNDKPTG 491 ********************************************************************* PP TIGR01236 483 avvgqqpfGGarlsGtndkaGapkillrfvsarsiketfkeltdfkypym 532 +vv qqpfGGar+sGtndkaG+ +++r++s+r+ike+f+++td++yp+m lcl|NCBI__GCF_900188115.1:WP_089299698.1 492 SVVNQQPFGGARASGTNDKAGSLFNMVRWTSPRAIKENFDAPTDHTYPHM 541 *************************************************8 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 10.43 // [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