Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate 8501416 DvMF_2146 delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq)
Query= BRENDA::Q9K9B2 (515 letters) >FitnessBrowser__Miya:8501416 Length = 1013 Score = 477 bits (1228), Expect = e-139 Identities = 236/512 (46%), Positives = 324/512 (63%) Query: 2 LQPYKHEPFTDFTVEANRKAFEEALGLVEKELGKEYPLIINGERVTTEDKIQSWNPARKD 61 L P+ +E D T+ ANR F A+ V + G PL I G+ VTT+D I S NPA+ Sbjct: 484 LPPFVNESMLDLTIPANRAGFVNAIAEVRGKAGGVIPLFIGGKDVTTDDTIASTNPAKPA 543 Query: 62 QLVGSVSKANQDLAEKAIQSADEAFQTWRNVNPEERANILVKAAAIIRRRKHEFSAWLVH 121 +++ V + + + AI++A +AF WR+ +P +RA L +AA I RRR E SAW V Sbjct: 544 EVIARVCQGGKPEVDAAIEAAQKAFPAWRDTSPADRAMFLHRAADIARRRMFELSAWQVL 603 Query: 122 EAGKPWKEADADTAEAIDFLEYYARQMIELNRGKEILSRPGEQNRYFYTPMGVTVTISPW 181 E GK W +A D E IDFL+YYA +M+ L + + PGE N FY P G+ I+PW Sbjct: 604 EVGKQWDQAFHDVGEGIDFLDYYAHEMLRLGTPRRMGRAPGELNHLFYQPKGIAAVIAPW 663 Query: 182 NFALAIMVGTAVAPIVTGNTVVLKPASTTPVVAAKFVEVLEDAGLPKGVINYVPGSGAEV 241 NF AI +G A A IVTGN V+ KP+S + E+ +AGLP+GV NYVPG + + Sbjct: 664 NFPFAIAIGMAAAAIVTGNPVIFKPSSIASRIGYNLTEIFREAGLPEGVFNYVPGRSSVM 723 Query: 242 GDYLVDHPKTSLITFTGSKDVGVRLYERAAVVRPGQNHLKRVIVEMGGKDTVVVDRDADL 301 GDYLV+HP+ S+I FTGS +VG+R+ E+AA V+PGQ KRVI EMGGK+ +++D DADL Sbjct: 724 GDYLVEHPQVSMICFTGSMEVGLRIQEKAAKVQPGQMQCKRVIAEMGGKNAIIIDDDADL 783 Query: 302 DLAAESILVSAFGFSGQKCSAGSRAVIHKDVYDEVLEKTVALAKNLTVGDPTNRDNYMGP 361 D A +L SAFGF GQKCSA SR ++ +YD +E+ V A+ + +G + NYMGP Sbjct: 784 DEAVLQVLYSAFGFQGQKCSACSRVIVLDPIYDRFVERLVKAAQAIKIGPSEDPANYMGP 843 Query: 362 VIDEKAFEKIMSYIEIGKKEGRLMTGGEGDSSTGFFIQPTIIADLDPEAVIMQEEIFGPV 421 V D + I+ Y+++ ++EG+++ + G ++ TI+ + P I QEEIFGPV Sbjct: 844 VADASLQKNILEYVKVAEQEGKVLVKRTDIPAEGCYVPLTIVEGIKPHHRIAQEEIFGPV 903 Query: 422 VAFSKANDFDHALEIANNTEYGLTGAVITRNRAHIEQAKREFHVGNLYFNRNCTGAIVGY 481 +A +A +FD AL IAN T + LTG V +R+ ++ +A+REF VGNLY NR TGA+V Sbjct: 904 LAVMRAGNFDEALAIANGTRFALTGGVFSRSPENLTKARREFRVGNLYLNRGSTGAMVER 963 Query: 482 HPFGGFKMSGTDSKAGGPDYLALHMQAKTVSE 513 PFGGFKMSG SK GGPDYL M + V+E Sbjct: 964 QPFGGFKMSGVGSKTGGPDYLLQFMDPRCVTE 995 Lambda K H 0.316 0.134 0.388 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: 1189 Number of extensions: 50 Number of successful extensions: 1 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: 515 Length of database: 1013 Length adjustment: 40 Effective length of query: 475 Effective length of database: 973 Effective search space: 462175 Effective search space used: 462175 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: 55 (25.8 bits)
Align candidate 8501416 DvMF_2146 (delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq))
to HMM TIGR01237 (pruA: putative delta-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/TIGR01237.hmm # target sequence database: /tmp/gapView.32080.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01237 [M=511] Accession: TIGR01237 Description: D1pyr5carbox2: putative delta-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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-204 666.2 0.0 2.2e-204 665.9 0.0 1.1 1 lcl|FitnessBrowser__Miya:8501416 DvMF_2146 delta-1-pyrroline-5-ca Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Miya:8501416 DvMF_2146 delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 665.9 0.0 2.2e-204 2.2e-204 10 510 .. 496 996 .. 487 997 .. 0.99 Alignments for each domain: == domain 1 score: 665.9 bits; conditional E-value: 2.2e-204 TIGR01237 10 adeelvqafkkalakvkellGkdyplvinGeeveteakidsinpadksevvGkvakasvedaeqalqaakkafeewk 86 + ++ f +a+a+v+ + G pl+i G+ v t++ i s npa++ ev+ +v++ + + a++aa+kaf++w+ lcl|FitnessBrowser__Miya:8501416 496 TIPANRAGFVNAIAEVRGKAGGVIPLFIGGKDVTTDDTIASTNPAKPAEVIARVCQGGKPEVDAAIEAAQKAFPAWR 572 5556788899******************************************************************* PP TIGR01237 87 ktdveeraaillkaaailkrrrhelsallvlevGkiyaeadaevaeaidfleyyaremiklakskevlsieGeknry 163 t++ +ra l +aa+i +rr +elsa+ vlevGk++++a +v e idfl+yya+em++l + +Ge n++ lcl|FitnessBrowser__Miya:8501416 573 DTSPADRAMFLHRAADIARRRMFELSAWQVLEVGKQWDQAFHDVGEGIDFLDYYAHEMLRLGTPRRMGRAPGELNHL 649 ***************************************************************************** PP TIGR01237 164 lyiplGvavvispwnfplailvGmtvapivtGncvvlkpaeaatviaaklveileeaGlpkGvlqfvpGkGsevGey 240 +y+p+G+a vi+pwnfp+ai++Gm++a+ivtGn v+ kp++ a+ i l ei++eaGlp+Gv+++vpG+ s++G+y lcl|FitnessBrowser__Miya:8501416 650 FYQPKGIAAVIAPWNFPFAIAIGMAAAAIVTGNPVIFKPSSIASRIGYNLTEIFREAGLPEGVFNYVPGRSSVMGDY 726 ***************************************************************************** PP TIGR01237 241 lvdhpktrlitftGsrevGlriyedaakvqpGqkhlkrviaelGGkdavivdesadieqavaaavtsafGfaGqkcs 317 lv+hp++++i+ftGs evGlri e+aakvqpGq krviae+GGk+a+i+d++ad+++av +++safGf+Gqkcs lcl|FitnessBrowser__Miya:8501416 727 LVEHPQVSMICFTGSMEVGLRIQEKAAKVQPGQMQCKRVIAEMGGKNAIIIDDDADLDEAVLQVLYSAFGFQGQKCS 803 ***************************************************************************** PP TIGR01237 318 aasrvvvlekvydevverfveatkslkvgktdeadvqvgpvidqksfdkikeyielgkaegklvlggedddskGyfi 394 a+srv+vl+++yd++ver+v+a+++ k+g+++++ ++gpv d+ +++i ey++++++egk+++ +d + +G ++ lcl|FitnessBrowser__Miya:8501416 804 ACSRVIVLDPIYDRFVERLVKAAQAIKIGPSEDPANYMGPVADASLQKNILEYVKVAEQEGKVLVKRTDIPAEGCYV 880 ***************************************************************************** PP TIGR01237 395 kptifkdvdrkarlaqeeifGpvvavlrakdfdealeiansteygltGgvisnsrerierakaefevGnlyfnrkit 471 ti++ + ++ r+aqeeifGpv+av+ra +fdeal ian+t ++ltGgv+s+s+e++ +a+ ef+vGnly+nr t lcl|FitnessBrowser__Miya:8501416 881 PLTIVEGIKPHHRIAQEEIFGPVLAVMRAGNFDEALAIANGTRFALTGGVFSRSPENLTKARREFRVGNLYLNRGST 957 ***************************************************************************** PP TIGR01237 472 GaivgvqpfGGfkmsGtdskaGGpdylaqflqaktvter 510 Ga+v +qpfGGfkmsG++sk+GGpdyl+qf++++ vte+ lcl|FitnessBrowser__Miya:8501416 958 GAMVERQPFGGFKMSGVGSKTGGPDYLLQFMDPRCVTEN 996 *************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (511 nodes) Target sequences: 1 (1013 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 20.99 // [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