Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate CCNA_00865 CCNA_00865 alpha-ketoglutaric semialdehyde dehydrogenase xylA
Query= curated2:B0T8I8 (484 letters) >FitnessBrowser__Caulo:CCNA_00865 Length = 478 Score = 217 bits (552), Expect = 8e-61 Identities = 159/470 (33%), Positives = 230/470 (48%), Gaps = 21/470 (4%) Query: 12 RAGAGAQATSVDPT-TGEVIWRQATASTAEVAAAVEAARKAFPAWADRSREERIAVLRRY 70 R A A A S++P+ T +V+ + AEV AAV+AARKAFPAWAD S E R +L + Sbjct: 13 RVAADAPAESLNPSNTNDVVAKVPMGGQAEVDAAVDAARKAFPAWADASPEVRSDLLDKV 72 Query: 71 KDVLVARTGTFAEALSRETGKALWETKAELGSMAGKVEASIKAYD-ERTGEHANDMAFGR 129 ++AR+ L+RE GK L E E AG++ R G++ G Sbjct: 73 GSTIIARSADIGRLLAREEGKTLAEGIGET-VRAGRIFKYFAGEALRRHGQNLESTRPGV 131 Query: 130 AVLRHR-AHGVMAVLGPFNFPGHLPNGHIVPALLAGDTVVFKPSEETPLAGQLLVEALEE 188 + +R A GV ++ P+NFP +P PAL G+TVV KP+ TP +L + + E Sbjct: 132 EIQTYRQAVGVYGLITPWNFPIAIPAWKAAPALAFGNTVVIKPAGPTPATANVLADIMAE 191 Query: 189 AGVPAGVINLVQGGREVGQALI-DQEIDGLLFTGSAAAGAFFRRHFADRPDVILALELGG 247 G PAGV N++ G +G ALI +++DG+ FTGS GA R + LE+GG Sbjct: 192 CGAPAGVFNMLFGRGSMGDALIKHKDVDGVSFTGSQGVGAQVAAAAVAR-QARVQLEMGG 250 Query: 248 NNPLVVWDAGDPEAVAALIVQSAFITTGQRCSCARRLIVSD---DAAGRAVIDAVAALSE 304 NPL+V D D E A+ + +F TGQRC+ + RLIV D D + + VAAL Sbjct: 251 KNPLIVLDDADLERAVAIALDGSFFATGQRCTASSRLIVQDGIHDKFVALLAEKVAALRV 310 Query: 305 RLVIGPWNGGQEPFMGPLISDRAAAMALAGAKAMPGQTLRAMTSVDGLSRA----FVSPG 360 + P +GP +S+ + + R +T D + +V P Sbjct: 311 GDALDP-----NTQIGPAVSEDQMETSYRYIDIAASEGGRVVTGGDRIKLDNPGWYVRPT 365 Query: 361 LVDVT--GETVPDEELFAPLLQVRRVGSFEEAIAAANATRYGLSAGLVSNETAHWDRFLT 418 L+ T G + +EE+F P+ RV S+EEA+ AN +GLSAG+ + H F Sbjct: 366 LIADTQAGMRINNEEVFGPVASTIRVKSYEEALEIANGVEFGLSAGIATTSLKHARHFQR 425 Query: 419 RIRAGVVNWNRPTTGAAGTMPFGGLGNSG-NHRPSAYYAADYCAYPVASF 467 RAG+ N T G +PFGG +S R + A ++ S+ Sbjct: 426 YARAGMTMVNLATAGVDYHVPFGGTKSSSYGAREQGFAAVEFFTQTKTSY 475 Lambda K H 0.318 0.134 0.395 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: 583 Number of extensions: 26 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: 484 Length of database: 478 Length adjustment: 34 Effective length of query: 450 Effective length of database: 444 Effective search space: 199800 Effective search space used: 199800 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 (21.7 bits) S2: 51 (24.3 bits)
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