Align Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate N515DRAFT_2488 N515DRAFT_2488 succinate-semialdehyde dehydrogenase / glutarate-semialdehyde dehydrogenase
Query= reanno::Smeli:SM_b20891 (477 letters) >FitnessBrowser__Dyella79:N515DRAFT_2488 Length = 463 Score = 236 bits (601), Expect = 2e-66 Identities = 154/461 (33%), Positives = 231/461 (50%), Gaps = 11/461 (2%) Query: 19 ANINPSNTDDVVGEYARASAEDAKAAIAAAKAAFPAWSRSGILERHAILKKTADEILARK 78 A INP T + V + A+ + A+ A+A F AW G+ R +L+K AD + Sbjct: 4 ATINPY-TGETVKTFPSATDAEVTQALDQAQAMFEAWKDVGVAARVKVLQKAADLLRESH 62 Query: 79 DELGRLLSREEGKTLAEGIGETVRAGQIFEFFAGETLRL-AGEVVPSVRPGIGVE-ITRE 136 + ++L+ E GK + E GE QI E++A +L A E + S P + Sbjct: 63 TQYAKVLTLEMGKVIGEAEGEVELCAQILEYYADHAEQLLAPEKLSSRHPSYTQSWVEHV 122 Query: 137 PAGVVGIITPWNFPIAIPAWKLAPALCYGNTIVFKPAELVPGCSWAIVDILHRAGLPKG- 195 P G++ + PWNFP AP L GN ++ K A VP C+ A + AGLP+G Sbjct: 123 PQGILLAVEPWNFPYYQIVRIAAPQLAAGNVLILKHASNVPQCAAAFERLFREAGLPQGG 182 Query: 196 VLNLVMGKGSVVGQAMLDSPDVQAITFTGSTATGKRVAVASVEHNRKYQLEMGGKNPFVV 255 NL + + +A+++ P VQ + TGS G VA + + +K +E+GG + FVV Sbjct: 183 FTNLYATRDQL--KAIIEDPRVQGVALTGSEGAGAVVAAQAGQALKKSTMELGGADAFVV 240 Query: 256 LDDADLSVAVEAAVNSAFFSTGQRCTASSRIIVTEGIHDRFVAAMGERIKGLVVDDALKP 315 L DADL AV+ AV ++ GQ C +S RIIV + I+D F+ + L D ++P Sbjct: 241 LADADLDKAVQWAVTGRHWNAGQVCCSSKRIIVVDEIYDAFLEKYKAGVARLRAGDPMEP 300 Query: 316 GTHIGPVVDQSQLNQDTDYIAIGKQEGAKL-AFGGEVISRDTPGFYLQPALFTEATNEMR 374 T + P+ + ++ + GAK+ G EV SR G + +P L + +++ Sbjct: 301 STTLAPMSSRGAVDDLKKQLEQAVAHGAKVEVIGAEVPSR---GAFFRPVLLSHVSDDNP 357 Query: 375 ISREEIFGPVAAVIRVKDYDEALAVANDTPFGLSSGIATTSLKHATHFKRNAEAGMVMVN 434 E FGPV+ VIR +D +A+ +AND+PFGL + TT +KH + GMV +N Sbjct: 358 ARYWEFFGPVSQVIRARDEADAIRIANDSPFGLGGSVFTTDIKHGIEVAKKISTGMVYIN 417 Query: 435 LPTAGVDFHVPFGGRKASSYGPREQGKYAAEFYTNVKTAYT 475 PT GV +PFGG + S YG G EF + A T Sbjct: 418 HPT-GVAADLPFGGVRRSGYGRELTGLGIKEFVNHKLIAVT 457 Lambda K H 0.317 0.134 0.391 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: 520 Number of extensions: 25 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: 477 Length of database: 463 Length adjustment: 33 Effective length of query: 444 Effective length of database: 430 Effective search space: 190920 Effective search space used: 190920 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