Align Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate GFF501 PGA1_c05130 aldehyde dehydrogenase
Query= reanno::Smeli:SM_b20891 (477 letters) >FitnessBrowser__Phaeo:GFF501 Length = 476 Score = 619 bits (1597), Expect = 0.0 Identities = 310/475 (65%), Positives = 372/475 (78%), Gaps = 2/475 (0%) Query: 4 HQNLIAGEWVGG-DGVANINPSNTDDVVGEYARASAEDAKAAIAAAKAAFPAWSRSGILE 62 ++NLIAG+W ANINPS+T DV+G A + AED + AIAAA+ A P W+ S + Sbjct: 3 YKNLIAGDWSETVAAAANINPSDTQDVLGYAANSPAEDMERAIAAARDAAPGWASSTPQQ 62 Query: 63 RHAILKKTADEILARKDELGRLLSREEGKTLAEGIGETVRAGQIFEFFAGETLRLAGEVV 122 R +L EILARK ELG+LLSREEGKTL EGIGE RAGQIF+FFAGETLR AGE++ Sbjct: 63 RFDVLDAIGTEILARKAELGKLLSREEGKTLPEGIGEAARAGQIFKFFAGETLRQAGEIL 122 Query: 123 PSVRPGIGVEITREPAGVVGIITPWNFPIAIPAWKLAPALCYGNTIVFKPAELVPGCSWA 182 SVRPG+GVE+TR P GVVG+ITPWNFPIAIPAWK+APAL YG+ +V KPAEL PGC+ A Sbjct: 123 GSVRPGVGVEVTRSPVGVVGLITPWNFPIAIPAWKIAPALAYGDAVVLKPAELTPGCAHA 182 Query: 183 IVDILHRAGLPKGVLNLVMGKGSVVGQAMLDSPDVQAITFTGSTATGKRVAVASVEHNRK 242 + +I++R+GLP+GV N+V G GS VGQ ++ S V AI+FTGS TG +A A +K Sbjct: 183 LAEIINRSGLPEGVFNIVFGTGSTVGQTLVQSRHVDAISFTGSVETGSAIAAACGAQRKK 242 Query: 243 YQLEMGGKNPFVVLDDADLSVAVEAAVNSAFFSTGQRCTASSRIIVTEGIHDRFVAAMGE 302 QLEMGGKNP VVLDDADL AV+A++N AFFSTGQRCTASSR+IVTEGIHDRFVAA+GE Sbjct: 243 LQLEMGGKNPMVVLDDADLETAVDASLNGAFFSTGQRCTASSRLIVTEGIHDRFVAALGE 302 Query: 303 RIKGLVVDDALKPGTHIGPVVDQSQLNQDTDYIAIGKQEGAKLAFGGEVISRDTPGFYLQ 362 R+ GL V +AL T IGPVVD+ QL +D Y+ + EG ++ GG+ + R T GFYL Sbjct: 303 RMTGLRVGNALDDSTQIGPVVDERQLEKDLYYLDVAASEGGQV-LGGQTLQRSTKGFYLA 361 Query: 363 PALFTEATNEMRISREEIFGPVAAVIRVKDYDEALAVANDTPFGLSSGIATTSLKHATHF 422 PAL TE +N+MRI++EE+FGP+A+VIRV DYDEAL VANDTPFGLS+GI T SLK+ATHF Sbjct: 362 PALVTETSNDMRINQEEVFGPLASVIRVADYDEALVVANDTPFGLSAGICTGSLKYATHF 421 Query: 423 KRNAEAGMVMVNLPTAGVDFHVPFGGRKASSYGPREQGKYAAEFYTNVKTAYTLA 477 K +AEAGM MVNLPTAGVD+HVPFGG K SS+G REQG +A EFYT VKTAYTLA Sbjct: 422 KAHAEAGMAMVNLPTAGVDYHVPFGGTKGSSFGAREQGSHAKEFYTKVKTAYTLA 476 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: 748 Number of extensions: 31 Number of successful extensions: 2 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: 476 Length adjustment: 33 Effective length of query: 444 Effective length of database: 443 Effective search space: 196692 Effective search space used: 196692 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