Align Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate YP_004139497.1 Mesci_0274 aldehyde dehydrogenase
Query= reanno::Smeli:SM_b20891 (477 letters) >NCBI__GCF_000185905.1:YP_004139497.1 Length = 479 Score = 762 bits (1968), Expect = 0.0 Identities = 382/478 (79%), Positives = 419/478 (87%), Gaps = 1/478 (0%) Query: 1 MTL-HQNLIAGEWVGGDGVANINPSNTDDVVGEYARASAEDAKAAIAAAKAAFPAWSRSG 59 MTL +NLI GEWVG G NINPS+T DVVG+YA A E A+ AIAAAKAAFPAWSRSG Sbjct: 1 MTLFRKNLIDGEWVGDAGSRNINPSDTGDVVGDYASAGVEQAQQAIAAAKAAFPAWSRSG 60 Query: 60 ILERHAILKKTADEILARKDELGRLLSREEGKTLAEGIGETVRAGQIFEFFAGETLRLAG 119 L RHA+LKK +DEILARKDE+GR L+REEGKTLAEGIGET+RA QIF+FFAGETLRL G Sbjct: 61 PLARHAVLKKASDEILARKDEIGRNLAREEGKTLAEGIGETIRAAQIFDFFAGETLRLTG 120 Query: 120 EVVPSVRPGIGVEITREPAGVVGIITPWNFPIAIPAWKLAPALCYGNTIVFKPAELVPGC 179 EVVPSVRPG+GVE+TRE GVVGIITPWNFPIAIPAWK+APAL +GNT+VFKPAELVP Sbjct: 121 EVVPSVRPGVGVEMTREAVGVVGIITPWNFPIAIPAWKIAPALTHGNTVVFKPAELVPES 180 Query: 180 SWAIVDILHRAGLPKGVLNLVMGKGSVVGQAMLDSPDVQAITFTGSTATGKRVAVASVEH 239 +W IVDILHRAGLPKGVLNLVMGKGSVVGQAMLDSPDV AI+FTGS TGKRVA AS+EH Sbjct: 181 AWTIVDILHRAGLPKGVLNLVMGKGSVVGQAMLDSPDVNAISFTGSVGTGKRVAAASIEH 240 Query: 240 NRKYQLEMGGKNPFVVLDDADLSVAVEAAVNSAFFSTGQRCTASSRIIVTEGIHDRFVAA 299 RK+QLEMGGKNP VVLDDADL++AV+ A+N AFFSTGQRCTASSR+IV +GIHDRFV A Sbjct: 241 MRKFQLEMGGKNPLVVLDDADLAIAVDCALNGAFFSTGQRCTASSRLIVADGIHDRFVDA 300 Query: 300 MGERIKGLVVDDALKPGTHIGPVVDQSQLNQDTDYIAIGKQEGAKLAFGGEVISRDTPGF 359 + +R+ LV+ DAL T IGPVVD +QL QD DYIAIG +EGA LAFGGE + R TPGF Sbjct: 301 LKDRMSKLVIGDALDAQTQIGPVVDATQLKQDEDYIAIGVREGATLAFGGERLDRKTPGF 360 Query: 360 YLQPALFTEATNEMRISREEIFGPVAAVIRVKDYDEALAVANDTPFGLSSGIATTSLKHA 419 YLQPAL TEATN MR SREEIFGPVA+VIRVKDYDEAL+VANDTPFGL+SGI T+SLKHA Sbjct: 361 YLQPALLTEATNAMRSSREEIFGPVASVIRVKDYDEALSVANDTPFGLTSGICTSSLKHA 420 Query: 420 THFKRNAEAGMVMVNLPTAGVDFHVPFGGRKASSYGPREQGKYAAEFYTNVKTAYTLA 477 THFKRN+EAGMVMVNLPTAGVDFHVPFGGRK SSYGPREQG YAAEFYT VKTAYT A Sbjct: 421 THFKRNSEAGMVMVNLPTAGVDFHVPFGGRKGSSYGPREQGHYAAEFYTTVKTAYTFA 478 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: 795 Number of extensions: 21 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: 477 Length of database: 479 Length adjustment: 34 Effective length of query: 443 Effective length of database: 445 Effective search space: 197135 Effective search space used: 197135 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 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