Align Aldehyde dehydrogenase [NAD(P)+] 2; EC 1.2.1.3 (characterized)
to candidate WP_011612882.1 TERY_RS16535 L-glutamate gamma-semialdehyde dehydrogenase
Query= SwissProt::P54114 (506 letters) >NCBI__GCF_000014265.1:WP_011612882.1 Length = 993 Score = 251 bits (642), Expect = 7e-71 Identities = 158/493 (32%), Positives = 264/493 (53%), Gaps = 24/493 (4%) Query: 10 IPQLKISLKQPLGLFINNEFCPSSDGKTIETVNPATG-EPITSFQAANEKDVDKAVKAAR 68 I Q+++ L + IN E+ ++ + ++++NP+ E + + + ++A++AA+ Sbjct: 493 IGQIRLELGKTYLPIINGEY--TNTAQIVDSLNPSNSKEVVGKIGLISVEQAEQAIQAAK 550 Query: 69 AAFDNVWSKTSSEQRGIYLSNLLKLIEEEQDTLAALETLDAGKPFHSNAKQDLAQIIELT 128 AAF + W KT +R L L+E+ + LAA L+ GKP + ++++ I+ Sbjct: 551 AAFPS-WKKTPVRERTRILRKAADLMEKRRHELAAWMVLEVGKPLNQG-NAEVSEAIDFC 608 Query: 129 RYYAGAVDKFNMGETIPLTFNKFAYTLKVPFGVVAQIVPWNYPLAMACRKMQGALAAGNT 188 RYYA +++ G + Y + P G+ I PWN+PLA+ +L GN Sbjct: 609 RYYADEMERLEQGYNYDVAGETDRYYYQ-PRGISLVISPWNFPLAIPTGMTVSSLVTGNC 667 Query: 189 VIIKPAENTSLSLLYFATLIKKAGFPPGVVNVIPGYGSVVGKALGTHMDIDKISFTGSTK 248 ++KPA +S+ + ++ +AGFP GV +PG GS VG + H ++ I+FTGS + Sbjct: 668 TLLKPAAVSSVIASKISEILLEAGFPKGVFQFVPGNGSTVGDFMVKHPSVNSITFTGSME 727 Query: 249 VGGSVLEASG-----QSNLKDITLECGGKSPALVFEDADLDKAIEWVANGIFFNSGQICT 303 VG + + Q +LK + E GGK+ +V E ADLD+A+ V F SGQ C+ Sbjct: 728 VGCHIYAQAAVLQPRQKHLKRVIAEMGGKNAIIVDESADLDQAVAGVVYSAFGYSGQKCS 787 Query: 304 ANSRVYVQSSIYDKFVEKFKETAKKEWDVAGKFDPFDEKCIVGPVISSTQYDRIKSYIER 363 A SRV V ++IYD FV + E A + ++ P + VGPVI RI+ YI + Sbjct: 788 ACSRVVVLATIYDSFVNRLVE-ATRSLNIGDAEKPSTQ---VGPVIDEKAQKRIQEYIVK 843 Query: 364 GKKEEKLDMFQTSEFPIGGAKGYFIPPTIFTDVPETSKLLRDEIFGPVVVVSKFTNYDDA 423 GK+E ++ + ++ GYF+ P IF DV ++ + ++EIFGPV+ V K N+ A Sbjct: 844 GKQEAEVAIEMSAP-----KDGYFVGPVIFKDVSPSATIAQEEIFGPVLAVMKADNFTQA 898 Query: 424 LKLANDTCYGLASAVFTKDVKKAHMFARDIKAGTVWINQ--TNQEEAKVPFGGFKMSGIG 481 L++AN T + L ++++ + + G ++IN+ T ++ PFGGFK+SG+G Sbjct: 899 LEIANGTNFALTGGLYSRTPSHIEQAKAEFEVGNLYINRGITGAIVSRQPFGGFKLSGVG 958 Query: 482 RESGDTGVDNYLQ 494 ++G G D LQ Sbjct: 959 SKAG--GPDYLLQ 969 Lambda K H 0.317 0.135 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: 1003 Number of extensions: 48 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: 506 Length of database: 993 Length adjustment: 39 Effective length of query: 467 Effective length of database: 954 Effective search space: 445518 Effective search space used: 445518 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: 54 (25.4 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