Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_090439664.1 BLS63_RS03170 aldehyde dehydrogenase family protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_1109 (481 letters) >NCBI__GCF_900100495.1:WP_090439664.1 Length = 478 Score = 818 bits (2114), Expect = 0.0 Identities = 404/477 (84%), Positives = 442/477 (92%) Query: 4 AKRYDNYINGEWVSGADYSANINPSELTDTIGDYAKADLAQVHAAIDAARAAFPAWSTSG 63 +KRYDNYI G+WV+G+DYS NINPS+L+D +G+YA+AD AQV AI AARAAFPAWSTS Sbjct: 2 SKRYDNYIGGQWVAGSDYSRNINPSDLSDLVGEYAQADAAQVEQAIAAARAAFPAWSTSA 61 Query: 64 IQARHDSLDKVGTEILARREELGTLLAREEGKTLPEAIGEVTRAGNIFKFFAGECLRLSG 123 IQAR D+LDKVG+EILARREELG+LLAREEGKTL EAIGEV+RAGNIFKFFAGECLR +G Sbjct: 62 IQARSDALDKVGSEILARREELGSLLAREEGKTLAEAIGEVSRAGNIFKFFAGECLRQAG 121 Query: 124 DYLPSVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVLKPADLVPGC 183 + L SVRPGV+VEVTRE LGV+GLITPWNFPIAIPAWKIAPALAYGNCVV KPADLVPGC Sbjct: 122 ELLASVRPGVSVEVTREPLGVIGLITPWNFPIAIPAWKIAPALAYGNCVVFKPADLVPGC 181 Query: 184 AWALAEIISRAGFPAGVFNLVMGSGRVVGDALVQSPKVDGISFTGSVGVGRQIAVSCVSR 243 AWA+AEII+RAGFPAGVFNLVMGSGRVVG+ LVQ P+VDG+SFTGSVGVGR IA CV+R Sbjct: 182 AWAIAEIIARAGFPAGVFNLVMGSGRVVGETLVQHPQVDGVSFTGSVGVGRSIAAVCVAR 241 Query: 244 QAKVQLEMGGKNPQIILDDADLKQAVELSVQSAFYSTGQRCTASSRFIVTAGIHDKFVEA 303 AKVQLEMGGKNPQ+ILDDADL AVELSVQSAFYSTGQRCTASSR IVTAGIHD+FVEA Sbjct: 242 GAKVQLEMGGKNPQVILDDADLNTAVELSVQSAFYSTGQRCTASSRLIVTAGIHDRFVEA 301 Query: 304 MAERMKSIKVGHALKTGTDIGPVVSQAQLEQDLKYIDIGQSEGARLVSGGGLVACDTEGY 363 MAERM+S++VGHAL+ G DIGPVVSQAQLEQDL+YI IG+ EGARLV GG V+C TEGY Sbjct: 302 MAERMRSLRVGHALERGVDIGPVVSQAQLEQDLRYIGIGRDEGARLVCGGERVSCATEGY 361 Query: 364 FLAPTLFADSTAAMRISREEIFGPVANIVRVADYEAALAMANDTEFGLSAGIATTSLKYA 423 FLAPTLFADSTAAMRI+REEIFGPVANI++VADYE ALAMANDTEFGLSAGI TTSLKYA Sbjct: 362 FLAPTLFADSTAAMRINREEIFGPVANILKVADYEEALAMANDTEFGLSAGICTTSLKYA 421 Query: 424 NHFKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGSREQGRYAQEFYTVVKTSYIG 480 NHFKRH+QAGMVMVNLPTAGVDYHVPFGGRKGSSYGSREQGRYAQEFYT VKT+Y+G Sbjct: 422 NHFKRHAQAGMVMVNLPTAGVDYHVPFGGRKGSSYGSREQGRYAQEFYTTVKTTYVG 478 Lambda K H 0.318 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: 774 Number of extensions: 10 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: 481 Length of database: 478 Length adjustment: 34 Effective length of query: 447 Effective length of database: 444 Effective search space: 198468 Effective search space used: 198468 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