Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate GFF374 Psest_0375 NAD-dependent aldehyde dehydrogenases
Query= reanno::pseudo1_N1B4:Pf1N1B4_1109 (481 letters) >FitnessBrowser__psRCH2:GFF374 Length = 480 Score = 771 bits (1992), Expect = 0.0 Identities = 381/480 (79%), Positives = 422/480 (87%) Query: 1 VADAKRYDNYINGEWVSGADYSANINPSELTDTIGDYAKADLAQVHAAIDAARAAFPAWS 60 +AD +RYDN+I+G+WV Y AN NPS+L+D IG+YA+AD AQV AI AAR AFPAW+ Sbjct: 1 MADVQRYDNFIDGQWVGSDRYQANTNPSDLSDVIGEYAQADAAQVEQAIAAARRAFPAWA 60 Query: 61 TSGIQARHDSLDKVGTEILARREELGTLLAREEGKTLPEAIGEVTRAGNIFKFFAGECLR 120 T GIQAR D+L+KVG EILARREELGTLLAREEGKTLPEAIGEV RAGNIFK+FAGECLR Sbjct: 61 TFGIQARADALEKVGLEILARREELGTLLAREEGKTLPEAIGEVARAGNIFKYFAGECLR 120 Query: 121 LSGDYLPSVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVLKPADLV 180 +G+ L SVRPGV VEVTRE LGV+GLITPWNFPIAIPAWKIAPALA+GNCVV+KPADLV Sbjct: 121 QAGETLQSVRPGVGVEVTREPLGVIGLITPWNFPIAIPAWKIAPALAFGNCVVIKPADLV 180 Query: 181 PGCAWALAEIISRAGFPAGVFNLVMGSGRVVGDALVQSPKVDGISFTGSVGVGRQIAVSC 240 PGCAWA+AEIISRAGFPAGVFNLVMG GR VG+A+V + VD +SFTGSVGVGR IA +C Sbjct: 181 PGCAWAIAEIISRAGFPAGVFNLVMGKGREVGEAIVNAKDVDAVSFTGSVGVGRGIAQTC 240 Query: 241 VSRQAKVQLEMGGKNPQIILDDADLKQAVELSVQSAFYSTGQRCTASSRFIVTAGIHDKF 300 V+R AKVQLEMGGKNPQI+LDDADL AVEL QSAFYSTGQRCTASSR IVT GI+D+F Sbjct: 241 VARGAKVQLEMGGKNPQIVLDDADLNVAVELCTQSAFYSTGQRCTASSRIIVTEGIYDRF 300 Query: 301 VEAMAERMKSIKVGHALKTGTDIGPVVSQAQLEQDLKYIDIGQSEGARLVSGGGLVACDT 360 VEAM ER+K IKVG AL+ G D+GPVVS+AQLEQDL+YI+IG+ EGARL GG V C T Sbjct: 301 VEAMVERIKKIKVGSALEQGVDVGPVVSEAQLEQDLRYIEIGKQEGARLACGGERVKCGT 360 Query: 361 EGYFLAPTLFADSTAAMRISREEIFGPVANIVRVADYEAALAMANDTEFGLSAGIATTSL 420 EGYFLAPTLF DS MRISREEIFGPVAN+V+V DY+ ALAMANDTEFGLSAGI TTSL Sbjct: 361 EGYFLAPTLFVDSDPNMRISREEIFGPVANVVKVKDYDEALAMANDTEFGLSAGICTTSL 420 Query: 421 KYANHFKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGSREQGRYAQEFYTVVKTSYIG 480 KYANHFKRH+QAGMVM+NLPTAGVDYHVPFGGRKGSSYG REQGRYAQEFYT VKT+YIG Sbjct: 421 KYANHFKRHAQAGMVMINLPTAGVDYHVPFGGRKGSSYGPREQGRYAQEFYTTVKTTYIG 480 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: 761 Number of extensions: 18 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: 480 Length adjustment: 34 Effective length of query: 447 Effective length of database: 446 Effective search space: 199362 Effective search space used: 199362 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 Apr 09 2024. 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