Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_009562902.1 RSPH17029_RS04350 betaine-aldehyde dehydrogenase
Query= reanno::pseudo1_N1B4:Pf1N1B4_1109 (481 letters) >NCBI__GCF_000015985.1:WP_009562902.1 Length = 483 Score = 288 bits (737), Expect = 3e-82 Identities = 179/443 (40%), Positives = 248/443 (55%), Gaps = 8/443 (1%) Query: 39 KADLAQVHAAIDAARAAFPAWSTSGIQARHDSLDKVGTEILARREELGTLLAREEGKTLP 98 +A A + AA+ + A AW+ R L + I AR EEL L + GK L Sbjct: 40 EATPAVIEAALASGARAQAAWAAMRPVERARILRRASDLIRARNEELSLLETLDTGKPLQ 99 Query: 99 EA-IGEVTRAGNIFKFFAGECLRLSGDYLPSVRPGVNVEVTREALGVVGLITPWNFPIAI 157 E + + + +FFAG ++G+ +P + V RE LG+ I WN+P I Sbjct: 100 ETLVADWASGADALEFFAGLAPAVTGETVPLGQDFVYT--IREPLGLCVGIGAWNYPSQI 157 Query: 158 PAWKIAPALAYGNCVVLKPADLVPGCAWALAEIISRAGFPAGVFNLVMGSGRVVGDALVQ 217 WK APALA GN +V KP+++ P A LAEI+ AG P G+FN+V G G VG ALV Sbjct: 158 ACWKAAPALALGNAMVFKPSEVTPLGALKLAEILIEAGLPPGLFNVVQGRG-AVGAALVT 216 Query: 218 SPKVDGISFTGSVGVGRQIAVSCVSRQAKVQLEMGGKNPQIILDDADLKQAVELSVQSAF 277 +V +S TGSV GR++ + V +E+GGK+P I+ DDADL+ A+ ++ F Sbjct: 217 DSRVAKVSLTGSVPTGRRVYAAAAEGVRHVTMELGGKSPLIVFDDADLESAIGAAMLGNF 276 Query: 278 YSTGQRCTASSRFIVTAGIHDKFVEAMAERMKSIKVGHALKTGTDIGPVVSQAQLEQDLK 337 YS GQ C+ +R V GI + F+ +AER +I++G L +GP+VSQAQLE+ L Sbjct: 277 YSAGQICSNGTRVFVQKGIKEAFLARLAERADAIRMGDPLDPEVQMGPLVSQAQLEKVLA 336 Query: 338 YIDIGQSEGARLVSGGGLVACDTEGYFLAPTLFADSTAAMRISREEIFGPVANIVRVADY 397 YI+ ++EG RLV GG A + G ++ PT+FAD T AM ++REE+FGPV ++ Sbjct: 337 YIEKARAEGGRLVCGG--EASVSPGCYVQPTVFADVTDAMTLAREEVFGPVMAVLDFETE 394 Query: 398 EAALAMANDTEFGLSAGIATTSLKYANHFKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSS 457 E A+A AN T+FGL+AG+ T L A+ QAG +N PFGG K S Sbjct: 395 EEAIARANATDFGLAAGVFTADLTRAHRVVAQLQAGTCWINAYNL-TPVEAPFGGVKLSG 453 Query: 458 YGSREQGRYAQEFYTVVKTSYIG 480 G RE GR A E YT VK+ Y+G Sbjct: 454 VG-RENGRAAVEHYTQVKSVYVG 475 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: 510 Number of extensions: 20 Number of successful extensions: 5 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: 483 Length adjustment: 34 Effective length of query: 447 Effective length of database: 449 Effective search space: 200703 Effective search space used: 200703 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: 52 (24.6 bits)
This GapMind analysis is from Apr 10 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