Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate CCNA_03695 CCNA_03695 aldehyde dehydrogenase
Query= reanno::pseudo1_N1B4:Pf1N1B4_1109 (481 letters) >FitnessBrowser__Caulo:CCNA_03695 Length = 506 Score = 263 bits (673), Expect = 8e-75 Identities = 178/486 (36%), Positives = 247/486 (50%), Gaps = 19/486 (3%) Query: 6 RYDNYINGEWVSGAD--YSANINPSELTDTIGDYAKADLAQVHAAIDAARAAFPAWSTSG 63 RYDN+I G+WV+ AD Y N +P I + A++ + A+DAA AA W+ + Sbjct: 18 RYDNFIGGQWVAPADGRYFDNSSPIH-GRKICEIARSQAIDIERALDAAHAAKAGWARTS 76 Query: 64 IQARHDSLDKVGTEILARREELGTLLAREEGKTLPEAIG-EVTRAGNIFKFFAGECLRLS 122 R L ++ + L T + GK + E + ++ A + F++FAG CLR Sbjct: 77 AADRSRILLRIADRMEENLAALATAETWDNGKPIRETLAADIPLAIDHFRYFAG-CLRSQ 135 Query: 123 GDYLPSVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVLKPADLVPG 182 + + E LGVVG I PWNFP+ + WK+APALA GNCVVLKPA+ P Sbjct: 136 EGSISEIDHDTIAYHFHEPLGVVGQIIPWNFPLLMACWKLAPALAAGNCVVLKPAEQTPA 195 Query: 183 CAWALAEIISRAGFPAGVFNLVMGSGRVVGDALVQSPKVDGISFTGSVGVGRQIAVSCVS 242 AE+I PAGV N+V G G G L SP++ I+FTG GR I Sbjct: 196 SIMVWAEMIGDL-LPAGVLNIVNGFGLEAGKPLASSPRIAKIAFTGETSTGRLIMQYAAQ 254 Query: 243 RQAKVQLEMGGKNPQIILDDAD------LKQAVELSVQSAFYSTGQRCTASSRFIVTAGI 296 V LE+GGK+P I DD L +A+E A + G+ CT SR +V I Sbjct: 255 NLIPVTLELGGKSPNIFFDDVAREDDDYLDKALEGFTMFAL-NQGEVCTCPSRALVQESI 313 Query: 297 HDKFVEAMAERMKSIKVGHALKTGTDIGPVVSQAQLEQDLKYIDIGQSEGARLVSGGG-- 354 ++KF+E +R+ ++ G L T IG S+ QL + L Y+DIG++EGA+L++GG Sbjct: 314 YEKFMERALKRVNAVVQGSPLDPATMIGAQASEEQLNKILGYMDIGRNEGAKLLAGGQRK 373 Query: 355 -LVACDTEGYFLAPTLFADSTAAMRISREEIFGPVANIVRVADYEAALAMANDTEFGLSA 413 L +GY++ PT+F + MRI +EEIFGPV + E AL +ANDT FGL A Sbjct: 374 ILPGQLADGYYVEPTVF-EGHNKMRIFQEEIFGPVLAVTTFKTEEEALEIANDTAFGLGA 432 Query: 414 GIATTSLKYANHFKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGSREQGRYAQEFYTV 473 G+ + F R +AG V N A H FGG K S G RE + + Y Sbjct: 433 GVWSRDANRCYRFGRGIEAGRVWTNCYHA-YPAHAAFGGYKQSGVG-RETHKMMLDHYQQ 490 Query: 474 VKTSYI 479 K + Sbjct: 491 TKNMLV 496 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: 496 Number of extensions: 25 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: 481 Length of database: 506 Length adjustment: 34 Effective length of query: 447 Effective length of database: 472 Effective search space: 210984 Effective search space used: 210984 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 Sep 17 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