Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_004305670.1 C665_RS08800 aldehyde dehydrogenase
Query= reanno::pseudo1_N1B4:Pf1N1B4_1109 (481 letters) >NCBI__GCF_000310185.1:WP_004305670.1 Length = 506 Score = 275 bits (702), Expect = 3e-78 Identities = 185/494 (37%), Positives = 254/494 (51%), Gaps = 30/494 (6%) Query: 2 ADAK-----RYDNYINGEWVSGA-----DYSANINPSELTDTIGDYAKADLAQVHAAIDA 51 ADAK RYDN+I G+WV+ D I + T A++ + A+DA Sbjct: 9 ADAKIQYKARYDNFIGGQWVAPVKGQYFDVVTPITGQKYTQA----ARSTAEDIELALDA 64 Query: 52 ARAAFPAWSTSGIQARHDSLDKVGTEILARREELGTLLAREEGKTLPEAIG-EVTRAGNI 110 A AAFP W + R + L K+ + A E L + GK + E + ++ A + Sbjct: 65 AHAAFPKWGKADATTRSNILLKIADRLEANLELLAYAETVDNGKPIRETLNADIPLAVDH 124 Query: 111 FKFFAGECLRLSGDYLPSVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGN 170 F++FAG CLR + + E LGVVG I PWNFPI + AWK+APAL GN Sbjct: 125 FRYFAG-CLRSQEGGISEIDENTMAYHIHEPLGVVGQIIPWNFPILMAAWKLAPALGAGN 183 Query: 171 CVVLKPADLVPGCAWALAEIISRAGFPAGVFNLVMGSGRVVGDALVQSPKVDGISFTGSV 230 CVVLKPA+ P L E+I+ P GV N+V G GR G L S ++ I+FTGS Sbjct: 184 CVVLKPAESTPISILVLMELIADL-LPPGVLNIVNGYGREAGMPLATSKRIAKIAFTGST 242 Query: 231 GVGRQIAVSCVSRQAKVQLEMGGKNPQII------LDDADLKQAVELSVQSAFYSTGQRC 284 GR IA + + LE+GGK+P I +DDA L +A+E V AF + G+ C Sbjct: 243 STGRVIAQAAANNLIPATLELGGKSPNIFFADVMDMDDAFLDKAIEGLVLFAF-NQGEVC 301 Query: 285 TASSRFIVTAGIHDKFVEAMAERMKSIKVGHALKTGTDIGPVVSQAQLEQDLKYIDIGQS 344 T SR ++ I+D+F+E +R+ +IK G L T T +G S Q+ + Y+ +G+ Sbjct: 302 TCPSRALIQESIYDRFIERAVKRVAAIKQGSPLDTDTMMGAQASSEQMSKIQSYLQLGKD 361 Query: 345 EGARLVSGGGLVACD---TEGYFLAPTLFADSTAAMRISREEIFGPVANIVRVADYEAAL 401 EGA+++ GG D +GY++ PTLF MRI +EEIFGPV + D AL Sbjct: 362 EGAQVLIGGARAQLDGDLADGYYIQPTLFKGHN-KMRIFQEEIFGPVLAVTTFKDEAEAL 420 Query: 402 AMANDTEFGLSAGIATTSLKYANHFKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGSR 461 A+ANDT +GL AG+ + + A R QAG V N A H FGG K S G R Sbjct: 421 AIANDTLYGLGAGVWSRNGNVAYRMGRAIQAGRVWTNCYHA-YPAHAAFGGYKESGIG-R 478 Query: 462 EQGRYAQEFYTVVK 475 E + + Y K Sbjct: 479 ETHKVMLDHYQQTK 492 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: 509 Number of extensions: 28 Number of successful extensions: 7 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 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