Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_011779095.1 MVAN_RS09340 aldehyde dehydrogenase
Query= reanno::pseudo1_N1B4:Pf1N1B4_1109 (481 letters) >NCBI__GCF_000015305.1:WP_011779095.1 Length = 488 Score = 392 bits (1006), Expect = e-113 Identities = 219/475 (46%), Positives = 293/475 (61%), Gaps = 10/475 (2%) Query: 11 INGEWV-SGADYSANINPSELTDTIGDYAKADLAQVHAAIDAARAAFPAWSTSGIQARHD 69 I+GEW+ G D ++NP+ T + + + A + V AA+ AA AA P+W+ +G+ R Sbjct: 11 IDGEWLPGGGDALVSVNPARPTVVVAEGSCAVASDVDAAVGAAAAAAPSWAATGMHQRGA 70 Query: 70 SLDKVGTEILARREELGTLLAREEGKTLPEAIGEVTRAGNIFKFFAGECLRLSGDYLPSV 129 L + E G LA EEGKT E +GEV RA I +++ E R +G+ S Sbjct: 71 RLLAAAEIVERNAERWGLELATEEGKTRAEGVGEVRRAAQILRYYGNEGDRQAGEIYSSP 130 Query: 130 RPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVLKPADLVPGCAWALAE 189 RPG + VTR+ LGVVG++TP+NFPIAIPAWKIAPAL YGN VV KPA VP A AE Sbjct: 131 RPGEQILVTRKPLGVVGVVTPFNFPIAIPAWKIAPALVYGNTVVWKPASTVPLLALRFAE 190 Query: 190 IISRAGFPAGVFNLVMGSGRVVGDALVQSPKVDGISFTGSVGVGRQIAVSCVSRQAKVQL 249 ++ AG P GV NLV+G G +GDA+V P +DGI+FTGS GVGR+IA + +R Q Sbjct: 191 ALTDAGLPPGVLNLVVG-GADIGDAIVNHPGIDGITFTGSTGVGRRIAAAAAARGVPAQA 249 Query: 250 EMGGKNPQIILDDADLKQAVELSVQSAFYSTGQRCTASSRFIVTAGIHDKFVEAMAERMK 309 EMGGKN ++LDDADL AVE + AF STGQ+CTA+SR IVTAGI D F EA+ + + Sbjct: 250 EMGGKNAAVVLDDADLDLAVEQVMLGAFRSTGQKCTATSRLIVTAGIADAFSEALLAQAR 309 Query: 310 SIKVGHALKTGTDIGPVVSQAQLEQDLKYIDIGQSEGARLVSGG-----GLVACDTEGYF 364 +++VG + T +GPVVS + + ID ++GA +++GG G +A EGYF Sbjct: 310 ALRVGDPVDDATQMGPVVSDSAQQSITAGIDTAVTQGATVLTGGRPYQDGALA---EGYF 366 Query: 365 LAPTLFADSTAAMRISREEIFGPVANIVRVADYEAALAMANDTEFGLSAGIATTSLKYAN 424 +APT+ A + + +E+FGPV I R D E A A+AND+EFGLSA + T + A Sbjct: 367 VAPTVVELGAAPVDVWTDELFGPVLAIRRATDAEEAFALANDSEFGLSAAVFTQDMTRAL 426 Query: 425 HFKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGSREQGRYAQEFYTVVKTSYI 479 G++ VN +AG D HVPFGG K S G +EQG A+EF+T T Y+ Sbjct: 427 QAVERIDVGVLHVNSESAGADPHVPFGGAKKSGLGPKEQGGAAREFFTHTTTVYL 481 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: 566 Number of extensions: 25 Number of successful extensions: 3 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: 488 Length adjustment: 34 Effective length of query: 447 Effective length of database: 454 Effective search space: 202938 Effective search space used: 202938 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