Align Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_009778838.1 MED217_RS02180 aldehyde dehydrogenase (NADP(+))
Query= reanno::pseudo6_N2E2:Pf6N2E2_612 (526 letters) >NCBI__GCF_000152985.1:WP_009778838.1 Length = 525 Score = 484 bits (1247), Expect = e-141 Identities = 259/520 (49%), Positives = 335/520 (64%), Gaps = 5/520 (0%) Query: 4 ILGHNYIGGARSAAGQTRLQSVDASTGEALPHDFIQATAEEVDAAAKAAAAAYPAYRSLS 63 I G NYIG SA G+T +++ F +AT EVDAAA+ AA A+ Y+ S Sbjct: 2 ITGKNYIGSKISAEGKTTYTTINPKLNIENEWQFTEATESEVDAAAQLAAEAFEVYKHKS 61 Query: 64 AVRRAEFLEAIADELDALGDEFVAVVCRETALPAARIQGERGRTSGQMRLFAKVLRRGDF 123 RA FL AI +E++ALG + + E+ LP R GERGRT GQ+ FA +L +GD+ Sbjct: 62 DKERAAFLRAIGEEIEALGQQLIDTYTTESGLPEGRAMGERGRTIGQLNAFASLLEQGDW 121 Query: 124 YGARIDRALPERTPLPRPDLRQYRIGLGPVAVFGASNFPLAFSTAGGDTASALAAGCPVV 183 A ID PERTP P+PDLR+ +I GPVAVFGASNFP AFSTAGGDTASALAAGCPVV Sbjct: 122 VQATIDHGNPERTPAPKPDLRKMQIATGPVAVFGASNFPFAFSTAGGDTASALAAGCPVV 181 Query: 184 FKAHSGHMATAEHVADAIIRAAEKTLMPAGVFNMIYGGG--VGEWLVKHPAIQAVGFTGS 241 K+H H AT E V+ AII+AA+KT MP GVF+ + G VGE LVKHPAI+ VGFTGS Sbjct: 182 VKSHPMHAATGELVSSAIIKAAQKTGMPDGVFSNLNSKGIAVGEQLVKHPAIKGVGFTGS 241 Query: 242 LKGGRALCDMAAARPQPIPVFAEMSSINPVIVLPQALETRAESVARDLTASVVQGCGQFC 301 +K G+AL + A R +PIPV+AEM SINPV++LP+AL+ ES A+ S+ G GQFC Sbjct: 242 IKAGKALVALGANREEPIPVYAEMGSINPVVILPEALKVNGESWAQKYAGSINLGAGQFC 301 Query: 302 TNPGLVIGIRSPQFTAFTQQVAALIGDQAPQTMLNAGTLQSYGKGLQKLLAHPGIEHLAG 361 TNPGL++GI + F + +A +G+Q ML+ +Y G Q +L G E LA Sbjct: 302 TNPGLILGIEGEELETFGKNLATHLGEQPAHCMLHPNIQSAYESGKQTMLDAAGTEVLAV 361 Query: 362 --RQQQGNQAQPQLFKADASLLINGDEALQEEVFGPTTVFVEVADQAQLTAALNGLHGQL 419 + N +P L K + + L EVFGP ++ V +AQL LN L GQL Sbjct: 362 TLEAEGANDGKPALVKVTGDNFL-ANTKLHAEVFGPFSMLVSCTSKAQLLEVLNALEGQL 420 Query: 420 TATMIGEPADFERFSELTPLLEQKVGRILLNGYPTGVEVCDSMVHGGPYPATSDARGTSV 479 T ++I E ++ ++++ L +VGRIL NG PTGVEVC +M HGGP+P++SDA+ TSV Sbjct: 421 TGSLIAETSEVATYTDVIDALRSRVGRILFNGVPTGVEVCPAMHHGGPFPSSSDAKFTSV 480 Query: 480 GTLAIDRFLRPVCFQNYPDSLLPEPLKNANPLGILRLVDG 519 G AI R++RPV +Q++P LLP+ LK NPLGILR VDG Sbjct: 481 GNDAIYRWVRPVSYQDWPQELLPDALKEENPLGILRKVDG 520 Lambda K H 0.319 0.135 0.395 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: 698 Number of extensions: 29 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: 526 Length of database: 525 Length adjustment: 35 Effective length of query: 491 Effective length of database: 490 Effective search space: 240590 Effective search space used: 240590 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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