Align isocitrate-homoisocitrate dehydrogenase (EC 1.1.1.286) (characterized)
to candidate GFF1981 Psest_2024 isocitrate dehydrogenase, NADP-dependent, prokaryotic type
Query= BRENDA::Q4J6C9 (411 letters) >FitnessBrowser__psRCH2:GFF1981 Length = 418 Score = 366 bits (939), Expect = e-106 Identities = 193/410 (47%), Positives = 269/410 (65%), Gaps = 9/410 (2%) Query: 8 PQDGEPIKFEKGKWV-VPNKPIILYIEGDGIGPEITNSAIRVVNKAVEKAYKSSREIKWL 66 P G+ I + VPN PII YIEGDGIG +I+ I+VV+ AV+KAY R+I W+ Sbjct: 9 PSSGDKITVNADNTLNVPNNPIIPYIEGDGIGVDISPVMIKVVDAAVQKAYGGQRKIAWM 68 Query: 67 EVYAGEKANKITGDR--FPKETQDMLLKYRVVLKGPLETPIGKGWKSINVAIRLMLDLYA 124 E+YAGEKA ++ PKET + + Y V +KGPL TP+G G +S+NVA+R LDLY Sbjct: 69 EIYAGEKATQVYDQDTWLPKETLEAVRDYVVSIKGPLTTPVGGGIRSLNVALRQELDLYV 128 Query: 125 NIRPVKYIEGLESPLKHPEKVDMIIFRENTDDLYRGIEFPYDSEEAKKIRKFLREEL--- 181 RPV++ G+ SP+K P VDM+IFREN++D+Y G+E+ S EA+K+ KFL EE+ Sbjct: 129 CQRPVRWFTGVPSPVKKPGDVDMVIFRENSEDIYAGVEWKAGSPEAEKVIKFLTEEMGVK 188 Query: 182 KVDIEDDTGIGLKVMSKFKTQRITRLALNYALQNSRKKVTVMHKGNVMKYTEGSFREWAY 241 K+ ++ GIG+K +S T+R+ R AL YA+ N R VT++HKGN+MK+TEG+F+EW Y Sbjct: 189 KIRFTENCGIGIKPVSLEGTKRLVRKALQYAVDNDRSSVTIVHKGNIMKFTEGAFKEWGY 248 Query: 242 EVALNEYRDKIVTEEEIN--RGVNSEGKVILNDRIADNMLQQIIIRPDEYDIILAPNVNG 299 EVA +E+ +++ + N+ +++ D IAD MLQQI++RP EYD+I N+NG Sbjct: 249 EVARDEFGAELLDGGPWMQFKNPNTGKNIVVKDAIADAMLQQILLRPAEYDVIATLNLNG 308 Query: 300 DYISDAAGALIGNIGMLGGANIGDTGGMFEAIHGTAPKYAGKNVANPTGIIKSCELMLYF 359 DY+SDA A +G IG+ GAN+ DT MFEA HGTAPKYAG++ NP +I S E+ML Sbjct: 309 DYLSDALAAEVGGIGIAPGANLSDTVAMFEATHGTAPKYAGQDKVNPGSLILSAEMMLRH 368 Query: 360 MGWSEAARLIEKAINESIKQKKVTQDIARYL-GITPLGTKEYTDTLVQIM 408 MGW EAA LI K+ +I K VT D R + G + ++ D ++ M Sbjct: 369 MGWVEAADLIIKSTESAIAAKTVTYDFERLMEGAQLMSCSQFGDAMISHM 418 Lambda K H 0.317 0.137 0.394 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: 500 Number of extensions: 21 Number of successful extensions: 4 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: 411 Length of database: 418 Length adjustment: 31 Effective length of query: 380 Effective length of database: 387 Effective search space: 147060 Effective search space used: 147060 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 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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