Align methanogen homoaconitase (EC 4.2.1.114) (characterized)
to candidate AZOBR_RS14130 AZOBR_RS14130 3-isopropylmalate dehydrogenase
Query= BRENDA::Q58991 (347 letters) >FitnessBrowser__azobra:AZOBR_RS14130 Length = 371 Score = 184 bits (466), Expect = 4e-51 Identities = 135/374 (36%), Positives = 197/374 (52%), Gaps = 45/374 (12%) Query: 3 KVCVIEGDGIGKEVIPEAIKILNELGE-----FEIIKGEAGLECLKKYGNALPEDTIEKA 57 K+ + GDGIG EV+ + ++++ L F++ +G G + YG L ++T+ A Sbjct: 6 KLLFLPGDGIGPEVMRQVRRVIDWLDRKRNVTFDVTEGLVGGAAIDAYGVPLKDETLADA 65 Query: 58 KEADIILFGAITSPKPGEVKNY----KSPIITLRKMFHLYANVRPINNFGIGQLIGKIAD 113 AD ++ GA+ PK +Y ++ +++LRK +L+AN+RP F + D Sbjct: 66 LAADAVMLGAVGGPKWDNPTDYTKRPEAGLLSLRKELNLFANLRPAVVFDA------LVD 119 Query: 114 YEFLNA---KNIDIVIIRENTEDLYVGRERLENDTAIAER------VITRKGSERIIRFA 164 L A K +DI+I+RE T +Y G R D ER V T R+ R A Sbjct: 120 ASTLKADVIKGLDILIVRELTGGVYFGEPRGITDIGNGERRGVNTQVYTTSEIRRVARVA 179 Query: 165 FEYAIKNNRKKVSCIHKANVLRITDGLFLEVFNEIKKHYNIEADDYLV-----DSTAMNL 219 FE A K K S + KANV+ GL E+ K + E D + D+ AM L Sbjct: 180 FELARKRGNKLHS-MEKANVME--SGLLWR--QEVTKLHQEEFSDVTLEHMYADNGAMQL 234 Query: 220 IKHPEKFDVIVTTNMFGDILSDEASALIGGLGLAPSANI------GDDKALFEPVHGSAP 273 +K+P++FDVIVT N+FGDILSDEA+ + G LG+ PSA++ G KAL+EPVHGSAP Sbjct: 235 LKNPKQFDVIVTDNLFGDILSDEAAMMTGSLGMLPSASLGAPDANGQRKALYEPVHGSAP 294 Query: 274 DIAGKGIANPMASILSIAMLFDY-IGEKEKGDLIREAVKYCLINKKVTPDLGGD----LK 328 DIAG+ +ANP A++LS AM Y E+ ++ +AV+ L T D+ Sbjct: 295 DIAGRDLANPCATLLSFAMCLRYSFNMDEEAKMLEKAVQNVLSGGMRTADIMAPGMARCS 354 Query: 329 TKDVGDEILNYIRK 342 T +GD IL + K Sbjct: 355 TTVMGDSILRELDK 368 Lambda K H 0.319 0.140 0.397 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: 323 Number of extensions: 15 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: 347 Length of database: 371 Length adjustment: 29 Effective length of query: 318 Effective length of database: 342 Effective search space: 108756 Effective search space used: 108756 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 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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