Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate RR42_RS16500 RR42_RS16500 fructose-bisphosphate aldolase
Query= BRENDA::Q8L207 (343 letters) >FitnessBrowser__Cup4G11:RR42_RS16500 Length = 340 Score = 341 bits (874), Expect = 2e-98 Identities = 192/323 (59%), Positives = 228/323 (70%), Gaps = 5/323 (1%) Query: 12 LVGAGKGILAADESTATIGKRFESIGVECTEDNRRAYREMLFTAKEAMESAISGVILFDE 71 LV AGKG+LAADES ATI KRFE IGV +E++RRA+R +L + + ISGVIL++E Sbjct: 14 LVQAGKGLLAADESGATIAKRFERIGVASSEESRRAWRNLLLSTP-GLGECISGVILYEE 72 Query: 72 TLRQKASTGQMLTDLIRDAGAVPGIKVDTGAKPLAAFPQETITEGLDGLRERLKDYYTLG 131 TL Q A G L L G VPGIKVD G LA P + ITEGLDGL +RL Y G Sbjct: 73 TLGQCADDGTPLPALAARHGIVPGIKVDKGKLALAHAPGDEITEGLDGLAKRLAAYRQQG 132 Query: 132 ARFAKWRAVIAIDAQTLPTRGAISQNAQALARYAALCQEAGLVPIVEPEVLMDGPSRQHS 191 ARFAKWRAV + + LP+R AI NAQALARYAA+CQE G+VPIVEPEVLMDG H+ Sbjct: 133 ARFAKWRAVYNVSGE-LPSRLAIQANAQALARYAAICQEMGVVPIVEPEVLMDGA---HA 188 Query: 192 ITRCFEVTKVVLHTVFKELFEARVLFEGMILKPNMVIDGKDARIASVEEVAEKTVHVLKQ 251 + RC EVT+ VLH VF L V+ E M+LKP+MV+ GKDA A+ EVA +TV VLK+ Sbjct: 189 MARCAEVTEAVLHDVFHALHRHAVVLEHMLLKPSMVLPGKDAGHAAPAEVAMQTVQVLKR 248 Query: 252 TVPAAVPGIAFLSGGQTDEEATAHLSAMNALGALPWKLTFSYGRALQAAALKAWAGKNEN 311 TVPAAVPGI FLSGGQT EATA+L AMN L LPW+L+FSYGRALQ L AW G+ N Sbjct: 249 TVPAAVPGIFFLSGGQTPIEATANLDAMNRLAPLPWRLSFSYGRALQEPPLLAWRGEAAN 308 Query: 312 IVVAQKAFCHRARMNHLAALGQW 334 AQ+A R+R+N LA+LGQ+ Sbjct: 309 AAQAQRALLQRSRLNGLASLGQY 331 Lambda K H 0.319 0.132 0.378 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: 328 Number of extensions: 11 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: 343 Length of database: 340 Length adjustment: 29 Effective length of query: 314 Effective length of database: 311 Effective search space: 97654 Effective search space used: 97654 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: 49 (23.5 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