Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate H281DRAFT_02805 H281DRAFT_02805 fructose-bisphosphate aldolase
Query= BRENDA::Q8L207 (343 letters) >FitnessBrowser__Burk376:H281DRAFT_02805 Length = 339 Score = 344 bits (883), Expect = 2e-99 Identities = 192/331 (58%), Positives = 232/331 (70%), Gaps = 6/331 (1%) Query: 12 LVGAGKGILAADESTATIGKRFESIGVECTEDNRRAYREMLFTAKEAMESAISGVILFDE 71 +V GKG+LAADES TI KRF++IG++ TE+NRRAYR +L T + +SGVIL++E Sbjct: 14 MVQPGKGLLAADESGPTIAKRFKTIGLDSTEENRRAYRNLLLTTP-GLGEFVSGVILYEE 72 Query: 72 TLRQKASTGQMLTDLIRDAGAVPGIKVDTGAKPLAAFPQETITEGLDGLRERLKDYYTLG 131 TL QKA G ++ G VPGIKVD G PLA P + ITEGLDGL R DY G Sbjct: 73 TLGQKADNGTPFPEVAAKNGIVPGIKVDLGKVPLAHAPGDEITEGLDGLARRFVDYKKQG 132 Query: 132 ARFAKWRAVIAIDAQTLPTRGAISQNAQALARYAALCQEAGLVPIVEPEVLMDGPSRQHS 191 ARFAKWRAV I A LP+R AI NA +LARYAA+ QEAG+VPIVEPEVLMDG H+ Sbjct: 133 ARFAKWRAVYNITAN-LPSRLAIEANADSLARYAAIAQEAGIVPIVEPEVLMDG---DHT 188 Query: 192 ITRCFEVTKVVLHTVFKELFEARVLFEGMILKPNMVIDGKD-ARIASVEEVAEKTVHVLK 250 I R EVT+ VLH VF L RV+ E M+LKP+MVI G + AR +S ++A TV +LK Sbjct: 189 IERSAEVTEAVLHEVFVALQRHRVVLEHMLLKPSMVIAGSESARQSSTADIAAYTVRILK 248 Query: 251 QTVPAAVPGIAFLSGGQTDEEATAHLSAMNALGALPWKLTFSYGRALQAAALKAWAGKNE 310 +TVPAAVPGI FLSGGQ+ EEATA+L AMN LG LPW L+FSYGRALQ L+AW G Sbjct: 249 RTVPAAVPGIVFLSGGQSPEEATANLDAMNRLGPLPWNLSFSYGRALQEPPLQAWKGAAS 308 Query: 311 NIVVAQKAFCHRARMNHLAALGQWTKDQEKS 341 N+ AQ+A RAR+N AALG++ QEK+ Sbjct: 309 NVEEAQQALLKRARLNSAAALGKYDAAQEKN 339 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: 301 Number of extensions: 12 Number of successful extensions: 5 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: 339 Length adjustment: 29 Effective length of query: 314 Effective length of database: 310 Effective search space: 97340 Effective search space used: 97340 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 Sep 17 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