Align D-tagatose-1,6-bisphosphate aldolase subunit GatZ (characterized)
to candidate 16202 b2095 D-tagatose 1,6-bisphosphate aldolase 2, subunit (NCBI)
Query= SwissProt::P0C8J8 (420 letters) >FitnessBrowser__Keio:16202 Length = 420 Score = 843 bits (2179), Expect = 0.0 Identities = 420/420 (100%), Positives = 420/420 (100%) Query: 1 MKTLIARHKAGEHIGICSVCSAHPLVIEAALAFDRNSTRKVLIEATSNQVNQFGGYTGMT 60 MKTLIARHKAGEHIGICSVCSAHPLVIEAALAFDRNSTRKVLIEATSNQVNQFGGYTGMT Sbjct: 1 MKTLIARHKAGEHIGICSVCSAHPLVIEAALAFDRNSTRKVLIEATSNQVNQFGGYTGMT 60 Query: 61 PADFREFVFTIADKVGFARERIILGGDHLGPNCWQQENADAAMEKSVELVKEYVRAGFSK 120 PADFREFVFTIADKVGFARERIILGGDHLGPNCWQQENADAAMEKSVELVKEYVRAGFSK Sbjct: 61 PADFREFVFTIADKVGFARERIILGGDHLGPNCWQQENADAAMEKSVELVKEYVRAGFSK 120 Query: 121 IHLDASMSCAGDPIPLAPETVAERAAVLCFAAESVATDCQREQLSYVIGTEVPVPGGEAS 180 IHLDASMSCAGDPIPLAPETVAERAAVLCFAAESVATDCQREQLSYVIGTEVPVPGGEAS Sbjct: 121 IHLDASMSCAGDPIPLAPETVAERAAVLCFAAESVATDCQREQLSYVIGTEVPVPGGEAS 180 Query: 181 AIQSVHITHVEDAANTLRTHQKAFIARGLTEALTRVIAIVVQPGVEFDHSNIIHYQPQEA 240 AIQSVHITHVEDAANTLRTHQKAFIARGLTEALTRVIAIVVQPGVEFDHSNIIHYQPQEA Sbjct: 181 AIQSVHITHVEDAANTLRTHQKAFIARGLTEALTRVIAIVVQPGVEFDHSNIIHYQPQEA 240 Query: 241 QPLAQWIENTRMVYEAHSTDYQTRTAYWELVRDHFAILKVGPALTFALREAIFALAQIEQ 300 QPLAQWIENTRMVYEAHSTDYQTRTAYWELVRDHFAILKVGPALTFALREAIFALAQIEQ Sbjct: 241 QPLAQWIENTRMVYEAHSTDYQTRTAYWELVRDHFAILKVGPALTFALREAIFALAQIEQ 300 Query: 301 ELIAPENRSGCLAVIEEVMLDEPQYWKKYYRTGFNDSLLDIRYSLSDRIRYYWPHSRIKN 360 ELIAPENRSGCLAVIEEVMLDEPQYWKKYYRTGFNDSLLDIRYSLSDRIRYYWPHSRIKN Sbjct: 301 ELIAPENRSGCLAVIEEVMLDEPQYWKKYYRTGFNDSLLDIRYSLSDRIRYYWPHSRIKN 360 Query: 361 SVETMMVNLEGVDIPLGMISQYLPKQFERIQSGELSAIPHQLIMDKIYDVLRAYRYGCAE 420 SVETMMVNLEGVDIPLGMISQYLPKQFERIQSGELSAIPHQLIMDKIYDVLRAYRYGCAE Sbjct: 361 SVETMMVNLEGVDIPLGMISQYLPKQFERIQSGELSAIPHQLIMDKIYDVLRAYRYGCAE 420 Lambda K H 0.321 0.135 0.401 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: 764 Number of extensions: 11 Number of successful extensions: 1 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: 420 Length of database: 420 Length adjustment: 32 Effective length of query: 388 Effective length of database: 388 Effective search space: 150544 Effective search space used: 150544 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 (21.9 bits) S2: 50 (23.9 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