Align D-tagatose-1,6-bisphosphate aldolase subunit KbaZ (characterized)
to candidate 7025549 Shewana3_2700 tagatose-bisphosphate aldolase noncatalytic subunit (RefSeq)
Query= SwissProt::P0C8K0 (426 letters) >FitnessBrowser__ANA3:7025549 Length = 428 Score = 416 bits (1068), Expect = e-121 Identities = 227/425 (53%), Positives = 278/425 (65%), Gaps = 8/425 (1%) Query: 1 MKHLTEMVRQHKAGKTNGIYAVCSAHPLVLEAAIRYASANQTPLLIEATSNQVDQFGGYT 60 M + ++ +KAG+ GI+AVCSA PLVL+AA+ A AN TPLLIEAT+NQV+QFGGYT Sbjct: 1 MSVIQTIIDANKAGQQAGIFAVCSAQPLVLQAALLQAKANGTPLLIEATANQVNQFGGYT 60 Query: 61 GMTPADFRGFVCQLADSLNFPQDALILGGDHLGPNRWQNLPAAQAMANADDLIKSYVAAG 120 GM P DF FV Q+ L L+ GGDHLGP W A +AM A+DLI YV AG Sbjct: 61 GMKPQDFIDFVTQMTVELGLNPSQLLFGGDHLGPVVWCQQAAEEAMQLAEDLIAEYVKAG 120 Query: 121 FKKIHLDCSMSCQDDPIPLTDDIVAERAARLAKVAEETCLEHFGEADLEYVIGTEVPVPG 180 F KIHLD SM+C D +PL D+++A RAARL VAE E L YVIGTEVP PG Sbjct: 121 FTKIHLDTSMACGGDVLPLADELIAARAARLCAVAE---AHRAPEQALCYVIGTEVPAPG 177 Query: 181 GAHETLSELAVTTPDAARATLEAHRHAFEKQGL-NAIWPRIIALVVQPGVEFDHTNVIDY 239 G E +ELAVT A TL HR AF GL +W ++IA+VVQPGVEFD++ V + Sbjct: 178 GVSEMEAELAVTPVSAIEHTLNCHRDAFAAAGLGEEVWQKVIAVVVQPGVEFDNSQVHLF 237 Query: 240 QPAKASALSQMVENYETLIFEAHSTDYQTPQSLRQLVIDHFAILKVGPALTFALREALFS 299 +P A S+ + Y L+FEAHSTDYQ + LV HFAILKVGP LTFALREALF+ Sbjct: 238 EPEATHAQSEFIRGYPRLVFEAHSTDYQLSMGYQALVQQHFAILKVGPQLTFALREALFA 297 Query: 300 LAAIEEELVPAKACSGLRQVLEDVMLDRPEYWQSHYHGDGNARRLARGYSYSDRVRYYWP 359 L+ IE L + CS LRQ ++M D P+YWQ Y D A + G+S+SDRVRYYWP Sbjct: 298 LSHIENVLCQPEQCSDLRQSCFELMRDNPKYWQGFY-ADNEALKWQLGFSFSDRVRYYWP 356 Query: 360 DSQIDDAFAHLVRNLADSPIPLPLISQYLPLQYVKVRSGELQPTPRELIINHIQDILAQY 419 Q + L+ NLA S IPLPLISQYLP QY V +GEL+PT REL+++ I ++LA Y Sbjct: 357 SLQ--NKVEQLLSNLAQS-IPLPLISQYLPNQYTAVLAGELKPTARELVLHKITEVLADY 413 Query: 420 HTACE 424 AC+ Sbjct: 414 ANACQ 418 Lambda K H 0.320 0.135 0.403 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: 568 Number of extensions: 28 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: 426 Length of database: 428 Length adjustment: 32 Effective length of query: 394 Effective length of database: 396 Effective search space: 156024 Effective search space used: 156024 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: 51 (24.3 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