Align D-tagatose-1,6-bisphosphate aldolase subunit KbaZ (characterized)
to candidate 6937021 Sama_1195 tagatose-6-phosphate kinase (RefSeq)
Query= SwissProt::P0C8K0 (426 letters) >FitnessBrowser__SB2B:6937021 Length = 422 Score = 405 bits (1040), Expect = e-117 Identities = 219/425 (51%), Positives = 283/425 (66%), Gaps = 10/425 (2%) Query: 1 MKHLTEMVRQHKAGKTNGIYAVCSAHPLVLEAAIRYASANQTPLLIEATSNQVDQFGGYT 60 M L ++ +K G+ GI+AVCSA PLVL AA+R+ +P+LIEAT+NQV+QFGGYT Sbjct: 1 MSVLKSIIEANKRGEQRGIFAVCSAQPLVLRAALRHGVETGSPVLIEATANQVNQFGGYT 60 Query: 61 GMTPADFRGFVCQLADSLNFPQDALILGGDHLGPNRWQNLPAAQAMANADDLIKSYVAAG 120 GM PADF FV LA++ P++ L+ GGDHLGP W++LPA +AMANA+ +++++V AG Sbjct: 61 GMVPADFIRFVESLAEAEGLPRERLLFGGDHLGPVAWKHLPADEAMANAEAMVRAFVNAG 120 Query: 121 FKKIHLDCSMSCQDDPIPLTDDIVAERAARLAKVAEETCLEHFGEADLEYVIGTEVPVPG 180 F+KIHLD SM CQ + PL D ++AERAARL K AEE L YVIGTEVP PG Sbjct: 121 FEKIHLDASMGCQGEAEPLGDSLIAERAARLCKAAEEAACGR----PLCYVIGTEVPPPG 176 Query: 181 GAHETLSELAVTTPDAARATLEAHRHAFEKQGL-NAIWPRIIALVVQPGVEFDHTNVIDY 239 G +L L VT A T+ AHR AF+ GL + +W R+IALVVQPGVEF H+++ Y Sbjct: 177 GV-ASLHALEVTPVPAIEQTVAAHRAAFDAAGLSDEVWQRVIALVVQPGVEFGHSDIHQY 235 Query: 240 QPAKASALSQMVENYETLIFEAHSTDYQTPQSLRQLVIDHFAILKVGPALTFALREALFS 299 + A + + L++EAHSTDYQ P+ + LV DHFAILKVGP LTFALREALF+ Sbjct: 236 NSSLLDAQRRFIRCQPGLVYEAHSTDYQLPEHYKSLVADHFAILKVGPELTFALREALFA 295 Query: 300 LAAIEEELVPAKACSGLRQVLEDVMLDRPEYWQSHYHGDGNARRLARGYSYSDRVRYYWP 359 L IE L+ +GLR + ED M P++WQ H++ D A G+SYSDR+RYYWP Sbjct: 296 LDHIEALLLEPSKRAGLRALCEDKMQADPKFWQ-HFYTDPLALDWQLGFSYSDRIRYYWP 354 Query: 360 DSQIDDAFAHLVRNLADSPIPLPLISQYLPLQYVKVRSGELQPTPRELIINHIQDILAQY 419 ++ A L+ NL D PIPLPLISQYLPLQY KV L T L+++HI +L +Y Sbjct: 355 --ELSQAIDTLLFNLKD-PIPLPLISQYLPLQYPKVLRQALPATALSLVLDHISLVLERY 411 Query: 420 HTACE 424 AC+ Sbjct: 412 EDACQ 416 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: 23 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: 426 Length of database: 422 Length adjustment: 32 Effective length of query: 394 Effective length of database: 390 Effective search space: 153660 Effective search space used: 153660 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