Align D-tagatose-1,6-bisphosphate aldolase subunit KbaZ (characterized)
to candidate WP_057508585.1 ABB28_RS10500 D-tagatose-bisphosphate aldolase, class II, non-catalytic subunit
Query= SwissProt::P0C8K0 (426 letters) >NCBI__GCF_001431535.1:WP_057508585.1 Length = 429 Score = 431 bits (1108), Expect = e-125 Identities = 229/425 (53%), Positives = 283/425 (66%), Gaps = 2/425 (0%) Query: 1 MKHLTEMVRQHKAGKTNGIYAVCSAHPLVLEAAIRYAS-ANQTPLLIEATSNQVDQFGGY 59 M L ++V +H+ G G+ ++CSAHPLV+EA++R+A + Q LL EAT NQV+Q GGY Sbjct: 1 MHALLDLVARHRQGHAIGVTSICSAHPLVIEASLRHAQRSGQALLLFEATCNQVNQDGGY 60 Query: 60 TGMTPADFRGFVCQLADSLNFPQDALILGGDHLGPNRWQNLPAAQAMANADDLIKSYVAA 119 TGM PADF FV +A + F ++LGGDHLGPN W +L AA AM A+ ++ +YVAA Sbjct: 61 TGMRPADFVRFVHGIAARVGFDTGRILLGGDHLGPNPWTSLDAAAAMDKAEVMVGAYVAA 120 Query: 120 GFKKIHLDCSMSCQDDPIPLTDDIVAERAARLAKVAEETCLEHFGEADLEYVIGTEVPVP 179 GF+KIHLDCSM+C+ DP PL + + RA RL + AE GEA + YVIGTEVPVP Sbjct: 121 GFRKIHLDCSMACKGDPEPLPEAEIVRRAVRLCRAAEAAWASAGGEAPV-YVIGTEVPVP 179 Query: 180 GGAHETLSELAVTTPDAARATLEAHRHAFEKQGLNAIWPRIIALVVQPGVEFDHTNVIDY 239 GGA E + LA+TTP AA T+EAHR AF + GL+A W R++A VVQPGVEFDH +VIDY Sbjct: 180 GGATEAIEGLALTTPAAALTTIEAHRVAFAEAGLDAAWQRVLASVVQPGVEFDHHDVIDY 239 Query: 240 QPAKASALSQMVENYETLIFEAHSTDYQTPQSLRQLVIDHFAILKVGPALTFALREALFS 299 KA LSQ V L+FEAHSTDYQT +L LV DHFAILKVGP LTFALREAL++ Sbjct: 240 DSDKAQPLSQAVTGVPQLVFEAHSTDYQTRDALAALVRDHFAILKVGPGLTFALREALWA 299 Query: 300 LAAIEEELVPAKACSGLRQVLEDVMLDRPEYWQSHYHGDGNARRLARGYSYSDRVRYYWP 359 L AIE E + + LR+V M + P YWQ +YHG G A YS SDR+RYYWP Sbjct: 300 LDAIEAEWIDDDRRARLREVTLRRMQESPGYWQRYYHGTGRALTTDLQYSLSDRIRYYWP 359 Query: 360 DSQIDDAFAHLVRNLADSPIPLPLISQYLPLQYVKVRSGELQPTPRELIINHIQDILAQY 419 D I+ A A L NL P PLPL+SQYLP VR+G P+ L + HI +L Y Sbjct: 360 DPAIEAARARLFDNLRADPPPLPLVSQYLPHALHAVRNGTATFDPQSLAMAHISAVLDDY 419 Query: 420 HTACE 424 H AC+ Sbjct: 420 HHACQ 424 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: 590 Number of extensions: 29 Number of successful extensions: 3 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: 429 Length adjustment: 32 Effective length of query: 394 Effective length of database: 397 Effective search space: 156418 Effective search space used: 156418 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 24 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