Align Inositol transport system ATP-binding protein (characterized)
to candidate SM_b20503 SM_b20503 sugar ABC transporter ATP-binding protein
Query= reanno::WCS417:GFF2332 (517 letters) >FitnessBrowser__Smeli:SM_b20503 Length = 512 Score = 423 bits (1087), Expect = e-123 Identities = 221/494 (44%), Positives = 331/494 (67%), Gaps = 5/494 (1%) Query: 23 LLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRL 82 +LEI N+SK F V AL V R+ G V AL GENGAGKSTLM +IAG+ QP GE+ + Sbjct: 6 VLEIRNVSKHFGAVKALTAVDFRLARGEVHALCGENGAGKSTLMNVIAGVLQPSEGEVLI 65 Query: 83 RGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCTA 142 G P+ +P AQ GIA++HQE+ L P +IAEN+++ ++N+ ++ R Sbjct: 66 EGAPVKIASPAVAQSLGIALVHQEIALCPDATIAENMFMAATNRRRSALMNYAQLERDAQ 125 Query: 143 ELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSI 202 ++ RL +D ++VG+L I+ +Q+VEIAKA++ D +LI DEPT+A+TE E LF I Sbjct: 126 AVMNRLA-PIDVSQKVGDLPISSQQLVEIAKALTLDCRVLIFDEPTAALTETEAQVLFGI 184 Query: 203 IADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGRELS 262 I DLK++G I+YI+H+M EVF++ D V VFRDG Y+ + + D ++ +MVGRE+S Sbjct: 185 IRDLKARGISIIYISHRMAEVFSLCDRVTVFRDGRYVATEMVSDVTPDDVVRLMVGREIS 244 Query: 263 QLFPLRETP---IGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIF 319 QL+P ++ +G+ +L+VRDL + F+DVSF+L GEILG+ GL+GSGRT +AE I Sbjct: 245 QLYPDKQPSSERLGEPILSVRDLGGER-FRDVSFELRYGEILGVGGLIGSGRTEIAEGIC 303 Query: 320 GITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHY 379 + P + G+I L K +R+ A + G L+EDRK SG+F LS+ +N+ L Sbjct: 304 ALRPVTQGEIRLHDKVLRLRRYSDAAKAGVVYLSEDRKGSGVFLDLSIAQNIAALDLKAL 363 Query: 380 TGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILD 439 T G + + RAL ED+ ++L V+ ++ + +LSGGNQQK +A+ L +P+++++D Sbjct: 364 TSLGLLNSREERALAEDLTRRLGVRMGGVDMPVSSLSGGNQQKVAIAKQLAVDPKVILMD 423 Query: 440 EPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRS 499 EPTRGIDVGAK+EI+RL+ LA G+ +++ISSELPE++G+ DRV+V+ EG + G + + Sbjct: 424 EPTRGIDVGAKSEIHRLLRELARAGIGILVISSELPELIGLCDRVLVVREGRIAGEVSGN 483 Query: 500 EATQEKVMQLASGM 513 E T+E +M+LASG+ Sbjct: 484 EMTEEVIMRLASGI 497 Lambda K H 0.320 0.136 0.381 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: 583 Number of extensions: 21 Number of successful extensions: 7 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: 517 Length of database: 512 Length adjustment: 35 Effective length of query: 482 Effective length of database: 477 Effective search space: 229914 Effective search space used: 229914 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: 52 (24.6 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