Align Inositol transport system ATP-binding protein (characterized)
to candidate WP_041937034.1 RL_RS36695 sugar ABC transporter ATP-binding protein
Query= reanno::WCS417:GFF2332 (517 letters) >NCBI__GCF_000009265.1:WP_041937034.1 Length = 512 Score = 417 bits (1071), Expect = e-121 Identities = 215/495 (43%), Positives = 327/495 (66%), Gaps = 5/495 (1%) Query: 23 LLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRL 82 +LEI N+SK F V AL +V + G V AL GENGAGKSTLM IIAG+ QP G++ + Sbjct: 6 VLEIRNVSKHFGAVKALTEVSFSLEKGEVHALCGENGAGKSTLMNIIAGVLQPTEGDVLV 65 Query: 83 RGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCTA 142 G P+ +P AQ G+ ++HQE+ L P ++AEN+++ +N+ + R Sbjct: 66 DGAPVKVTSPAVAQSLGLGLVHQEIALCPDATVAENMFMAATNRRRSPFMNYGRLERDAQ 125 Query: 143 ELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSI 202 ++ RL +D +VG+LSI+ +Q+VEIAKA++ D +LI DEPT+A+TE E LF+I Sbjct: 126 VVMNRLA-PIDVRRKVGDLSISSQQLVEIAKALTLDCRVLIFDEPTAALTESETQVLFAI 184 Query: 203 IADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGRELS 262 I DLK+QG I+YI+H+M E+F++ D V VFRDG Y+ +++ + D ++ MVGRE++ Sbjct: 185 IRDLKAQGISIIYISHRMAEIFSLCDRVTVFRDGRYVSMEKVADVTPDDVVRRMVGREIT 244 Query: 263 QLFPLRETP---IGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIF 319 QL+P ++ P +++L+VR+L F DV+FDL GEILG+ GL+GSGRT +AE I Sbjct: 245 QLYPEKQAPAERTDEIILSVRNLGDGSRFTDVNFDLRKGEILGVGGLIGSGRTEIAEGIC 304 Query: 320 GITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHY 379 G+ P G++ L G+ +R A + G L+EDRK SG+F LS+ +N+ + L Sbjct: 305 GLRPVIDGKVQLHGQRLRARSYAQAAQAGVVYLSEDRKGSGIFLDLSIAQNIAVLDLKSL 364 Query: 380 TGN-GFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLIL 438 TG G + KA ++ ++L V+ ++ + +LSGGNQQK +A+ L +P+++++ Sbjct: 365 TGPLGLLNSKAEADRAHNLVRRLGVRMGGIDMPVSSLSGGNQQKVAIAKQLAVDPKVILM 424 Query: 439 DEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDR 498 DEPTRGIDVGAK+EI+RL+ LA G+ +++ISSELPE+LG+ DRV+V+HEG + G ++ Sbjct: 425 DEPTRGIDVGAKSEIHRLLRDLARSGIGIVVISSELPELLGLCDRVLVIHEGTVAGEVEG 484 Query: 499 SEATQEKVMQLASGM 513 T+E +M+LASG+ Sbjct: 485 EAMTEEAIMRLASGI 499 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: 576 Number of extensions: 23 Number of successful extensions: 9 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 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