Align Inositol transport system ATP-binding protein (characterized)
to candidate SM_b21376 SM_b21376 sugar uptake ABC transporter ATP-binding protein
Query= reanno::WCS417:GFF2332 (517 letters) >FitnessBrowser__Smeli:SM_b21376 Length = 503 Score = 421 bits (1083), Expect = e-122 Identities = 230/497 (46%), Positives = 330/497 (66%), Gaps = 12/497 (2%) Query: 23 LLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRL 82 +L+I +++K F V AL ++L VR G V L+GENGAGKSTLMKI+AG++ +GEI L Sbjct: 9 ILKITDVTKSFGQVAALKGMRLEVRRGRVHTLLGENGAGKSTLMKILAGVHGATSGEIVL 68 Query: 83 RGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCTA 142 G+ P A G+A++ QEL+L ++++AENI RE +N + + Sbjct: 69 DGQAYRPANPQEAASLGLAIVFQELSLCNNLTVAENILATREP-RRFGFINDKALVAKAH 127 Query: 143 ELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSI 202 ++A LR+ +D E+VGNLSIA+RQ+VEIAK +S+D+ ++I+DEPTS++++ E LF I Sbjct: 128 RIVADLRLPIDVTEKVGNLSIAQRQLVEIAKGLSHDAKVVILDEPTSSLSDSEAEILFEI 187 Query: 203 IADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGRELS 262 I L+ +G I+YI+H+M E+ ++D++ V RDG Y+ D + ++LI++MVGR + Sbjct: 188 IGRLRQRGAAIIYISHRMEEIMRLSDDITVIRDGEYVSTHARDEVTIETLIALMVGRRMD 247 Query: 263 QLFPLRETPIGDL------LLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAE 316 +++P P+ + +L V LT +G F+DVSFD+ AGEILG GL+GSGR+ V Sbjct: 248 EIYP---PPVHHVAADRAPVLAVDRLTREGEFQDVSFDVRAGEILGFFGLVGSGRSEVMN 304 Query: 317 TIFGITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVL 376 +FG+ S++G + LDG+ VR P AI +G +TE+RK GL SV N+ MA L Sbjct: 305 ALFGMK-SAAGTVRLDGEVVRFRSPDQAIARGVGFVTENRKEEGLVLGHSVEWNISMAAL 363 Query: 377 PHYTGN-GFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRL 435 + G GFI+ A RA + KL +KT SLE LSGGNQQK +LA+WL+T P++ Sbjct: 364 ADFAGGLGFIRNGAERAAASEQVGKLSIKTNSLETPAGALSGGNQQKIVLAKWLLTRPKV 423 Query: 436 LILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGT 495 LILDEPTRG+DVGAK EIY++I LA+EG A+++ISS+LPEVLGMSDRV+VMHEG T Sbjct: 424 LILDEPTRGVDVGAKFEIYKIIRELAAEGTAILLISSDLPEVLGMSDRVVVMHEGAPGAT 483 Query: 496 LDRSEATQEKVMQLASG 512 L+ S T E +M A+G Sbjct: 484 LEGSALTPETIMAHATG 500 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: 592 Number of extensions: 29 Number of successful extensions: 8 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: 503 Length adjustment: 34 Effective length of query: 483 Effective length of database: 469 Effective search space: 226527 Effective search space used: 226527 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