Align Inositol transport system ATP-binding protein (characterized)
to candidate SM_b20713 SM_b20713 sugar uptake ABC transporter ATP-binding protein
Query= reanno::WCS417:GFF2332 (517 letters) >FitnessBrowser__Smeli:SM_b20713 Length = 513 Score = 629 bits (1623), Expect = 0.0 Identities = 318/491 (64%), Positives = 396/491 (80%), Gaps = 1/491 (0%) Query: 22 YLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIR 81 YLL + K FPGVVAL DV+ +++ GTV ALMGENGAGKSTLMKI+AGIY PD GE++ Sbjct: 22 YLLTAEGVRKEFPGVVALDDVEFKLKRGTVHALMGENGAGKSTLMKILAGIYYPDQGEVK 81 Query: 82 LRGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCT 141 LRG I ++PL A + GIAMIHQELNLMP M++AENIWI RE N V+H EM R T Sbjct: 82 LRGAGIRLKSPLDALENGIAMIHQELNLMPFMTVAENIWIRREPKNRFGFVDHGEMRRMT 141 Query: 142 AELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFS 201 A+L RL+I+LDPE +V +LS+A RQMVEIAKAVSY+SD+LIMDEPTSA+TE+EVAHLF Sbjct: 142 AKLFERLKIDLDPEIEVRHLSVANRQMVEIAKAVSYESDVLIMDEPTSALTEREVAHLFE 201 Query: 202 IIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGREL 261 II DL+SQG GIVYITHKMNE+F IADE +VFRDG YIG ++ + D +I MMVGRE+ Sbjct: 202 IIRDLRSQGIGIVYITHKMNELFEIADEFSVFRDGKYIGTHLSNEVTRDDIIRMMVGREI 261 Query: 262 SQLFPLRETPIGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIFGI 321 +Q+FP E PIGD++L+V++LTL+GVF+DVSFD+ AGEILG+AGL+GSGR+NVAET+FG+ Sbjct: 262 TQMFPKEEVPIGDVVLSVKNLTLNGVFRDVSFDVRAGEILGVAGLVGSGRSNVAETLFGV 321 Query: 322 TPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVL-PHYT 380 TP+SSG I +DGK V I + AI A LTEDRK +G L +LENM++AVL + Sbjct: 322 TPASSGTIAIDGKEVVIDSANKAIRHRMAFLTEDRKDTGCLLILDILENMQIAVLQDKFV 381 Query: 381 GNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILDE 440 GF+ ++ + A CE+M +KLRVKTP+L++ ++ LSGGNQQK L+ RWL+TNPR+LILDE Sbjct: 382 KRGFVSEREVTAACEEMSRKLRVKTPNLQERVENLSGGNQQKVLIGRWLLTNPRILILDE 441 Query: 441 PTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRSE 500 PTRGIDVGAKAEI+RL+ LA G+AVIMISSE+PEVLGMSDR+MVMHEG + G LDR+E Sbjct: 442 PTRGIDVGAKAEIHRLVTELARNGVAVIMISSEMPEVLGMSDRIMVMHEGRVTGILDRAE 501 Query: 501 ATQEKVMQLAS 511 ATQ KVM+LA+ Sbjct: 502 ATQIKVMELAA 512 Score = 94.4 bits (233), Expect = 9e-24 Identities = 62/241 (25%), Positives = 124/241 (51%), Gaps = 16/241 (6%) Query: 282 LTLDGVFK---------DVSFDLHAGEILGIAGLMGSGRTNVAETIFGITPSSSGQITLD 332 LT +GV K DV F L G + + G G+G++ + + + GI G++ L Sbjct: 24 LTAEGVRKEFPGVVALDDVEFKLKRGTVHALMGENGAGKSTLMKILAGIYYPDQGEVKLR 83 Query: 333 GKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGNGFIQQKALRA 392 G +R+ P A+E G A++ ++ L P ++V EN+ + P GF+ +R Sbjct: 84 GAGIRLKSPLDALENGIAMIHQELNL---MPFMTVAENIWIRREPK-NRFGFVDHGEMRR 139 Query: 393 LCEDMCKKLRVKT-PSLEQCIDTLSGGNQQKALLARWLMTNPRLLILDEPTRGIDVGAKA 451 + + ++L++ P +E + LS N+Q +A+ + +LI+DEPT + A Sbjct: 140 MTAKLFERLKIDLDPEIE--VRHLSVANRQMVEIAKAVSYESDVLIMDEPTSALTEREVA 197 Query: 452 EIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRSEATQEKVMQLAS 511 ++ +I L S+G+ ++ I+ ++ E+ ++D V +G+ +GT +E T++ ++++ Sbjct: 198 HLFEIIRDLRSQGIGIVYITHKMNELFEIADEFSVFRDGKYIGTHLSNEVTRDDIIRMMV 257 Query: 512 G 512 G Sbjct: 258 G 258 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: 688 Number of extensions: 27 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 517 Length of database: 513 Length adjustment: 35 Effective length of query: 482 Effective length of database: 478 Effective search space: 230396 Effective search space used: 230396 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