Align Inositol transport system ATP-binding protein (characterized)
to candidate WP_011653997.1 RL_RS23960 sugar ABC transporter ATP-binding protein
Query= reanno::WCS417:GFF2332 (517 letters) >NCBI__GCF_000009265.1:WP_011653997.1 Length = 513 Score = 623 bits (1606), Expect = 0.0 Identities = 318/491 (64%), Positives = 389/491 (79%), Gaps = 1/491 (0%) Query: 22 YLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIR 81 YLL + K FPGVVAL DVQ R++ +V ALMGENGAGKSTLMKI+AGIY PD G+IR Sbjct: 22 YLLSAEGVRKEFPGVVALDDVQFRLKRASVHALMGENGAGKSTLMKILAGIYTPDKGDIR 81 Query: 82 LRGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCT 141 L+G I ++PL A + GIAMIHQELNLMP M++AENIWI RE N L ++H MHR T Sbjct: 82 LKGIEIQLKSPLDALENGIAMIHQELNLMPFMTVAENIWIRREPKNRLGFIDHGVMHRMT 141 Query: 142 AELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFS 201 EL RL I +DP+ +V LS+A RQMVEIAKAVSY+SD+LIMDEPTSA+TE+EV HLF Sbjct: 142 EELFTRLNIAIDPDIEVRFLSVANRQMVEIAKAVSYNSDVLIMDEPTSALTEREVEHLFR 201 Query: 202 IIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGREL 261 II DLK+QG GIVYITHKMNE+F IADE +VFRDG YIG + + D +I MMVGRE+ Sbjct: 202 IIRDLKAQGIGIVYITHKMNELFEIADEFSVFRDGRYIGTHASTDVTRDDIIRMMVGREI 261 Query: 262 SQLFPLRETPIGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIFGI 321 +Q+FP E PIG+++L+V+DL L+GVFK+VSF++ AGEILG+AGL+GSGR+NVAET+FG+ Sbjct: 262 TQMFPKEEVPIGEVMLSVKDLCLNGVFKNVSFEVRAGEILGVAGLVGSGRSNVAETLFGV 321 Query: 322 TPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVL-PHYT 380 TP+SSG I L GK V IS P AI A LTEDRK +G L +LENM++AVL Y Sbjct: 322 TPASSGSIELYGKPVAISSPTEAIRNRMAFLTEDRKDTGCLLILDILENMQIAVLQDRYV 381 Query: 381 GNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILDE 440 GF+QQ A+ A CEDM KKLRVKTP+L + ++ LSGGNQQK L+ RWL+TNPR+LILDE Sbjct: 382 KGGFVQQGAVEATCEDMAKKLRVKTPNLYERVENLSGGNQQKVLIGRWLLTNPRILILDE 441 Query: 441 PTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRSE 500 PTRGIDVGAKAEI+RL+ +A +G+AV+MISSE+PEVLGMSDR+MVMHEG + G L+R E Sbjct: 442 PTRGIDVGAKAEIHRLVTEMARDGVAVVMISSEMPEVLGMSDRIMVMHEGRVTGFLNRDE 501 Query: 501 ATQEKVMQLAS 511 ATQ KVM+LA+ Sbjct: 502 ATQIKVMELAA 512 Score = 90.5 bits (223), Expect = 1e-22 Identities = 56/224 (25%), Positives = 115/224 (51%), Gaps = 7/224 (3%) Query: 290 DVSFDLHAGEILGIAGLMGSGRTNVAETIFGITPSSSGQITLDGKAVRISDPHMAIEKGF 349 DV F L + + G G+G++ + + + GI G I L G +++ P A+E G Sbjct: 41 DVQFRLKRASVHALMGENGAGKSTLMKILAGIYTPDKGDIRLKGIEIQLKSPLDALENGI 100 Query: 350 ALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGNGFIQQKALRALCEDMCKKLRVKT-PSL 408 A++ ++ L P ++V EN+ + P GFI + + E++ +L + P + Sbjct: 101 AMIHQELNL---MPFMTVAENIWIRREPK-NRLGFIDHGVMHRMTEELFTRLNIAIDPDI 156 Query: 409 EQCIDTLSGGNQQKALLARWLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMAVI 468 E + LS N+Q +A+ + N +LI+DEPT + ++R+I L ++G+ ++ Sbjct: 157 E--VRFLSVANRQMVEIAKAVSYNSDVLIMDEPTSALTEREVEHLFRIIRDLKAQGIGIV 214 Query: 469 MISSELPEVLGMSDRVMVMHEGELMGTLDRSEATQEKVMQLASG 512 I+ ++ E+ ++D V +G +GT ++ T++ ++++ G Sbjct: 215 YITHKMNELFEIADEFSVFRDGRYIGTHASTDVTRDDIIRMMVG 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: 680 Number of extensions: 26 Number of successful extensions: 6 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 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