Align Inositol transport system ATP-binding protein (characterized)
to candidate RR42_RS04800 RR42_RS04800 ABC transporter
Query= reanno::WCS417:GFF2332 (517 letters) >FitnessBrowser__Cup4G11:RR42_RS04800 Length = 529 Score = 278 bits (712), Expect = 3e-79 Identities = 181/514 (35%), Positives = 276/514 (53%), Gaps = 21/514 (4%) Query: 17 TLEEPYLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPD 76 TL L + +ISK +PGV A DV L V PG + A++GENGAGKSTLMKII G +PD Sbjct: 2 TLSTTPRLALAHISKRYPGVTANDDVSLVVAPGEIHAVLGENGAGKSTLMKIIFGAVKPD 61 Query: 77 AGEIRLRGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIG-----REQLNSLHM 131 AG++ G P A+ GIAM+ Q +L +++AENI +G + S H Sbjct: 62 AGDMHFNGARAAIHNPHDARNLGIAMVFQHFSLFDTLTVAENIALGLPRGSKTAAGSPHA 121 Query: 132 -VNHREMHRCTAELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSA 190 N +++ E R + L+P V LS+ ERQ VEI +A+ +LI+DEPTS Sbjct: 122 GTNMKQLAEQIRETALRYGLPLEPNRHVHTLSVGERQRVEIVRALLAKPQLLILDEPTSV 181 Query: 191 ITEKEVAHLFSIIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSD 250 +T + V LF + L ++G I+YI+HK++E+ + V R G G+ ++ Sbjct: 182 LTPQAVQTLFITLRQLAAEGTSILYISHKLDEIRELCHSATVMRMGRVTGVCDPRQESAA 241 Query: 251 SLISMMVGRELSQLFPLRETPIGDLLLTVRDLTLD------GVFKDVSFDLHAGEILGIA 304 SL +M+G E + ++ P G L VR+L+L +S DL AGEI+GIA Sbjct: 242 SLSRLMIGGEPPREARVQTEP-GVCRLAVRELSLPRSHAFATELAGISLDLRAGEIVGIA 300 Query: 305 GLMGSGRTNVAETIFG-ITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFP 363 G+ G+G+ + + G ++ ITLD K V D G A + E+R G P Sbjct: 301 GVSGNGQQELLAALSGEDVRAARDAITLDNKPVGKLDARQRRRAGLAFVPEERLGRGAVP 360 Query: 364 CLSVLENMEMAVLPH----YTGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGN 419 +S+ N+ +L H Y G I KA L + + +LRVK +LSGGN Sbjct: 361 GMSLAANI---LLSHQSAPYVQRGMISPKAAAGLAQAVIARLRVKASGPHALAKSLSGGN 417 Query: 420 QQKALLARWLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLG 479 QK ++ R + + P++LI+ +PT G+DVGA A+I+ + L + G A++++S EL E+ Sbjct: 418 LQKFIVGREIESGPKVLIVAQPTWGVDVGAAAQIHNELLALKATGCALLVVSEELDELFA 477 Query: 480 MSDRVMVMHEGELMGTLDRSEATQEKVMQLASGM 513 + DR+ V+ +G L ++ +AT+E+V SG+ Sbjct: 478 ICDRLHVIAKGRLSPSIPTRDATREQVGLWMSGL 511 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: 593 Number of extensions: 27 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: 529 Length adjustment: 35 Effective length of query: 482 Effective length of database: 494 Effective search space: 238108 Effective search space used: 238108 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