Align Inositol transport system ATP-binding protein (characterized)
to candidate BWI76_RS19640 BWI76_RS19640 galactose/methyl galactoside ABC transporter ATP-binding protein MglA
Query= reanno::WCS417:GFF2332 (517 letters) >FitnessBrowser__Koxy:BWI76_RS19640 Length = 506 Score = 462 bits (1190), Expect = e-134 Identities = 237/493 (48%), Positives = 342/493 (69%), Gaps = 4/493 (0%) Query: 22 YLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIR 81 YLLE+ NI+K FPGV AL +V L+VRP ++ ALMGENGAGKSTL+K + GIYQ D+G I Sbjct: 12 YLLEMTNINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGSIL 71 Query: 82 LRGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCT 141 +G+ I F + A + GI+M+HQELNL+ S+ +N+W+GR + V+ +M+R T Sbjct: 72 FQGQEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGV-FVDQDKMYRDT 130 Query: 142 AELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFS 201 + L I++DP +VG LS+++ QM+EIAKA SY++ I+IMDEPTS++TEKEV HLF Sbjct: 131 KAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFK 190 Query: 202 IIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGREL 261 II LK +G GIVYI+HKM E+F + DE+ + RDG +I Q + ++ D +I+MMVGR L Sbjct: 191 IIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDKIIAMMVGRSL 250 Query: 262 SQLFPLRETPIGDLLLTVRDLT--LDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIF 319 +Q FP +E G+++L VR+LT +D+SFDLH GEILGIAGL+G+ RT++ ET+F Sbjct: 251 NQRFPNKENKPGEVILEVRNLTSLRQPSIRDISFDLHKGEILGIAGLVGAKRTDIVETLF 310 Query: 320 GITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHY 379 GI + G I L GK + + AI GFAL+TE+R+ +G++ L + N ++ + Y Sbjct: 311 GIREKAGGTIRLHGKKINNHSANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIKKY 370 Query: 380 TGN-GFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLIL 438 G + +++ + + +RVKTP I +LSGGNQQK ++ RWL+T P +L+L Sbjct: 371 KNKVGLLDNSRMKSDTQWVIDSMRVKTPGQHTQIGSLSGGNQQKVIIGRWLLTQPEILML 430 Query: 439 DEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDR 498 DEPTRGIDVGAK EIY+LIA LA + +I+ISSE+PE+LG++DR++VM G + G ++ Sbjct: 431 DEPTRGIDVGAKFEIYQLIAELAKKDKGIIIISSEMPELLGITDRILVMSNGLVAGIVET 490 Query: 499 SEATQEKVMQLAS 511 TQ ++++LAS Sbjct: 491 KTTTQNEILRLAS 503 Score = 70.9 bits (172), Expect = 1e-16 Identities = 47/223 (21%), Positives = 103/223 (46%), Gaps = 6/223 (2%) Query: 290 DVSFDLHAGEILGIAGLMGSGRTNVAETIFGITPSSSGQITLDGKAVRISDPHMAIEKGF 349 +V+ + I + G G+G++ + + +FGI SG I G+ + A+E G Sbjct: 31 NVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGSILFQGQEIDFHSAKEALENGI 90 Query: 350 ALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGNGFIQQKALRALCEDMCKKLRVKTPSLE 409 +++ ++ L SV++NM + P T F+ Q + + + +L + Sbjct: 91 SMVHQELNL---VLQRSVMDNMWLGRYP--TKGVFVDQDKMYRDTKAIFDELDIDIDPRA 145 Query: 410 QCIDTLSGGNQQKALLARWLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIM 469 + + TLS Q +A+ N +++I+DEPT + ++++I L G ++ Sbjct: 146 R-VGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFKIIRKLKERGCGIVY 204 Query: 470 ISSELPEVLGMSDRVMVMHEGELMGTLDRSEATQEKVMQLASG 512 IS ++ E+ + D + ++ +G+ + T +K++ + G Sbjct: 205 ISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDKIIAMMVG 247 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: 615 Number of extensions: 29 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 517 Length of database: 506 Length adjustment: 35 Effective length of query: 482 Effective length of database: 471 Effective search space: 227022 Effective search space used: 227022 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