Align Inositol transport system ATP-binding protein (characterized)
to candidate WP_061533937.1 CAter10_RS14380 D-xylose ABC transporter ATP-binding protein
Query= reanno::WCS417:GFF2332 (517 letters) >NCBI__GCF_001584165.1:WP_061533937.1 Length = 518 Score = 379 bits (974), Expect = e-109 Identities = 219/503 (43%), Positives = 316/503 (62%), Gaps = 17/503 (3%) Query: 22 YLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDA--GE 79 YLLE+ I K F V AL + L+VR G + L GENGAGKSTLMK+++G+Y + GE Sbjct: 4 YLLEMKGIVKQFGAVRALDGIALKVRAGECVGLCGENGAGKSTLMKVLSGVYPHGSWEGE 63 Query: 80 IRLRGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHR 139 I G+P+ ++ + AGI +IHQEL L+P +S+AENI++G E +N+ M+R Sbjct: 64 ILWDGQPLKAQSIRDTEAAGIVIIHQELMLVPELSVAENIFMGHELTLPGGRMNYPAMYR 123 Query: 140 CTAELLARLRINLDPEEQVG----NLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKE 195 EL+ L++ PE V +Q+VEIAKA++ + +LI+DEP+S++T E Sbjct: 124 RADELVRELKM---PEMNVALPVMQYGGGHQQLVEIAKALNKKARLLILDEPSSSLTTSE 180 Query: 196 VAHLFSIIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISM 255 +A L II DLK++G VYI+HK++EV AI D V+V RDG +I +N + +I+ Sbjct: 181 IAVLLDIIRDLKAKGVACVYISHKLDEVAAICDTVSVIRDGQHIATTPMQELNVEYIIAQ 240 Query: 256 MVGRELSQLFPLRETPIGDLLLTVRDLTLDGV-------FKDVSFDLHAGEILGIAGLMG 308 MVGRE++ L+P +E IG+++ R ++ V D+SF L GEILG+AGL+G Sbjct: 241 MVGREMNNLYPKQEHAIGEVVFEARHISCYDVDNPARKKVDDISFSLRKGEILGVAGLVG 300 Query: 309 SGRTNVAETIFGITPS-SSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSV 367 +GRT + ++G P G++ LDGK V P ++ G ++ EDRK G+ L+V Sbjct: 301 AGRTELVSALYGAYPGRQEGEVWLDGKQVDTGSPMKSLRLGLCMVPEDRKRHGIVADLNV 360 Query: 368 LENMEMAVLPHYTGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLAR 427 +N+ + VL ++ G I +A + KLR+KT S I +LSGGNQQKA+LA+ Sbjct: 361 GQNITLTVLQEFSRFGRIDAEAELQTIQQQIGKLRLKTASPFLPITSLSGGNQQKAVLAK 420 Query: 428 WLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVM 487 L+ PR+LILDEPTRG+DVGAK EIY+L+ LA +G+A+IM+SSEL EVLG+SDRV+V+ Sbjct: 421 MLLAKPRVLILDEPTRGVDVGAKYEIYKLMFDLAEQGVAIIMVSSELAEVLGVSDRVLVI 480 Query: 488 HEGELMGTLDRSEATQEKVMQLA 510 EG+L G TQE V+ A Sbjct: 481 GEGKLRGDFVNQGLTQETVLAAA 503 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: 600 Number of extensions: 28 Number of successful extensions: 9 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: 518 Length adjustment: 35 Effective length of query: 482 Effective length of database: 483 Effective search space: 232806 Effective search space used: 232806 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