Align Inositol transport system ATP-binding protein (characterized)
to candidate WP_041936920.1 RL_RS31840 sugar ABC transporter ATP-binding protein
Query= reanno::WCS417:GFF2332 (517 letters) >NCBI__GCF_000009265.1:WP_041936920.1 Length = 511 Score = 419 bits (1077), Expect = e-121 Identities = 213/504 (42%), Positives = 331/504 (65%) Query: 9 QPPSLQPQTLEEPYLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKI 68 Q + +T + P +LE+ IS+ FPGV AL +V + + PGTV AL+GENGAGKSTL+KI Sbjct: 6 QQTATDSKTGDAPAILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKI 65 Query: 69 IAGIYQPDAGEIRLRGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNS 128 + GIY+P+ GEI + G+P+ F + AA AG+ IHQE L +++AENI++G Sbjct: 66 LTGIYRPNEGEILVDGQPVTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTR 125 Query: 129 LHMVNHREMHRCTAELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPT 188 L ++ + M+ LL L N+DP ++ + SIA+R +V IA+A+S ++ I+IMDEPT Sbjct: 126 LRTIDWQAMNSRAKALLTALESNIDPTIRLKDFSIAQRHLVAIARALSIEARIVIMDEPT 185 Query: 189 SAITEKEVAHLFSIIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMN 248 +A++ KE+ LF I+ LK +GK I++I+HK +EV+ IAD+ VFRDG +G R Sbjct: 186 AALSRKEIDDLFRIVRGLKEKGKAILFISHKFDEVYEIADDFVVFRDGRAVGQGRLKETP 245 Query: 249 SDSLISMMVGRELSQLFPLRETPIGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMG 308 D ++ MMVGR++ FP + G +L +R+ + F+D+SF L GEILGI GL+G Sbjct: 246 QDEIVRMMVGRDVENAFPKVDVAFGGPVLEIRNYSHRTEFRDISFTLRQGEILGIYGLIG 305 Query: 309 SGRTNVAETIFGITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVL 368 +GR+ +++++FGIT SG++ L+G+ + I P AI G + E+R GL + + Sbjct: 306 AGRSELSQSLFGITRPLSGKMMLEGREITIHSPQDAIRAGIVYVPEERGRHGLALPMPIF 365 Query: 369 ENMEMAVLPHYTGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARW 428 +NM + L + GF++ AL ++L ++ +L + TLSGGNQQK ++ +W Sbjct: 366 QNMTLPSLTRTSRRGFLRAAEEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKW 425 Query: 429 LMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMH 488 L T P+++ILDEPT+GID+G+KA ++ I+ LA+EG+++IM+SSELPE++GMSDRV+VM Sbjct: 426 LATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMK 485 Query: 489 EGELMGTLDRSEATQEKVMQLASG 512 EG G +R+E + E +++ A+G Sbjct: 486 EGLAAGIFERAELSPEALVRAATG 509 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: 588 Number of extensions: 30 Number of successful extensions: 6 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: 511 Length adjustment: 35 Effective length of query: 482 Effective length of database: 476 Effective search space: 229432 Effective search space used: 229432 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