Align Inositol transport system sugar-binding protein (characterized)
to candidate HSERO_RS12110 HSERO_RS12110 sugar ABC transporter substrate-binding protein
Query= reanno::Phaeo:GFF715 (316 letters) >FitnessBrowser__HerbieS:HSERO_RS12110 Length = 331 Score = 326 bits (836), Expect = 4e-94 Identities = 161/335 (48%), Positives = 220/335 (65%), Gaps = 32/335 (9%) Query: 10 LATTVAAAPMMLATTASAEGEKYILVSHAPDSDSWWNTIKNGIALAGEQMNVEVEYRNPP 69 +A AA P + + A E+++L+SHAPDSDSWWNTIKN I AGE +V V+YRNP Sbjct: 1 MALLAAATP----SPSVAANERFVLISHAPDSDSWWNTIKNAIKQAGEDFDVSVDYRNPS 56 Query: 70 TGDLADMARIIEQAAASGPNGIITTLSDYDVLSGPIKAAVDSGVDVIIMNSGTPDQAREV 129 GDLADMAR++EQAAA NG++ +++D+ VL PI+ V + VI +NSGT Q+ ++ Sbjct: 57 NGDLADMARLVEQAAARNYNGVVVSIADFSVLKKPIEMVVAKNIPVITINSGTQQQSEQL 116 Query: 130 GALMYVGQPEYDAGHAAGMRAKADGVGSFLCVNHYISSPSSTERCQGFADGLGVDLGDQM 189 GALM+VGQPEYDAG+ AG +AKA G+ SFLCVNHY ++PSS ERC+GFA+ +G D Sbjct: 117 GALMHVGQPEYDAGYGAGQKAKAAGIKSFLCVNHYATNPSSFERCRGFAEAIGADYKKST 176 Query: 190 IDSGQDPAEIKNRVLAYLNTNPETDAILTLGPTSADPTLLALDENGMAGDIYFGTFDLGE 249 +D+G DP ++++V AYL NP T A+L LGP SA P+L AL + G+ I+F TFDL E Sbjct: 177 LDTGIDPNAVESKVSAYLRNNPGTQAVLALGPDSAVPSLRALQKMGLKSKIWFATFDLSE 236 Query: 250 EIVKGLKSGVINWGIDQQPFLQAYLPVVVLT-------------------------NYHR 284 EI G+K G + + IDQQP+LQ Y+PV +L Sbjct: 237 EIANGIKDGSVQFAIDQQPYLQGYIPVAILALSRQLKTNDVAVLQDKLKGNAKFQARLAE 296 Query: 285 YGVLP---GNNINSGPGFVTKDGLEKVEEFAGEYR 316 YG+ P +I+SGPG++T+D L+KV ++AG+YR Sbjct: 297 YGLAPIYGPRHISSGPGYITRDNLDKVLKYAGQYR 331 Lambda K H 0.315 0.134 0.393 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: 348 Number of extensions: 10 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 316 Length of database: 331 Length adjustment: 28 Effective length of query: 288 Effective length of database: 303 Effective search space: 87264 Effective search space used: 87264 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 48 (23.1 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