Align Inositol transport system ATP-binding protein (characterized)
to candidate GFF2274 PGA1_c23060 ribose import ATP-binding protein RbsA
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__Phaeo:GFF2274 Length = 503 Score = 166 bits (420), Expect = 9e-46 Identities = 88/246 (35%), Positives = 142/246 (57%), Gaps = 4/246 (1%) Query: 1 MSMSQPLIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPT 60 M+ P++R++GI K F V AL GVS+ + PGE H L+G+NGAGKST +K + G+H+P Sbjct: 1 MTEQSPVLRLEGIVKTFPGVRALDGVSLTILPGEVHALMGENGAGKSTLMKVLGGIHQPD 60 Query: 61 KGDILFEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFD 120 +G I+ QP+ + P DA A GI +HQ L++ +SV+ N ++G P ++ G + + Sbjct: 61 EGQIIVAEQPVVMSGPLDAKAKGIVFIHQELSLADELSVAENIYLGELPRKRFGLVDWAE 120 Query: 121 HDYANRITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALG 180 + +E++ K+G N + VG LS +Q V IARA+ AK +I DEPT++L Sbjct: 121 LEAKTNAILEKL-KVGFNAK---TRVGDLSIANQQMVEIARALTVDAKAVIFDEPTASLT 176 Query: 181 VRQTANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEEL 240 + + I +++QGV + +I+H + + DR +VL G+ GT + + E + Sbjct: 177 DAEKVVLFEVISDLQEQGVGIAYISHRMEEIFKITDRISVLRDGQYQGTVNTAETNEENV 236 Query: 241 QDMMAG 246 MM G Sbjct: 237 TQMMIG 242 Score = 91.3 bits (225), Expect = 4e-23 Identities = 66/225 (29%), Positives = 104/225 (46%), Gaps = 7/225 (3%) Query: 26 VSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILFEGQPLHFADPRDAIAAGIA 85 V+ +V GE G GAG++ +T+ G+ PT G I +G + P DAI GI+ Sbjct: 275 VNFEVRRGEVVGFYGLVGAGRTEIAETLFGLRNPTSGSIFLDGAEVAITSPHDAIERGIS 334 Query: 86 TVHQHL---AMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANRITMEEMR-KMGINLRG 141 V + ++ M+ N + K GP F D A ++ R K+ I G Sbjct: 335 LVPEDRKGQGLVLGMNCRDNMTLPQVDDLKAGP---FVADGAEIAIFDQYRDKLDIRTPG 391 Query: 142 PDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTANVLATIDKVRKQGVAV 201 Q VG LSGG +Q + I + + VLI+DEPT + V A + + + QG AV Sbjct: 392 WKQLVGNLSGGNQQKIVIGKWLSMRPNVLIVDEPTRGIDVGSKAEIHNLLRDLAAQGYAV 451 Query: 202 VFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDMMAG 246 + I+ + L V DR + G+ + T +++ E L ++G Sbjct: 452 IVISSEMPEVLHVADRIVAMYSGRIMRTFTSEEVTEENLIAAISG 496 Lambda K H 0.321 0.137 0.395 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: 309 Number of extensions: 13 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 261 Length of database: 503 Length adjustment: 29 Effective length of query: 232 Effective length of database: 474 Effective search space: 109968 Effective search space used: 109968 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 (21.9 bits) S2: 49 (23.5 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