Align Inositol transport system ATP-binding protein (characterized)
to candidate GFF2274 PGA1_c23060 ribose import ATP-binding protein RbsA
Query= reanno::WCS417:GFF2332 (517 letters) >FitnessBrowser__Phaeo:GFF2274 Length = 503 Score = 427 bits (1097), Expect = e-124 Identities = 218/495 (44%), Positives = 324/495 (65%) Query: 19 EEPYLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAG 78 E+ +L + I K FPGV AL V L + PG V ALMGENGAGKSTLMK++ GI+QPD G Sbjct: 3 EQSPVLRLEGIVKTFPGVRALDGVSLTILPGEVHALMGENGAGKSTLMKVLGGIHQPDEG 62 Query: 79 EIRLRGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMH 138 +I + +P+V PL A+ GI IHQEL+L +S+AENI++G +V+ E+ Sbjct: 63 QIIVAEQPVVMSGPLDAKAKGIVFIHQELSLADELSVAENIYLGELPRKRFGLVDWAELE 122 Query: 139 RCTAELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAH 198 T +L +L++ + + +VG+LSIA +QMVEIA+A++ D+ +I DEPT+++T+ E Sbjct: 123 AKTNAILEKLKVGFNAKTRVGDLSIANQQMVEIARALTVDAKAVIFDEPTASLTDAEKVV 182 Query: 199 LFSIIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVG 258 LF +I+DL+ QG GI YI+H+M E+F I D ++V RDG Y G N +++ MM+G Sbjct: 183 LFEVISDLQEQGVGIAYISHRMEEIFKITDRISVLRDGQYQGTVNTAETNEENVTQMMIG 242 Query: 259 RELSQLFPLRETPIGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETI 318 R+L +G++ L VR L+ +F+DV+F++ GE++G GL+G+GRT +AET+ Sbjct: 243 RKLDLSRNEAHHELGEVALEVRGLSCGSLFEDVNFEVRRGEVVGFYGLVGAGRTEIAETL 302 Query: 319 FGITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPH 378 FG+ +SG I LDG V I+ PH AIE+G +L+ EDRK GL ++ +NM + + Sbjct: 303 FGLRNPTSGSIFLDGAEVAITSPHDAIERGISLVPEDRKGQGLVLGMNCRDNMTLPQVDD 362 Query: 379 YTGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLIL 438 F+ A A+ + KL ++TP +Q + LSGGNQQK ++ +WL P +LI+ Sbjct: 363 LKAGPFVADGAEIAIFDQYRDKLDIRTPGWKQLVGNLSGGNQQKIVIGKWLSMRPNVLIV 422 Query: 439 DEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDR 498 DEPTRGIDVG+KAEI+ L+ LA++G AVI+ISSE+PEVL ++DR++ M+ G +M T Sbjct: 423 DEPTRGIDVGSKAEIHNLLRDLAAQGYAVIVISSEMPEVLHVADRIVAMYSGRIMRTFTS 482 Query: 499 SEATQEKVMQLASGM 513 E T+E ++ SG+ Sbjct: 483 EEVTEENLIAAISGL 497 Score = 84.0 bits (206), Expect = 1e-20 Identities = 59/229 (25%), Positives = 114/229 (49%), Gaps = 5/229 (2%) Query: 41 DVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRLRGKPIVFETPLAAQKAGI 100 DV VR G V+ G GAG++ + + + G+ P +G I L G + +P A + GI Sbjct: 274 DVNFEVRRGEVVGFYGLVGAGRTEIAETLFGLRNPTSGSIFLDGAEVAITSPHDAIERGI 333 Query: 101 AMIHQELN---LMPHMSIAENIWIGR-EQLNSLHMVNHREMHRCTAELLARLRINLDPEE 156 +++ ++ L+ M+ +N+ + + + L + V + +L I + Sbjct: 334 SLVPEDRKGQGLVLGMNCRDNMTLPQVDDLKAGPFVADGAEIAIFDQYRDKLDIRTPGWK 393 Query: 157 Q-VGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSIIADLKSQGKGIVY 215 Q VGNLS +Q + I K +S ++LI+DEPT I A + +++ DL +QG ++ Sbjct: 394 QLVGNLSGGNQQKIVIGKWLSMRPNVLIVDEPTRGIDVGSKAEIHNLLRDLAAQGYAVIV 453 Query: 216 ITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGRELSQL 264 I+ +M EV +AD + G + ++ + ++LI+ + G + ++ Sbjct: 454 ISSEMPEVLHVADRIVAMYSGRIMRTFTSEEVTEENLIAAISGLDTEKV 502 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: 610 Number of extensions: 31 Number of successful extensions: 5 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: 517 Length of database: 503 Length adjustment: 34 Effective length of query: 483 Effective length of database: 469 Effective search space: 226527 Effective search space used: 226527 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