Align Inositol transport system ATP-binding protein (characterized)
to candidate PP_2455 PP_2455 ribose ABC transporter - ATP-binding subunit
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__Putida:PP_2455 Length = 524 Score = 129 bits (324), Expect = 1e-34 Identities = 80/243 (32%), Positives = 125/243 (51%), Gaps = 5/243 (2%) Query: 4 SQPLIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGD 63 ++ ++ G+ K + + L VS+ + GE L G+NGAGKST K +SG+ PT G Sbjct: 13 NEVVLAASGLGKTYAQPV-LGEVSLSLRAGEVLALTGENGAGKSTLSKLISGLEVPTTGH 71 Query: 64 ILFEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDY 123 + + GQ +A G+ V Q L ++P ++V+ N F+ N P R H Sbjct: 72 MTYRGQAYAPGSRGEAERLGVRMVMQELNLLPTLTVAENLFLDNLPSR----FGWISHKR 127 Query: 124 ANRITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQ 183 ++ M ++G++ PD VG L G +Q V IAR + VLILDEPT+ L R+ Sbjct: 128 LRQLATAAMARVGLDAIDPDTPVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTARE 187 Query: 184 TANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDM 243 A + I+++R +GVA+V+I+H + V R VL GK + S+ EL ++ Sbjct: 188 VALLFTQIERLRARGVAIVYISHRLEELQRVAQRIVVLRDGKLVCDEPIQRYSSAELVNL 247 Query: 244 MAG 246 M G Sbjct: 248 MVG 250 Score = 93.6 bits (231), Expect = 8e-24 Identities = 62/221 (28%), Positives = 110/221 (49%), Gaps = 9/221 (4%) Query: 26 VSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILFEGQP---LHFADPRDAIAA 82 VS +V GE + G GAG++ ++ + G + G I GQP + P+ A+ A Sbjct: 283 VSFEVRAGEIFGISGLIGAGRTELLRLIYGADRADSGGIAL-GQPPQAVSIDSPKAAVRA 341 Query: 83 GIATVHQHL---AMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANRITMEEMRKMGINL 139 GIA + + ++ S+S N +GN + + + D + + +++ M I Sbjct: 342 GIALITEDRKGEGLLLTQSISANIALGN--LGAVSRAGVLDSEAEKALAERQIQAMRIRS 399 Query: 140 RGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTANVLATIDKVRKQGV 199 G Q VG LSGG +Q V I R + +VL+ DEPT + V ++ + ++ +QG Sbjct: 400 AGAQQVVGELSGGNQQKVVIGRWLERDCQVLLFDEPTRGIDVGAKFDIYGLLAELARQGK 459 Query: 200 AVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEEL 240 A+V ++ ++R + + DR VL+ G+ + T R S ++L Sbjct: 460 ALVVVSSDLRELMLICDRIAVLSAGRLIDTFARDHWSQDQL 500 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: 306 Number of extensions: 21 Number of successful extensions: 3 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: 524 Length adjustment: 30 Effective length of query: 231 Effective length of database: 494 Effective search space: 114114 Effective search space used: 114114 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