Align Inositol transport system ATP-binding protein (characterized)
to candidate PfGW456L13_2121 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2121 Length = 514 Score = 137 bits (346), Expect = 3e-37 Identities = 76/240 (31%), Positives = 129/240 (53%), Gaps = 6/240 (2%) Query: 8 IRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILFE 67 +R GI K F V AL +S PG+ H L+G+NGAGKST +K + G + P G + Sbjct: 16 LRFNGIGKTFPGVKALDNISFVAHPGQVHALMGENGAGKSTLLKILGGAYTPCSGALQIG 75 Query: 68 GQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANRI 127 + + F D+I +G+A +HQ L ++P M+V+ N F+G+ P L + + Sbjct: 76 ERTMDFKSTADSIGSGVAVIHQELHLVPEMTVAENLFLGHLP----ASFGLINRSTLRQQ 131 Query: 128 TMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTANV 187 + ++ + + P + VG LS G+RQ V IA+A+ GA V+ DEPTS+L R+ + Sbjct: 132 ALACLKGLADEI-DPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRL 190 Query: 188 LATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGT-AQRGDISAEELQDMMAG 246 +A I ++R +G V++++H + + + TV G+ + T ++ ++L M G Sbjct: 191 MAIIGRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFDDMSQLTHDQLVTCMVG 250 Score = 92.0 bits (227), Expect = 2e-23 Identities = 64/223 (28%), Positives = 109/223 (48%), Gaps = 15/223 (6%) Query: 26 VSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILFEGQPLHFADPRDAIAAGIA 85 VS +V GE L G GAG++ ++ +SG+ + + G + G L PRDAIAAGI Sbjct: 283 VSFEVHKGEILGLFGLVGAGRTELLRLLSGLARHSAGQLKLRGHELKLRSPRDAIAAGIL 342 Query: 86 TVHQHL---AMIPLMSVSRNFFMGNEPIRK-IGPLK--LFDHDYANRITMEEMRKMGINL 139 + ++PL SV+ N + G L L++ D A ++++ + + Sbjct: 343 LCPEDRKKEGILPLASVAENINISARGAHSTFGCLLRGLWEKDNAE----QQIKALKVKT 398 Query: 140 RGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTANVLATIDKVRKQGV 199 Q + LSGG +Q + R + KVL+LDEPT + + A + I + +G+ Sbjct: 399 PNAAQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNLAAEGI 458 Query: 200 AVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQD 242 AV+ ++ ++ + + DR VL G A RG++S E+ + Sbjct: 459 AVIVVSSDLMEVMGISDRILVLCEG-----ALRGELSREQANE 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: 339 Number of extensions: 18 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: 514 Length adjustment: 29 Effective length of query: 232 Effective length of database: 485 Effective search space: 112520 Effective search space used: 112520 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