Align Inositol transport system ATP-binding protein (characterized)
to candidate GFF1357 Psest_1392 ABC-type uncharacterized transport systems, ATPase components
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__psRCH2:GFF1357 Length = 518 Score = 125 bits (314), Expect = 2e-33 Identities = 79/242 (32%), Positives = 126/242 (52%), Gaps = 8/242 (3%) Query: 8 IRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILFE 67 +++ GI K + +A + + + PGE H LLG+NGAGKST +K + GV +P G+I ++ Sbjct: 9 LQLCGITKQYPGCLANDRIDLSIQPGEIHALLGENGAGKSTLMKIIYGVTQPDAGEIHWQ 68 Query: 68 GQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANRI 127 G+ + DP A GI V QH ++ +SV+ N + K G K + Sbjct: 69 GERVTMRDPAQARERGIGMVFQHFSLFETLSVAENIALALG--AKAGTPKQLEPK----- 121 Query: 128 TMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTANV 187 E ++ G+ L P + V +LS GERQ V I R + ++LILDEPTS L ++ + Sbjct: 122 IREVSQRYGMPLE-PQRLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADEL 180 Query: 188 LATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDMMAGG 247 T+ ++ +G +++FI+H + A+ TVL G+ G + S EL +M G Sbjct: 181 FVTLRRLAAEGCSILFISHKLNEVRALCQSATVLRAGRVSGECIPAECSDLELARLMVGD 240 Query: 248 QE 249 E Sbjct: 241 AE 242 Score = 47.4 bits (111), Expect = 6e-10 Identities = 52/251 (20%), Positives = 95/251 (37%), Gaps = 12/251 (4%) Query: 6 PLIRMQGIEKH----FGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTK 61 P +R++ + H FG ++L V ++V GE + G G G+ + +SG + Sbjct: 256 PFLRVERLSWHNADPFG--VSLKEVDLEVRAGEIVGIAGVAGNGQDELLALLSGEQRLQA 313 Query: 62 GD---ILFEGQPLHFADPRDAIAAGIATVHQHL---AMIPLMSVSRNFFMGNEPIRKIGP 115 I F G + P G+A V +P MS++ N + + Sbjct: 314 AQAMRIRFLGDDVAHLRPGARRRHGMAFVPAERLGHGAVPSMSLADNGLLTAYQQTGMVE 373 Query: 116 LKLFDHDYANRITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEP 175 L + +++ + +LSGG Q + R + K+LI P Sbjct: 374 QGLIRRGRVRAFAEQVIQRFAVKTPDAQTPAASLSGGNLQKFILGREILQQPKLLIAAHP 433 Query: 176 TSALGVRQTANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDI 235 T + V A + + ++R G A++ I+ ++ + DR L+ G+ Sbjct: 434 TWGVDVGAAAAIHRALIELRDAGAAILVISEDLEELFQISDRIAALSDGRLSPQRATAST 493 Query: 236 SAEELQDMMAG 246 E+ MAG Sbjct: 494 CPVEVGRWMAG 504 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: 278 Number of extensions: 12 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: 518 Length adjustment: 30 Effective length of query: 231 Effective length of database: 488 Effective search space: 112728 Effective search space used: 112728 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