Align Inositol transport system ATP-binding protein (characterized)
to candidate 206505 DVU1070 branched chain amino acid ABC transporter, ATP-binding protein (TIGR)
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__DvH:206505 Length = 524 Score = 145 bits (366), Expect = 2e-39 Identities = 82/242 (33%), Positives = 136/242 (56%), Gaps = 9/242 (3%) Query: 6 PLIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDIL 65 P++R++GI K FG V A +++D+ PG LLG+NGAGKST + +SG G I Sbjct: 33 PVVRLEGIGKSFGPVRANHDITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTGIIH 92 Query: 66 FEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYAN 125 +G+ + F P+DA+ AGI V+QH ++ M+V+ N +G + P+ + + Sbjct: 93 VDGEAVRFRSPKDALKAGIGMVYQHFMLVDSMTVAENVLLGQSG-AWLSPV------HMS 145 Query: 126 RITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTA 185 R+ E + G+++ P V LS GERQ V I + ++ ++VLILDEPT+ L +T Sbjct: 146 RVVAELAARYGLDI-DPAARVCDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGETE 204 Query: 186 NVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAE-ELQDMM 244 + + ++ + G A+VFI+H ++ LA+ D +L RG+ + ++ E EL + M Sbjct: 205 QLFEALHRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVDEFHESEVPGEAELANRM 264 Query: 245 AG 246 G Sbjct: 265 VG 266 Score = 72.0 bits (175), Expect = 2e-17 Identities = 54/228 (23%), Positives = 98/228 (42%), Gaps = 6/228 (2%) Query: 23 LAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILFEGQP---LHFADPRDA 79 L G+S +V GE + G G G+ ++ ++G+ +P +G++ G P PR Sbjct: 295 LKGLSFEVRKGEVFAIAGVAGNGQRELVECVTGLRRPAEGEVELLGIPWRQFFTKAPRQG 354 Query: 80 IAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANRITMEEMRKMGINL 139 A I Q LA + + NF + GP D A+ + + + + Sbjct: 355 GLAYIPEDRQGLATCLSLDLVDNFLLTARGCFTRGP--FLDRKSADAAARDILAEYNVQP 412 Query: 140 RGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTANVLATIDKVRKQGV 199 + +LSGG Q + + R + +++ + PT L + T V A + +VR Sbjct: 413 GRAEAPARSLSGGNLQKLVVGREFYRKPSLIVAENPTQGLDIAATEEVWARLLEVRSH-A 471 Query: 200 AVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDMMAGG 247 V+ ++ ++ LA+ DR V+ RG +G R D + + +M G Sbjct: 472 GVLLVSGDLNEVLALADRVAVMYRGCFIGLLDRSDTNKVDAIGLMMAG 519 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: 329 Number of extensions: 18 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: 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 Apr 09 2024. 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