Align Inositol transport system ATP-binding protein (characterized)
to candidate Ac3H11_609 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_609 Length = 505 Score = 153 bits (386), Expect = 8e-42 Identities = 90/244 (36%), Positives = 137/244 (56%), Gaps = 9/244 (3%) Query: 7 LIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGV--HKPTKGDI 64 L+ M+ I K F V+AL V++ V GE H ++G+NGAGKST +K +SGV H G I Sbjct: 2 LLEMRNIRKTFPGVVALNQVNLQVQAGEIHAIVGENGAGKSTLMKVLSGVYPHGSYSGQI 61 Query: 65 LFEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYA 124 LF+GQ FA RD+ GI +HQ LA++PL+S++ N F+GNE R + D A Sbjct: 62 LFDGQEREFAGIRDSEHLGIIIIHQELALVPLLSIAENIFLGNETARH----GVIDWMAA 117 Query: 125 NRITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQT 184 + + K+G+ PD VG L G++Q V IA+A+ ++LILDEPT++L + Sbjct: 118 HSRAQALLHKVGLG-ESPDTPVGQLGVGKQQLVEIAKALSRKVRLLILDEPTASLNENDS 176 Query: 185 ANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLG--TAQRGDISAEELQD 242 +L + +++ QG+ + I+H + V D TVL G T+ + G +S + + Sbjct: 177 QALLDLLLELKAQGITCILISHKLNEISRVADAITVLRDGSTVQMLDCREGPVSEDRVIQ 236 Query: 243 MMAG 246 M G Sbjct: 237 AMVG 240 Score = 79.3 bits (194), Expect = 1e-19 Identities = 55/223 (24%), Positives = 103/223 (46%), Gaps = 7/223 (3%) Query: 23 LAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVH--KPTKGDILFEGQPLHFADPRDAI 80 L G+ ++V GE + G GAG++ ++ G + G++ GQP+ + A+ Sbjct: 277 LKGIDLNVRRGEIVGIAGLMGAGRTELAMSIFGRSWGQRISGEVRLHGQPIDVSTVEKAV 336 Query: 81 AAGIATVHQHL---AMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANRITMEEMRKMGI 137 + G+A V + ++ + N + N P + + D +R+ + K+ I Sbjct: 337 SHGLAYVTEDRKGNGLVLNEDIQFNTSLANLP--GVSFASVIDSGQEHRVAQDYREKLRI 394 Query: 138 NLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTANVLATIDKVRKQ 197 G DQ LSGG +Q V +++ + +VLILDEPT + V + I ++ + Sbjct: 395 RCSGVDQKTLNLSGGNQQKVVLSKWLFTSPEVLILDEPTRGIDVGAKYEIYTLIAQLAAE 454 Query: 198 GVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEEL 240 G V+ I+ + L + DR V+N G+ + + S E++ Sbjct: 455 GKCVIVISSEMPELLGITDRIYVMNEGRFVAEMPTSEASQEKI 497 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: 16 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: 505 Length adjustment: 29 Effective length of query: 232 Effective length of database: 476 Effective search space: 110432 Effective search space used: 110432 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