Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 6936480 Sama_0668 iron(III) ABC transporter, ATP-binding protein (RefSeq)
Query= uniprot:A0A165KQ08 (355 letters) >FitnessBrowser__SB2B:6936480 Length = 341 Score = 191 bits (484), Expect = 3e-53 Identities = 113/299 (37%), Positives = 175/299 (58%), Gaps = 13/299 (4%) Query: 3 SSLDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTE 62 S+L I G++ + + +VLR +++ + GE L+GPSGCGK+TLL IAGL + + Sbjct: 2 STLSIQGLHSDY----RGEQVLRGLNLTLTQGEITALLGPSGCGKTTLLRTIAGLQDISA 57 Query: 63 GEIRIGGKNVVG----MPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKR 118 G I I GK V + P R I M+FQ YAL+P L+VADNI F + R++ K R R Sbjct: 58 GSIAINGKTVSADGCFVAPEKRSIGMIFQDYALFPHLTVADNILFGV--RQLDKQSRSVR 115 Query: 119 IDEVAAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMR 178 ++E+ +++++ L R P +LSGGQ+QRV++ RALA +P L L DEP SN+DA++R + Sbjct: 116 LEEMLSLVKLEGLGKRYPHELSGGQQQRVSIARALAYEPDLLLLDEPFSNIDAQVRRALM 175 Query: 179 AEIKRLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATF 238 EI+ + +A +++V+VTH + EA +A+ + G + Q G P+ +Y P YVA F Sbjct: 176 LEIRAILKARNVSAVFVTHSKDEAFAFADTLALFEAGRIVQHGIPETLYQSPNTPYVADF 235 Query: 239 IGSPTMNLLRGAVTGGQFGIQGAALNLAPPPSSANEV-LLGVRPEHLVMQETAPWRGRV 296 +G+ N L + GQ A L +A+E +RPE L+++ A G + Sbjct: 236 LGA--SNYLDVRLEAGQLISTLGAFPLPQDFKAASETGRWLLRPEQLLIEARADGAGEI 292 Lambda K H 0.318 0.135 0.388 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: 263 Number of extensions: 9 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 355 Length of database: 341 Length adjustment: 29 Effective length of query: 326 Effective length of database: 312 Effective search space: 101712 Effective search space used: 101712 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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