Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate GFF4127 HP15_4067 spermidine/putrescine ABC transporter ATPase subunit
Query= uniprot:A0A165KQ08 (355 letters) >FitnessBrowser__Marino:GFF4127 Length = 362 Score = 222 bits (566), Expect = 1e-62 Identities = 137/367 (37%), Positives = 197/367 (53%), Gaps = 24/367 (6%) Query: 1 MASSLDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEP 60 M S L G+ +RFG S + V + V G F ++GPSGCGK+TLL ++AG D+P Sbjct: 1 MDSDLFCEGLVRRFG----SNAAVDHVSLDVPAGTFFSILGPSGCGKTTLLRLLAGFDKP 56 Query: 61 TEGEIRIGGKNVVGMPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRID 120 +G+I I G+ + +PP R + MVFQ AL+PT++V DNI + L+ RKMP ER+KRI Sbjct: 57 DQGDIHIRGERMNDVPPNRRPVNMVFQHLALFPTMTVGDNIAYGLKRRKMPLVERRKRIA 116 Query: 121 EVAAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAE 180 V + + L R P +LSGGQRQRVA+ R L +P L L DEPL LD KLR +M+ E Sbjct: 117 RVLEQVGLPDLEHRNPQELSGGQRQRVALARCLVLEPTLLLLDEPLGALDLKLREQMKVE 176 Query: 181 IKRLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIG 240 +K L + G T VY+THDQ EAM + ++AVM+ G Q+ P+E+Y PA +VA F+G Sbjct: 177 LKHLQKQFGTTFVYITHDQSEAMVMSDQVAVMRDGRFDQVAPPEELYREPATPFVAGFVG 236 Query: 241 SPTMNLLRGAVTGGQFGIQGAALN---------LAPPPSSANEVLLGVRPEHLVMQETA- 290 N L G + + + L+ + + + L +RPE LV+ A Sbjct: 237 D--NNRLSGELVSVRDSLAELRLDDGVLVQGRVASDNLQAGHRAELYIRPESLVLSGDAL 294 Query: 291 -----PWRGRVSVVEPTGPDTYVMVDTAAGSVTLR---TDAQTRVQPGEHVGLALAPAHA 342 + +V G ++ V +T V R + R+ + LA P+ A Sbjct: 295 SPGFSSMQAKVRTTLFDGANSRVEAETCGQPVYARLPQDGSAPRLSVDSSIRLAWNPSLA 354 Query: 343 HWFDAQS 349 F A+S Sbjct: 355 RVFGAES 361 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: 343 Number of extensions: 16 Number of successful extensions: 1 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: 362 Length adjustment: 29 Effective length of query: 326 Effective length of database: 333 Effective search space: 108558 Effective search space used: 108558 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