Align ABC transporter (characterized, see rationale)
to candidate GFF1645 PGA1_c16680 sugar ABC transporter, ATP-binding protein
Query= uniprot:A0A166QFW2 (381 letters) >FitnessBrowser__Phaeo:GFF1645 Length = 355 Score = 347 bits (891), Expect = e-100 Identities = 188/358 (52%), Positives = 246/358 (68%), Gaps = 8/358 (2%) Query: 1 MIKLKLDNVNKQLGGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDL 60 M +++L +V K+ G + +LRD++L+I GEF+V VGPSGCGKSTLLR+IAGL+ I GD Sbjct: 1 MARIELRDVAKRYGAVEVLRDINLDIQDGEFIVLVGPSGCGKSTLLRMIAGLEPITSGDF 60 Query: 61 LIDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQI 120 IDG+R+ND+ PR+R + MVFQSYALYPHM V N+ F +++ K R RV + A+ Sbjct: 61 EIDGQRMNDVRPRDRDIAMVFQSYALYPHMDVARNMGFSMEIRKDPAEERRSRVARAAET 120 Query: 121 LQLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLH 180 L L L+ R PK LSGGQRQRVAMGRA+ R+P LFDEPLSNLDA+LRV+MR EIARLH Sbjct: 121 LGLSSLVDRLPKALSGGQRQRVAMGRAIIRDPRAFLFDEPLSNLDAALRVEMRLEIARLH 180 Query: 181 DRLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMN 240 +LG+TMIYVTHDQVEA+TLAD+IVVLNGG ++QVGSP ELYERPA++FVA F+GSP MN Sbjct: 181 KQLGATMIYVTHDQVEALTLADRIVVLNGGDIQQVGSPLELYERPANKFVAQFIGSPTMN 240 Query: 241 FLSARLQTPGETSLVDTLVWGITSLPFDSSNLAAGTPLSLGIRPEHVS-LKAADGTAGVV 299 L G S V + +L AA + LGIRPEH+ ++ +G V Sbjct: 241 I----LPVSGAASGVMATNGMMLTLDHMHDTAAA---VELGIRPEHLDVVEPGEGHLIAV 293 Query: 300 VTAVEYLGSETYVHLETGQDEPLICRCEVSAGWQAGDRVELLLDLDNLHLFDADGVAL 357 VE LGS+T ++ + PL+ R + ++G+R+ L + N H+FD G+AL Sbjct: 294 ADVVERLGSDTNIYAKVDGLGPLMVRKHGNVPVRSGERLGLRVQAQNAHIFDDRGIAL 351 Lambda K H 0.320 0.137 0.394 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: 381 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: 381 Length of database: 355 Length adjustment: 30 Effective length of query: 351 Effective length of database: 325 Effective search space: 114075 Effective search space used: 114075 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 (21.8 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