Align ABC transporter (characterized, see rationale)
to candidate GFF857 Psest_0871 ABC-type sugar transport systems, ATPase components
Query= uniprot:A0A166QFW2 (381 letters) >lcl|FitnessBrowser__psRCH2:GFF857 Psest_0871 ABC-type sugar transport systems, ATPase components Length = 371 Score = 379 bits (972), Expect = e-109 Identities = 211/364 (57%), Positives = 251/364 (68%), Gaps = 5/364 (1%) Query: 1 MIKLKLDNVNKQLGGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDL 60 M + L ++ K G I R + L+I GEFVVFVGPSGCGKSTLLRLIAGL+ I GDL Sbjct: 1 MASVTLRDICKSYDGTPITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGDL 60 Query: 61 LIDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQI 120 LID +RVNDL P++R VGMVFQSYALYPHM+V +N++FGLKLA DK ++ RV A+I Sbjct: 61 LIDNQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVAEI 120 Query: 121 LQLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLH 180 LQLDKLL+RKPK+LSGGQRQRVA+GR M REP + LFDEPLSNLDA LRVQMR EIARLH Sbjct: 121 LQLDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIARLH 180 Query: 181 DRLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMN 240 R+ STMIYVTHDQVEAMTLADKIVVLN G + QVG P LY P +RFVAGFLGSP+MN Sbjct: 181 QRIRSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQMN 240 Query: 241 FLSAR-LQTPGETSLVDTLVWGITSLPFDSSNLAAGTPLSLGIRPEH-VSLKAADGTAGV 298 F+ R + ET ++ +LP D S ++ G PL+LGIRPEH V AD T Sbjct: 241 FVEVRAISASPETVTIELPSGYPLTLPVDGSAVSPGDPLTLGIRPEHFVMPDEADFTFHG 300 Query: 299 VVTAVEYLGSET--YVHLETGQDEPLICRCEVSAGWQAGDRVELLLDLDNLHLFDADGVA 356 +T E LG Y+ LE QD +C + + G+ L D HLF +G A Sbjct: 301 QITVAERLGQYNLLYLTLERLQDVITLC-VDGNLRVTEGETFAAGLKADKCHLFRENGEA 359 Query: 357 LSRH 360 +RH Sbjct: 360 CTRH 363 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: 388 Number of extensions: 13 Number of successful extensions: 2 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: 371 Length adjustment: 30 Effective length of query: 351 Effective length of database: 341 Effective search space: 119691 Effective search space used: 119691 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: 50 (23.9 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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