Align ABC transporter (characterized, see rationale)
to candidate H281DRAFT_05701 H281DRAFT_05701 glycerol 3-phosphate ABC transporter ATP-binding protein
Query= uniprot:A0A166QFW2 (381 letters) >FitnessBrowser__Burk376:H281DRAFT_05701 Length = 362 Score = 332 bits (850), Expect = 1e-95 Identities = 180/358 (50%), Positives = 240/358 (67%), Gaps = 11/358 (3%) Query: 1 MIKLKLDNVNKQLGGMR-ILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGD 59 M L L V K G + +L + +++ GEFVV VGPSGCGKSTLLR++AGL+ I G Sbjct: 1 MAALTLQGVKKTYDGKQFVLHGIDVDVNDGEFVVMVGPSGCGKSTLLRMVAGLERISEGT 60 Query: 60 LLIDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQ 119 + I G+ VN+LEP++R + MVFQ+YALYPHMSV +N+ + LK+A D+ + +RV AQ Sbjct: 61 ISIAGKVVNELEPKDRNIAMVFQNYALYPHMSVAENMGYALKIAGVDRAQIAQRVNAAAQ 120 Query: 120 ILQLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARL 179 IL+L+ LLQRKP+ELSGGQRQRVAMGRA+ REP + LFDEPLSNLDA LRVQMR EI RL Sbjct: 121 ILELEPLLQRKPRELSGGQRQRVAMGRAIVREPAVFLFDEPLSNLDARLRVQMRLEIQRL 180 Query: 180 HDRLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRM 239 H RL +T +YVTHDQ+EAMTLA +++V+N G EQ+G+P E+YERPA+ FVAGF+GSP M Sbjct: 181 HARLATTSLYVTHDQIEAMTLAQRVIVMNKGHAEQIGAPTEVYERPATVFVAGFIGSPGM 240 Query: 240 NFLSARLQTPGETSLV-----DTLVWGITSLPFDSSNLAAGTPLSLGIRPEHVSLKAADG 294 N L R+ G T V + G+ S+ +A G +LGIRPEH+S AD Sbjct: 241 NLLEGRVSDDGSTFDVAGNGPQLPLAGVASI---GREVAKGREWTLGIRPEHMSPGQADA 297 Query: 295 T-AGVVVTAVEYLGSETYVHLETGQDEPLICRCEVSAGWQAGDRVELLLDLDNLHLFD 351 + V + E LG++ H G+ + + R + AG+ +++ L +LH FD Sbjct: 298 PHTTLTVDSCELLGADNLAHGRWGKHD-VTARLPHAHRPAAGEALQVALPARHLHFFD 354 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: 393 Number of extensions: 19 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: 362 Length adjustment: 30 Effective length of query: 351 Effective length of database: 332 Effective search space: 116532 Effective search space used: 116532 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