Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate 6939439 Sama_3531 molybdenum ABC transporter, ATP-binding protein (RefSeq)
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__SB2B:6939439 Length = 370 Score = 145 bits (367), Expect = 1e-39 Identities = 111/348 (31%), Positives = 177/348 (50%), Gaps = 28/348 (8%) Query: 30 GEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGTVVND------LPARERNVAMVFQ 83 GEF+ ++GPSG GK+T+LRMIAGL G++R G + D + R++ V Q Sbjct: 28 GEFLAVVGPSGGGKTTLLRMIAGLAKPENGSIRCGKRIWFDSDEGIHCSPQNRHIGFVPQ 87 Query: 84 NYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAAL--LNLEALLERKPRAMSGGQQQ 141 ++ L+P +S NI L L P+ E RR R +AAL +NL L +R P +SGGQ+Q Sbjct: 88 HFGLFPKLSALGNIMAALDHL--PSQE--RRPRALAALEKVNLHGLTDRLPSQLSGGQKQ 143 Query: 142 RAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRTTTVYVTHDQLEAMTL 201 R A+ARA+ + P V L DEP S +D + R +L ++ RL L + VTHD EA+ L Sbjct: 144 RVALARALAREPRVLLLDEPFSAVDRETRERLYLELARLKAELNIPVIMVTHDLNEALLL 203 Query: 202 ADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAMNFLSGTVQRQD---GQLFIET 258 AD ++L+ G ++Q G+P +++ PRN A +G N + V QD G +++ Sbjct: 204 ADSMLLISQGHMLQHGTPQDVFSRPRNEAVARQMG--LRNIFNAHVVAQDCAKGVTWLKF 261 Query: 259 AHQRWALTGERFSRLRHAMAVKLAVRPDHVR---IAGEREPAASLTCPVSVELVEILGAD 315 + + + R+ V+ + +R IA R + P+ ++ + LG Sbjct: 262 GDR--LIASDSLPRVNIGDKVRWVIPNQGIRFNSIASGRLCRSFNILPIHIDNMLTLGES 319 Query: 316 ALLTTRCGD--QTLTALVP---ADRLP-QPGATLTLALDQHELHVFDV 357 L D + L +P A +L GA +AL ++H+ ++ Sbjct: 320 VRLEASVQDSGERLNVEIPLHLAHKLALTQGAATEVALKSDQVHILEM 367 Lambda K H 0.321 0.137 0.403 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: 320 Number of extensions: 10 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: 406 Length of database: 370 Length adjustment: 30 Effective length of query: 376 Effective length of database: 340 Effective search space: 127840 Effective search space used: 127840 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:
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