Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate WP_086508166.1 BZY95_RS01120 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= reanno::psRCH2:GFF857 (371 letters) >NCBI__GCF_002151265.1:WP_086508166.1 Length = 371 Score = 437 bits (1123), Expect = e-127 Identities = 216/369 (58%), Positives = 274/369 (74%) Query: 1 MASVTLRDICKSYDGTPITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGDL 60 M +TL I K Y G ++R IDL IEDGEFVVFVGPSGCGKSTLLR+IAGLEDI+ G++ Sbjct: 1 MGRLTLAGIGKDYAGVEVSRDIDLTIEDGEFVVFVGPSGCGKSTLLRMIAGLEDISHGEM 60 Query: 61 LIDNQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVAEI 120 +D +R+N++PP++R +GMVFQSYALYPHMTVAENMAFGLKLA DK EI+RRVE AE+ Sbjct: 61 RLDGERINEVPPQERDIGMVFQSYALYPHMTVAENMAFGLKLARTDKAEIRRRVEHAAEM 120 Query: 121 LQLDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIARLH 180 L L +LLERKPK+LSGGQRQRVAIGRT+V+EP VFLFDEPLSNLDA LRV MR++IA LH Sbjct: 121 LHLGELLERKPKELSGGQRQRVAIGRTLVKEPAVFLFDEPLSNLDAALRVDMRVQIAELH 180 Query: 181 QRIRSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQMN 240 +R+ +TMIYVTHDQVEAMTLAD+IV+L G IAQVG PL LYH+P VA F+GSP++N Sbjct: 181 RRLGATMIYVTHDQVEAMTLADRIVLLAGGRIAQVGAPLSLYHFPATLEVARFIGSPRIN 240 Query: 241 FVEVRAISASPETVTIELPSGYPLTLPVDGSAVSPGDPLTLGIRPEHFVMPDEADFTFHG 300 + V + + ++ LP G L + VDG+ + GD TL +R E FV P +AD Sbjct: 241 VIPVEVLDPGRQRTSVRLPDGATLAVAVDGARLRAGDKATLAVRAEDFVTPADADARLTA 300 Query: 301 QITVAERLGQYNLLYLTLERLQDVITLCVDGNLRVTEGETFAAGLKADKCHLFRENGEAC 360 ++ VAERLG L +L +E + + +T +DG R+ +G+ GL ++CHLF +G+AC Sbjct: 301 RLMVAERLGYETLAHLRVEGVSETLTQRLDGLTRLEDGQAVELGLSGERCHLFAADGKAC 360 Query: 361 TRHYREPAI 369 R R P + Sbjct: 361 PRQVRIPGV 369 Lambda K H 0.322 0.139 0.405 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: 495 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: 371 Length of database: 371 Length adjustment: 30 Effective length of query: 341 Effective length of database: 341 Effective search space: 116281 Effective search space used: 116281 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 (21.9 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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