Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate GFF3855 PGA1_78p00190 sn-glycerol-3-phosphate import ATP-binding protein UgbC
Query= reanno::psRCH2:GFF857 (371 letters) >FitnessBrowser__Phaeo:GFF3855 Length = 361 Score = 306 bits (784), Expect = 6e-88 Identities = 174/362 (48%), Positives = 227/362 (62%), Gaps = 14/362 (3%) Query: 3 SVTLRDICKSYDGTPITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGDLLI 62 SV +RD+ + + ++LDIE GEF+V +G SGCGKSTLL IAGL DI+ G + I Sbjct: 7 SVEIRDLDLHFGELQVLHQLNLDIEQGEFLVLLGSSGCGKSTLLNCIAGLLDISDGQIFI 66 Query: 63 DNQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVAEILQ 122 Q V P +R +GMVFQSYALYP MTV N++FGLK A + K EI +RV AE+LQ Sbjct: 67 QGQNVTWAEPSERGIGMVFQSYALYPQMTVEGNLSFGLKNARLPKAEIAKRVARAAEVLQ 126 Query: 123 LDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIARLHQR 182 ++ LL+RKP LSGGQRQRVAIGR +VR+ VFLFDEPLSNLDA LR +R+E+ RLHQ+ Sbjct: 127 IEPLLKRKPAALSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRADLRVELKRLHQQ 186 Query: 183 IRSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQMNFV 242 + +TMIYVTHDQVEAMTLAD+I ++ G I Q+ P +Y+ P+N +VAGF+GSP MN + Sbjct: 187 LANTMIYVTHDQVEAMTLADRIAIMKGGRIMQLSSPDEIYNRPQNLYVAGFIGSPAMNLI 246 Query: 243 EVRAISASPETVTIELP-SGYPL-TLPVDGSAVSPGDPLTLGIRPEHFVMPDE---ADFT 297 E I ++ LP Y P G+AV +GIRPEH + ++ AD T Sbjct: 247 EGVLIDGVFHAGSLALPMQRYDYRNGPHHGAAV-------IGIRPEHILTGEQITRADAT 299 Query: 298 FHGQITVAERLGQYNLLYLTLERLQDVITLCVDGNLRVTEGETFAAGLKADKCHLFRENG 357 + + E LG L+Y T + L +DG RV+ G+ G + LF N Sbjct: 300 AEVLVDLVEGLGSDTLVYAT--HGAQNLRLRMDGASRVSAGDRLRIGFDTGRASLFDPNT 357 Query: 358 EA 359 EA Sbjct: 358 EA 359 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: 388 Number of extensions: 15 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: 361 Length adjustment: 30 Effective length of query: 341 Effective length of database: 331 Effective search space: 112871 Effective search space used: 112871 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 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