Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate Ac3H11_2066 SN-glycerol-3-phosphate transport ATP-binding protein UgpC (TC 3.A.1.1.3)
Query= reanno::psRCH2:GFF857 (371 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2066 Length = 355 Score = 283 bits (723), Expect = 7e-81 Identities = 152/341 (44%), Positives = 213/341 (62%), Gaps = 13/341 (3%) Query: 18 ITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGDLLIDNQRVNDLPPKDRSV 77 + R +D+ + GEF++ VGPSGCGKSTLL +IAGL++ T G++ I + V +PP+DR + Sbjct: 23 VLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEGEIRIGGKNVVGMPPRDRDI 82 Query: 78 GMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVAEILQLDKLLERKPKDLSGG 137 MVFQSYALYP ++VA+N+ F L++ + K E ++R++ VA +LQ+ LL+R+P LSGG Sbjct: 83 AMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRIDEVAAMLQISHLLDRRPSQLSGG 142 Query: 138 QRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIARLHQRIRSTMIYVTHDQVEA 197 QRQRVA+GR + R+P++FLFDEPLSNLDA LRV+MR EI RLHQ T +YVTHDQVEA Sbjct: 143 QRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAEIKRLHQASGITSVYVTHDQVEA 202 Query: 198 MTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQMNFVEVRAISASPETVTIE 257 MTL +I V+ G + Q+G P +Y+ P N +VA F+GSP MN + A++ + Sbjct: 203 MTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIGSPTMNLLR-GAVTGGQFGI--- 258 Query: 258 LPSGYPLTLPVDGSAVSPGDPLTLGIRPEHFVMPDEADFTFHGQITVAERLGQYNLLYLT 317 G L L S + + LG+RPEH VM + A + G+++V E G Y+ Sbjct: 259 --QGAALNL---APPPSSANEVLLGVRPEHLVMQETA--PWRGRVSVVEPTGPDT--YVM 309 Query: 318 LERLQDVITLCVDGNLRVTEGETFAAGLKADKCHLFRENGE 358 ++ +TL D RV GE L H F E Sbjct: 310 VDTAAGSVTLRTDAQTRVQPGEHVGLALAPAHAHWFDAQSE 350 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: 335 Number of extensions: 18 Number of successful extensions: 3 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: 355 Length adjustment: 29 Effective length of query: 342 Effective length of database: 326 Effective search space: 111492 Effective search space used: 111492 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