Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate RR42_RS27800 RR42_RS27800 ABC transporter ATP-binding protein
Query= reanno::psRCH2:GFF857 (371 letters) >FitnessBrowser__Cup4G11:RR42_RS27800 Length = 357 Score = 230 bits (587), Expect = 4e-65 Identities = 138/319 (43%), Positives = 190/319 (59%), Gaps = 18/319 (5%) Query: 3 SVTLRDICKSY-DGTPITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGDLL 61 ++TLR K++ DGT + +DLDI GE VV +GPSGCGK+T LR+IAGLE +G ++ Sbjct: 6 TITLRHCGKTFADGTLALQPLDLDIGAGETVVLLGPSGCGKTTTLRIIAGLEFPDAGGVV 65 Query: 62 I--DNQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVAE 119 + DN V LP + R VGMVFQSYAL+P+MTVAEN+A+GL++ +D +RRV+ + Sbjct: 66 MFGDND-VTPLPIEQRGVGMVFQSYALFPNMTVAENIAYGLRVRRIDAAARRRRVDEMLA 124 Query: 120 ILQLDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIARL 179 ++ L ER+ LSGGQRQRVA+ R + +P+V L DEPL+ LDA LR +R +I +L Sbjct: 125 MMHLGPFAERRIDQLSGGQRQRVALARAIAVQPRVLLLDEPLTALDAKLRDALRADINQL 184 Query: 180 HQRIRSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQM 239 + + T +YVTHDQ EAM L D+I+V++ G IAQ G P +Y P N FVA F+G+ Sbjct: 185 LRSLHITAVYVTHDQAEAMALGDRIIVMDRGRIAQTGTPQQIYRAPANAFVADFIGT--- 241 Query: 240 NFVEVRAISASPETVTIELPSGYPLTLPVDGSAVS----PGDPLTLGIRPEHFVMPDEAD 295 + + A E +P G +P G+A S P L RPE + D Sbjct: 242 ----MNRLPAVLEADAWRVPGG---LVPRHGTAASLAAAPSPRAELLFRPEDVALAQAED 294 Query: 296 FTFHGQITVAERLGQYNLL 314 G + A LG Y L Sbjct: 295 AHLGGSVVTALFLGNYTRL 313 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: 348 Number of extensions: 15 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: 357 Length adjustment: 29 Effective length of query: 342 Effective length of database: 328 Effective search space: 112176 Effective search space used: 112176 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