Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate PfGW456L13_1569 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= reanno::Smeli:SM_b21216 (360 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1569 Length = 372 Score = 233 bits (593), Expect = 8e-66 Identities = 141/364 (38%), Positives = 206/364 (56%), Gaps = 18/364 (4%) Query: 3 ALEIRNIRKRYGEVET----LKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGG 58 A+ IR++RK YG+ +T LK ID+ + EF LLG SGCGK+TLL +IAG P+ G Sbjct: 11 AVSIRSVRKVYGDPKTGPVALKSIDLDIRDNEFFTLLGPSGCGKTTLLRMIAGFEFPTEG 70 Query: 59 DILIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHD----KAV 114 +IL+ ++ P R + VFQ YAL+P++++A N+ FGLE + + H + V Sbjct: 71 EILLYGENIADRPPFQRPVNTVFQHYALFPHMTIAENLAFGLESHPMGKVLHKTQLAERV 130 Query: 115 RDTARLLQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRT 174 R+ L+Q+E +RKP+QLSGGQ+QRVA+ RAL +P+V L DEPLS LD KLR MR Sbjct: 131 REMLALVQMERFANRKPAQLSGGQQQRVALARALAPHPKVLLLDEPLSALDLKLRQAMRE 190 Query: 175 ELKRLHQMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFV 234 ELK + T ++VTHDQ EA+T++ RIAV+ +G ++Q+ P+++Y+RP +VA F+ Sbjct: 191 ELKTIQARTGITFIFVTHDQEEALTMSDRIAVLSEGEVQQVGRPEDIYERPRNRFVADFI 250 Query: 235 GSPPMNILDAEMT--ANGLKIEGCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLAAGSE 292 G N ++ +T +GL PLPA G V + +RPE L L + Sbjct: 251 GE--TNFIEGTVTRVEDGLAWFAGPAGHPLPAQPCSDVRVGANVTLSVRPERLHLVPATT 308 Query: 293 AQRLTASVEVVELTGPELVTTATV--GSQ---RITACLPPRTAVGMGSAHAFTFD-GTAL 346 L +E G +L ++ GS+ R C+ +GS FD G+A Sbjct: 309 ENALPCRIEAQIYLGTDLQYQVSLSDGSRLTVRTPNCVDQSKRFAVGSQAGLLFDQGSAS 368 Query: 347 HLFD 350 L D Sbjct: 369 VLHD 372 Lambda K H 0.320 0.136 0.385 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: 327 Number of extensions: 19 Number of successful extensions: 4 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: 360 Length of database: 372 Length adjustment: 30 Effective length of query: 330 Effective length of database: 342 Effective search space: 112860 Effective search space used: 112860 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: 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