Align ABC transporter for D-Glucosamine, putative ATPase component (characterized)
to candidate Ac3H11_2553 Cell division transporter, ATP-binding protein FtsE (TC 3.A.5.1.1)
Query= reanno::pseudo6_N2E2:Pf6N2E2_2050 (263 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2553 Length = 265 Score = 227 bits (579), Expect = 2e-64 Identities = 126/249 (50%), Positives = 162/249 (65%), Gaps = 5/249 (2%) Query: 11 QPLLDIRGLRKQYGPLEVLKGVDLSMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQI 70 +P++ IRGLRK +G VL G+D + VV +IG SGSGK+T LRC N LE+ +GG + Sbjct: 16 EPIVRIRGLRKAFGSHVVLNGIDFDVLPSQVVVVIGPSGSGKSTFLRCCNGLEQPEGGSV 75 Query: 71 MLDGESIGYDDIDGKRVRHPEKVIARHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKL 130 + G ++ D G+ + P+ + R GM FQ FNLFPHL+ L NVTLG K++ L Sbjct: 76 EICGRTLVQD---GRML--PDHDLNALREEVGMVFQSFNLFPHLSVLDNVTLGPRKLRGL 130 Query: 131 PKDEAVALAEKWLERVGLLERRDHFPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALD 190 + EA A+ L +VGL + P LSGGQ+QRVAIARA+AM P +MLFDE TSALD Sbjct: 131 SRKEAEERAQALLTKVGLAHKAPAMPASLSGGQKQRVAIARALAMEPRVMLFDEPTSALD 190 Query: 191 PELVGEVLNVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFERPQ 250 PELVGEVL V+K LA +GMTM++VTHEM FA EV D +V M+ G I E G P +F P Sbjct: 191 PELVGEVLQVMKLLASEGMTMMVVTHEMDFAREVGDVVVVMDGGGIIEAGAPATIFTNPT 250 Query: 251 SPRLAEFLK 259 R FL+ Sbjct: 251 QERTRSFLQ 259 Lambda K H 0.320 0.138 0.392 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: 177 Number of extensions: 8 Number of successful extensions: 2 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: 263 Length of database: 265 Length adjustment: 25 Effective length of query: 238 Effective length of database: 240 Effective search space: 57120 Effective search space used: 57120 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: 47 (22.7 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