Align ABC-type sugar transport system, periplasmic component protein (characterized, see rationale)
to candidate Ac3H11_1842 Ribose ABC transport system, periplasmic ribose-binding protein RbsB (TC 3.A.1.2.1)
Query= uniprot:D8IUD0 (314 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1842 Length = 317 Score = 402 bits (1034), Expect = e-117 Identities = 213/315 (67%), Positives = 250/315 (79%), Gaps = 5/315 (1%) Query: 3 KFTRRHFAIAALACAV---LPGAAMAQTPAKPKVALVMKSLANEFFLNMENGAREYQKAN 59 +FTRR AA V L A AQ KPK+AL+MKSLANEFF ME+GA+ +QKA+ Sbjct: 2 QFTRRSVQTAAALAVVGSLLASPAFAQD--KPKIALIMKSLANEFFRTMEDGAKAHQKAH 59 Query: 60 ASKFDLIANGIKDEQDTANQIKIVEQMIVSKVNALVIAPADSKALVPVVKKAIDAGIIVV 119 A ++ L+ANGIK+E DTA QIK++EQ + KV+A+V+APADSKALVPVVK AID GI+VV Sbjct: 60 AKEYTLVANGIKNETDTAAQIKMIEQAMAQKVSAIVLAPADSKALVPVVKAAIDKGILVV 119 Query: 120 NIDNKLDDAALKEKGITVPFVGPDNRKGAKLAGDYLGKQLQKGDKVAIIEGVSTTFNAQQ 179 NIDN+LD ALKEK ITVPFVGPDNR GAKL GD+L K L+ GDKV IIEGVSTTFNAQQ Sbjct: 120 NIDNQLDADALKEKNITVPFVGPDNRAGAKLVGDHLAKTLKAGDKVGIIEGVSTTFNAQQ 179 Query: 180 RTLGFQDAMKDVGANVVTVQSGQWEIDQGNKVAASILNAHPDIKAILAGNDNMALGAVAA 239 RTLG+QDAMK VV VQSG WEI++GN VAA ++ HPD+ A+LAGND+MALGAVAA Sbjct: 180 RTLGYQDAMKAANITVVGVQSGNWEIEKGNTVAAGMMREHPDLVALLAGNDSMALGAVAA 239 Query: 240 IRAAGKTGKVQLVGYDNINAIKPMLKDGRVLATVDQFAQQQAVFGIETALKALSEKKPQS 299 ++AAGKTGKVQ+VGYDNI AIKPML DGRVLAT DQ+A +QAVFGIE A KAL+ K PQ+ Sbjct: 240 VKAAGKTGKVQVVGYDNIGAIKPMLADGRVLATADQYAAKQAVFGIELAQKALAAKTPQN 299 Query: 300 ALGGVVETKVSLVTK 314 L V+T V LVTK Sbjct: 300 QLPATVKTDVVLVTK 314 Lambda K H 0.315 0.131 0.355 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: 316 Number of extensions: 11 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: 314 Length of database: 317 Length adjustment: 27 Effective length of query: 287 Effective length of database: 290 Effective search space: 83230 Effective search space used: 83230 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 48 (23.1 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