Align ABC transporter for D-Glucosamine, permease component 2 (characterized)
to candidate BWI76_RS03135 BWI76_RS03135 sugar ABC transporter permease
Query= reanno::Smeli:SM_b21220 (293 letters) >FitnessBrowser__Koxy:BWI76_RS03135 Length = 290 Score = 120 bits (301), Expect = 4e-32 Identities = 84/274 (30%), Positives = 131/274 (47%), Gaps = 7/274 (2%) Query: 1 MTGTWISTRAWLLMLPLLVVMTAVIGWPLVDTVRLSFTDAKLVGTEGGFVGTANYIKMLG 60 M TW+ WL++ P L+ + +PL +V S D ++V G +VG N+ ++ Sbjct: 1 MRKTWLP---WLILSPSLLFLLLFTWFPLGRSVYDSLFDTRMVSDGGQYVGLENFSRLFA 57 Query: 61 GSNFQRALVTTTWFAVISVAAEMVLGVLAALLLNQQFRGRTALRALMILPWALPTVVNAT 120 S F ++LV + +++V + L +L A+ L + R LR P +P V A Sbjct: 58 DSVFWQSLVNNLLYILLTVVPGVTLALLLAVALTENHRVNRWLRTAFFFPMIIPMVSAAA 117 Query: 121 LWRLIYNPEYGALNAALTQL-GLLDSYRSWLGEPGTALAALIVADCWKNFPLVALIALAA 179 LW I+ P G L+ L +L G +++ +WLG +AL AL + WK L LA Sbjct: 118 LWLFIFMPGLGLLDHYLAKLFGPMNN--NWLGRSNSALLALALIGVWKFAGYYMLFFLAG 175 Query: 180 LQAVPRDITAASLVDGAGPFNRFRFVIMPYLAGPLLVALVLRTIEAFKVFDIIWVMTRGG 239 LQ++P A++++GA F V +P L L + I + D + VMTRGG Sbjct: 176 LQSIPASTREAAIMEGATRTQVFFKVTLPLLRPTLSFVITTALIYSITQIDHVAVMTRGG 235 Query: 240 PANSTRTLSILVYQEAFSFQRAGSGASLALIVTL 273 P N+T L + A+ G AS A +TL Sbjct: 236 PDNATTVLLYYIQNLAWDTHDLGK-ASAATFLTL 268 Lambda K H 0.326 0.138 0.417 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: 234 Number of extensions: 11 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 293 Length of database: 290 Length adjustment: 26 Effective length of query: 267 Effective length of database: 264 Effective search space: 70488 Effective search space used: 70488 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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