Align ABC transporter for D-Glucosamine, permease component 2 (characterized)
to candidate Pf1N1B4_5113 Maltose/maltodextrin ABC transporter, permease protein MalF
Query= reanno::Smeli:SM_b21220 (293 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5113 Length = 295 Score = 210 bits (535), Expect = 3e-59 Identities = 114/290 (39%), Positives = 174/290 (60%), Gaps = 15/290 (5%) Query: 10 AWLLMLPLLVVMTAVIGWPLVDTVRLSFTDAKLVGTEGG-FVGTANYIKMLGGS------ 62 AWL + P+L+ + V WPL+ T S TDA L T GG F+G NY+ G S Sbjct: 4 AWLFLTPMLLCLALVAAWPLLRTFWFSLTDANLADTGGGTFIGFGNYLFHNGSSWSGILV 63 Query: 63 --NFQRALVTTTWFAVISVAAEMVLGVLAALLLNQQFRGRTALRALMILPWALPTVVNAT 120 + A+ T +F V+SV E+VLG+L ALLLN +F GR +RAL+++PWA+PT+V+A Sbjct: 64 DPQWWNAVRNTLYFTVVSVGLEVVLGLLVALLLNIKFTGRALVRALILIPWAIPTIVSAK 123 Query: 121 LWRLIYNPEYGALNAALTQLGLLDSYRSWLGEPGTALAALIVADCWKNFPLVALIALAAL 180 +W + N ++G +N + LGL+D+ +W + ++ A+I+ D WK P V L+ LAAL Sbjct: 124 IWSWMLNDQFGIINHLMLSLGLIDAPLAWTADADLSMWAVIIVDVWKTVPFVTLLMLAAL 183 Query: 181 QAVPRDITAASLVDGAGPFNRFRFVIMPYLAGPLLVALVLRTIEAFKVFDIIWVMTRGGP 240 Q +P D A+ VDG P F V +P L LLVA + R +++ +VFD+I+V+T Sbjct: 184 QMLPSDCYEAARVDGIHPLKVFWRVTLPLLMPALLVAAIFRILDSLRVFDVIYVLT---- 239 Query: 241 ANSTRTLSILVY--QEAFSFQRAGSGASLALIVTLLVTILAAAYAALLRK 288 +NS+ T+S+ VY Q FQ G G++ + ++ L+V ++A Y L R+ Sbjct: 240 SNSSSTMSMSVYARQHLVEFQDVGYGSAASTLLFLVVAVIALLYLYLGRR 289 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: 273 Number of extensions: 12 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: 293 Length of database: 295 Length adjustment: 26 Effective length of query: 267 Effective length of database: 269 Effective search space: 71823 Effective search space used: 71823 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