Align ABC transporter for L-Fucose, permease component 2 (characterized)
to candidate WP_042615044.1 ABB28_RS00970 carbohydrate ABC transporter permease
Query= reanno::Smeli:SM_b21105 (288 letters) >NCBI__GCF_001431535.1:WP_042615044.1 Length = 278 Score = 151 bits (382), Expect = 1e-41 Identities = 88/268 (32%), Positives = 139/268 (51%), Gaps = 7/268 (2%) Query: 21 GLFLAMLVICLPGLWIVLSSLRPTVEIMAKPPVWIPETLSLDAYRAMFSGAGQGGVPVWD 80 GL + LV P LW+V S+ P E PP P ++ Y +F+ G G Sbjct: 18 GLLVLALVSLAPLLWMVSVSVMPAGEATTFPPPLTPSHVTFANYHELFARTGMGV----- 72 Query: 81 YFRNSLIVSVTSTVIALAIGLSGGYAFARYRFKAKSAIFLGFMLTRAVPGIALSLPLFML 140 F NSL+VSV T+ +L + GYAFA+ RF + +F M +P LPLF+L Sbjct: 73 NFANSLLVSVAITLGSLLLNTMAGYAFAKLRFVGRDRLFQVLMAALVIPAQVAMLPLFLL 132 Query: 141 YARTGIIDTHFSLILTYVALNVPFTIWLIDGFFRQVPKDLAEAAQIDGCTPWQAFWQVEF 200 + G++++ +I+ AL F I+L+ + R +P +L EAA++DG + F+Q+ Sbjct: 133 MKQLGLVNSFGGVIVP--ALATVFGIFLVRQYARSIPDELLEAARMDGAGEMRIFFQIVL 190 Query: 201 PLAGPGIASAGIFAFLTSWNEYALASQITRSVNSKTLPVGLLDYTAEFTIDWRGMCALAV 260 P+ P + + IF F+ +WN++ + TLPV L + E +D M A AV Sbjct: 191 PMLKPVLVTLSIFTFMGAWNDFMWPLIVLTDQEHYTLPVALATLSREHIMDVEMMMAGAV 250 Query: 261 VMIVPALTLTFIIQKHLVSGLTFGAVKG 288 V ++P L L ++Q++ + GL G+VKG Sbjct: 251 VTVIPVLALFLLLQRYYIQGLMLGSVKG 278 Lambda K H 0.328 0.141 0.442 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: 223 Number of extensions: 13 Number of successful extensions: 3 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: 288 Length of database: 278 Length adjustment: 26 Effective length of query: 262 Effective length of database: 252 Effective search space: 66024 Effective search space used: 66024 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 (21.8 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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