Align ABC transporter for L-Fucose, permease component 2 (characterized)
to candidate Pf1N1B4_4848 Various polyols ABC transporter, permease component 2
Query= reanno::Smeli:SM_b21105 (288 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4848 Length = 276 Score = 148 bits (373), Expect = 2e-40 Identities = 88/290 (30%), Positives = 152/290 (52%), Gaps = 17/290 (5%) Query: 1 MDTNASHRLRRRLLKVAHLAGLFLAMLVICLPGLWIVLSSLRPTVEIMAKPPVWIPETLS 60 M S RL+ LL A ++I P W+VL+S + ++ A PP +I T + Sbjct: 1 MTLQQSRRLQSLLLGTLAWA----IAILIFFPIFWMVLTSFKTEIDAFATPPQFI-FTPT 55 Query: 61 LDAYRAMFSGAGQGGVPVWDYFR---NSLIVSVTSTVIALAIGLSGGYAFARYRFKAKSA 117 L+ Y + + DYF NS+++S ++T + L I + Y+ A Y + Sbjct: 56 LENYLHINERS--------DYFSFAWNSVVISFSATALCLLIAVPAAYSMAFYETQRTKG 107 Query: 118 IFLGFMLTRAVPGIALSLPLFMLYARTGIIDTHFSLILTYVALNVPFTIWLIDGFFRQVP 177 L + T+ +P + + +P+++L G++DT +LI+ Y +N+P +W+I +F+ +P Sbjct: 108 TLLWMLSTKMLPPVGVLMPIYLLAKSFGLLDTRIALIVIYTLINLPIVVWMIYTYFKDIP 167 Query: 178 KDLAEAAQIDGCTPWQAFWQVEFPLAGPGIASAGIFAFLTSWNEYALASQITRSVNSKTL 237 KD+ EAA++DG T WQ +V P+A G+AS + + + WNE + +T S + L Sbjct: 168 KDILEAARLDGATLWQEMVRVLLPIAKGGLASTVLLSLILCWNEAFWSLNLTSS-QAAPL 226 Query: 238 PVGLLDYTAEFTIDWRGMCALAVVMIVPALTLTFIIQKHLVSGLTFGAVK 287 + Y++ + W + A++ + P L +I QK LV GL+FGAVK Sbjct: 227 TALIASYSSPEGLFWAKLSAVSTLACAPILIFGWISQKQLVRGLSFGAVK 276 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: 220 Number of extensions: 12 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: 276 Length adjustment: 26 Effective length of query: 262 Effective length of database: 250 Effective search space: 65500 Effective search space used: 65500 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 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