Align sugar transport protein 6 (characterized)
to candidate CA265_RS01275 CA265_RS01275 hypothetical protein
Query= CharProtDB::CH_091493 (507 letters) >FitnessBrowser__Pedo557:CA265_RS01275 Length = 462 Score = 189 bits (480), Expect = 2e-52 Identities = 144/483 (29%), Positives = 228/483 (47%), Gaps = 53/483 (10%) Query: 20 YVFICVMIAAVGGLIFGYDIGISGGVSAMDDFLKEFFPAVWERKKHVHENNYCKYDNQFL 79 ++F+ +IAA+GG +FG+D+ + G+ E +Y Sbjct: 9 FIFLITLIAALGGFLFGFDMAVVSGII---------------------EPLKSQYGLSSA 47 Query: 80 Q--LFTSSLYLAALVASFVASATCSKLGRRPTMQFASIFFLIGVGLTAGAVNLVMLIIGR 137 Q LF S L +V + K+GRR + A+I FL+ A +V +LI R Sbjct: 48 QEGLFVSCALLGCIVGVSFSGYLSDKVGRRKVLFLAAILFLVSAVGFAFSVAYPVLIFFR 107 Query: 138 LFLGFGVGFGNQAVPLFLSEIAPAQLRGGLNIVFQLMVTIGILIANIVNYFT---ATVHP 194 + G GVG + PL++SE+AP+Q RG L + +QL +TIGIL A I N F ATVH Sbjct: 108 VLAGMGVGVASNVSPLYISEVAPSQKRGRLVVFYQLAITIGILAAYISNLFLQRYATVHA 167 Query: 195 YG-------------WRIALGGAGIPAVILLFGSLLIIETPTSLIERNKNEEGKEALRKI 241 WR +PA L++ E+P L++ +NEE L KI Sbjct: 168 GAGEGILHWLFVENVWRGMFIVGVVPAAAFCLLLLIVPESPRWLVQYGRNEEALNTLIKI 227 Query: 242 RGVDDINDEYESIVHACDIASQVKDPYRKLLKPASRPPFIIGMLLQLFQQFTGINAIMFY 301 G + E +SI ++ASQ Y++L++ + +L QF+GIN ++FY Sbjct: 228 NGAETGRLELDSIK---EMASQKSGGYKELMRLPLSKLLALATILTALSQFSGINGVIFY 284 Query: 302 APVLFQTVGFGSDAALLSAVITGSINVLATFVGIYLVDRTGRRFLLLQSSVHMLICQLII 361 P + ++ G + AL VI GS NVL TF+ I VD GRR L + S+ + Sbjct: 285 GPTILKSAGIVTSDALFYQVILGSANVLFTFIAISKVDTWGRRPLYIIGSLCAAGALALT 344 Query: 362 GIILAKDLGVTGTLGRPQALVVVIFVCVYVMGFAWSWGPLGWLIPSETFPLETRSAGFAV 421 G D +TG ++ + ++++ FA+S GPL ++I +E FP R ++ Sbjct: 345 GFCFLMD--ITGWF-------MLFSIILFLLFFAFSLGPLKFVISTEIFPTHIRGTALSM 395 Query: 422 AVSCNMFFTFVIAQAFLSMLCGMR-SGIFFFFSGWIIVMGLFAFFFIPETKGIAIDDMRE 480 + +V+ F M G+ + FF FS + I+ L+A + ETKG +++++ E Sbjct: 396 CIMTMWVSDWVVNMLFPIMRDGLGIATTFFIFSFFCILSFLYAKKKLFETKGKSLEEI-E 454 Query: 481 SVW 483 W Sbjct: 455 KAW 457 Lambda K H 0.329 0.144 0.446 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: 642 Number of extensions: 32 Number of successful extensions: 6 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: 507 Length of database: 462 Length adjustment: 34 Effective length of query: 473 Effective length of database: 428 Effective search space: 202444 Effective search space used: 202444 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: 52 (24.6 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