Align sugar transport protein 13 (characterized)
to candidate 353923 BT4397 xylose/H+ symporter (NCBI ptt file)
Query= CharProtDB::CH_091463 (526 letters) >FitnessBrowser__Btheta:353923 Length = 460 Score = 181 bits (458), Expect = 7e-50 Identities = 138/480 (28%), Positives = 222/480 (46%), Gaps = 48/480 (10%) Query: 27 CIMAATGGLMFGYDVGVSGGVTSMPDFLEKFFPVVYRKVVAGADKDSNYCKYDNQGLQLF 86 C+++A GGL+FGYD V GG F E +F + D+ +Q Sbjct: 13 CLVSAMGGLLFGYDWVVIGGAKP---FYELYFGIA-----------------DSPTMQGL 52 Query: 87 TSSLYLAG-LTATFFASYTTRTLGRRLTMLIAGVFFIIGVALNAGAQDLAMLIAGRILLG 145 S+ L G L A GR+ +LI+ F+ + +A R L G Sbjct: 53 AMSVALLGCLIGAMVAGMMADRYGRKPLLLISAFIFLSSAYATGAFSVFSWFLAARFLGG 112 Query: 146 CGVGFANQAVPLFLSEIAPTRIRGGLNILFQLNVTIGILFANLVN----------YGTAK 195 G+G A+ P++++E+APT IRG L L QL + +GIL A + N + A Sbjct: 113 IGIGIASGLSPMYIAEVAPTSIRGKLVSLNQLTIVLGILGAQIANWLIAEPIPADFTPAD 172 Query: 196 IKGGW----GWRLSLGLAGIPALLLTVGALLVTETPNSLVERGRLDEGKAVLRRIRGTDN 251 I W GWR A PA + + A + E+P L +G+ ++ +VL RI G Sbjct: 173 ICASWNGQMGWRWMFWGAAFPAAVFLLLACFIPESPRWLAMKGKREKAWSVLSRIGGNRY 232 Query: 252 VEPEFADLLEASRLAKEVKHPFRNLLQRRNRPQLVIAVALQIFQQCTGINAIMFYAPVLF 311 E E + + S A + + + L R R LV+ V + +FQQ G N I YA +F Sbjct: 233 AEQELQMVEQTS--ASKSEGGLKLLFSRPFRKVLVLGVIVAVFQQWCGTNVIFNYAQEIF 290 Query: 312 STLGFGSDASLYSAVVTGAVNVLSTLVSIYSVDKVGRRVLLLEAGVQMFFSQVVIAIILG 371 + G+ L++ VVTG NV+ T V+IY+V+++GRR L+L + +V+ Sbjct: 291 QSAGYSLGDVLFNIVVTGVANVIFTFVAIYTVERLGRRALMLLGAGGLAGIYLVLGTCYF 350 Query: 372 VKVTDTSTNLSKGFAILVVVMICTYVAAFAWSWGPLGWLIPSETFPLETRSAGQSVTVCV 431 +V+ GF ++V+V++ +A +A S GP+ W++ +E FP R + Sbjct: 351 FQVS--------GFFMVVLVVLA--IACYAMSLGPITWVLLAEIFPNRVRGVAMATCTFA 400 Query: 432 NLLFTFIIAQAF-LSMLCHFKFGIFIFFSAWVLIMSVFVMFLLPETKNIPIEEMTERVWK 490 + +F + F L +G F +SA + +F + LPETK +E + + + K Sbjct: 401 LWVGSFTLTYTFPLLNTALGSYGTFWIYSAICVFGFLFFLRALPETKGKSLETLEKDLIK 460 Lambda K H 0.326 0.141 0.425 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: 645 Number of extensions: 44 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: 526 Length of database: 460 Length adjustment: 34 Effective length of query: 492 Effective length of database: 426 Effective search space: 209592 Effective search space used: 209592 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: 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