Align Glucose/galactose porter (characterized)
to candidate BWI76_RS22920 BWI76_RS22920 MFS transporter
Query= TCDB::P0C105 (412 letters) >FitnessBrowser__Koxy:BWI76_RS22920 Length = 436 Score = 242 bits (618), Expect = 1e-68 Identities = 148/431 (34%), Positives = 227/431 (52%), Gaps = 22/431 (5%) Query: 3 TSIPTNNPLHTETSSQKNYGFALTSLTLLFFMWGFITCLNDILIPHLKNVFQLNYTQSML 62 T+I T + ET K Y L LFF+W LNDIL+P + F L Q+ L Sbjct: 4 TTIQTQSFRAVETGKSKRYIIPFALLCSLFFLWAVANNLNDILLPQFQQAFTLTNFQAGL 63 Query: 63 IQFCFFGAYFIVSLPAGQLVKRISYKRGIVVGLIVAAIGCALFIPAASYRVYALFLGALF 122 IQ F+ YF++ +PAG L+K++SYK GI+ GL + A G ALF PAA Y LFL LF Sbjct: 64 IQSAFYFGYFVIPIPAGILMKKLSYKAGIITGLFLYAFGAALFWPAAEVMNYTLFLIGLF 123 Query: 123 VLASGVTILQVAANPYVTILGKPETAASRLTLTQAFNSLGTTVAPVFGAVLILS------ 176 ++A+G+ L+ AANP+VT+LG RL L Q FNS G +A VFG LILS Sbjct: 124 IIAAGLGCLETAANPFVTVLGPESGGHFRLNLAQTFNSFGAIIAVVFGQSLILSNVPHQS 183 Query: 177 ---------AATDATVNAEADAVRFPYLLLALAFTVLAIIFAILKPPDVQEDEPALSDKK 227 A ++ +V+ PY+++ ++A++ + K P +Q D+ + + + Sbjct: 184 QDVLDKMAPEQLSAYKHSLVLSVQTPYMIIVAVVLLVALLIMLTKFPALQSDDHSDATQS 243 Query: 228 EGSA-----WQYRHLVLGAIGIFVYVGAEVSVGSFLVNFLSDPTVAGLSETDAAHHVAYF 282 SA + RH + F YVGA+ + S+L+ + + + G++ AA+++ Sbjct: 244 SFSASLARLVRVRHWRWAVLAQFCYVGAQTACWSYLIRYAIE-EIPGMTPGFAANYLTGT 302 Query: 283 WGGAMVGRFIGSAAMRYIDDGKALAFNAFVAIILLFITVATTGHIAMWSVLAIGLFNSIM 342 +GRF G+ + K LA A +++IL I+ T GH+ + ++ F SI Sbjct: 303 MVCFFIGRFSGTWLISRFAPHKVLAAYALLSMILCLISAFTGGHVGLLALTLCSAFMSIQ 362 Query: 343 FPTIFSLALHGLGSHTSQGSGILCLAIVGGAIVPLIQGALADAIG-IHLAFLMPIICYAY 401 +PTIFSL + LG T GS + + I+GG IV + G ++DA G I A L+P +C+A Sbjct: 363 YPTIFSLGIKNLGQDTKYGSSFIVMTIIGGGIVTPVMGFVSDAAGNIPTAELVPALCFAV 422 Query: 402 IAFYGLIGSKS 412 I + S++ Sbjct: 423 IFIFARFRSQT 433 Lambda K H 0.328 0.141 0.420 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: 518 Number of extensions: 36 Number of successful extensions: 5 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: 412 Length of database: 436 Length adjustment: 32 Effective length of query: 380 Effective length of database: 404 Effective search space: 153520 Effective search space used: 153520 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: 51 (24.3 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