Align ProY of 457 aas and 12 TMSs (characterized)
to candidate PfGW456L13_318 Histidine transport protein (permease)
Query= TCDB::P0AAE2 (457 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_318 Length = 468 Score = 578 bits (1490), Expect = e-169 Identities = 276/439 (62%), Positives = 351/439 (79%), Gaps = 1/439 (0%) Query: 7 LKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGPSVLLAYIIGGIAAYIIMRALGEMS 66 LKRGLS RHIRFMALGSAIGTGLFYGSA AI+MAGP+VLLAY+IGG A +++MRALGEM+ Sbjct: 8 LKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMRALGEMA 67 Query: 67 VHNPAASSFSRYAQENLGPLAGYITGWTYCFEILIVAIADVTAFGIYMGVWFPTVPHWIW 126 VHNP A SF +YA LGP+AG+I GWTY FE++IV +ADVTAFGIYMG WFP V WIW Sbjct: 68 VHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFPEVSRWIW 127 Query: 127 VLSVVLIICAVNLMSVKVFGELEFWFSFFKVATIIIMIVAGFGIIIWGIGNG-GQPTGIH 185 VL VV I+ +NL +VKVFGE+EFW S KVA I+ MI+ GFGI+ +GI + GQ T I Sbjct: 128 VLGVVSIVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMWFGISSAPGQATDIS 187 Query: 186 NLWSNGGFFSNGWLGMVMSLQMVMFAYGGIEIIGITAGEAKDPEKSIPRAINSVPMRILV 245 NLWS+GGF NG G++ S +VMFA+GGIEIIG+TAGEAKDP+ +PRAIN+VP+RIL+ Sbjct: 188 NLWSHGGFMPNGMGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQHVLPRAINAVPLRILL 247 Query: 246 FYVGTLFVIMSIYPWNQVGTAGSPFVLTFQHMGITFAASILNFVVLTASLSAINSDVFGV 305 FYV T+ V+MSI+PW Q+G+ GSPFV F +GI+ AA+ILN VV+TA++SAINSD+FG Sbjct: 248 FYVLTMLVLMSIFPWQQIGSQGSPFVQIFDKLGISSAATILNIVVITAAISAINSDIFGA 307 Query: 306 GRMLHGMAEQGSAPKIFSKTSRRGIPWVTVLVMTTALLFAVYLNYIMPENVFLVIASLAT 365 GRM+ G+A+QG APK F++ SR G+PW+TV+VM+ ALL V LNY++PENVFL+IAS+AT Sbjct: 308 GRMMFGLAQQGHAPKGFARLSRNGVPWMTVVVMSAALLLGVLLNYLIPENVFLLIASVAT 367 Query: 366 FATVWVWIMILLSQIAFRRRLPPEEVKALKFKVPGGVATTIGGLIFLLFIIGLIGYHPDT 425 FATVWVW+MIL++Q+A RR + E+V LKF VP + F+LFI G++GY PDT Sbjct: 368 FATVWVWLMILVTQVAMRRSMSAEQVAQLKFPVPLWPYAPAAAIAFMLFIFGVLGYFPDT 427 Query: 426 RISLYVGFAWIVVLLIGWM 444 + +L VG WIV+L++ ++ Sbjct: 428 QAALIVGVVWIVLLVLAYL 446 Lambda K H 0.329 0.143 0.449 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: 695 Number of extensions: 38 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: 457 Length of database: 468 Length adjustment: 33 Effective length of query: 424 Effective length of database: 435 Effective search space: 184440 Effective search space used: 184440 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: 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