Align ProY of 457 aas and 12 TMSs (characterized)
to candidate Pf1N1B4_1580 Histidine transport protein (permease)
Query= TCDB::P0AAE2 (457 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1580 Length = 469 Score = 580 bits (1495), Expect = e-170 Identities = 273/440 (62%), Positives = 355/440 (80%), Gaps = 2/440 (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 VHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFPEVDRWIW 127 Query: 127 VLSVVLIICAVNLMSVKVFGELEFWFSFFKVATIIIMIVAGFGIIIWGIGN--GGQPTGI 184 VL +V ++ +NL +VKVFGE+EFW S KVA I+ MI+ GFGI+++GI G Q T I Sbjct: 128 VLGIVSVVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAPGAQATDI 187 Query: 185 HNLWSNGGFFSNGWLGMVMSLQMVMFAYGGIEIIGITAGEAKDPEKSIPRAINSVPMRIL 244 NLWS+GGF NG G++ S +VMFA+GGIEIIG+TAGEAKDP++ +PRAIN+VP+RIL Sbjct: 188 SNLWSHGGFMPNGVGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQRVLPRAINAVPLRIL 247 Query: 245 VFYVGTLFVIMSIYPWNQVGTAGSPFVLTFQHMGITFAASILNFVVLTASLSAINSDVFG 304 +FYV T+ V+MSI+PW Q+G+ GSPFV F ++GI+ AA+ILN VV++A++SAINSD+FG Sbjct: 248 LFYVLTMLVLMSIFPWQQIGSQGSPFVQIFDNLGISSAATILNIVVISAAVSAINSDIFG 307 Query: 305 VGRMLHGMAEQGSAPKIFSKTSRRGIPWVTVLVMTTALLFAVYLNYIMPENVFLVIASLA 364 GRM++G+A+QG APK F++ SR G+PW+TV+VM++ALL V LNY++PENVFL+IAS+A Sbjct: 308 AGRMMYGLAQQGHAPKGFARLSRNGVPWLTVVVMSSALLLGVLLNYLIPENVFLLIASVA 367 Query: 365 TFATVWVWIMILLSQIAFRRRLPPEEVKALKFKVPGGVATTIGGLIFLLFIIGLIGYHPD 424 TFATVWVW+MIL +Q+A RR + E+V LKF VP + + F+LFI G++GY PD Sbjct: 368 TFATVWVWLMILFTQVAMRRSMSAEQVAQLKFPVPFWPYAPMAAIAFMLFIFGVLGYFPD 427 Query: 425 TRISLYVGFAWIVVLLIGWM 444 T+ +L VG WIV+L++ ++ Sbjct: 428 TQAALIVGVVWIVLLVLAYL 447 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: 678 Number of extensions: 31 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: 469 Length adjustment: 33 Effective length of query: 424 Effective length of database: 436 Effective search space: 184864 Effective search space used: 184864 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