Align Histidine permease HisP (characterized)
to candidate RR42_RS11100 RR42_RS11100 gamma-aminobutyrate permease
Query= SwissProt::A2RI97 (477 letters) >FitnessBrowser__Cup4G11:RR42_RS11100 Length = 509 Score = 468 bits (1205), Expect = e-136 Identities = 228/472 (48%), Positives = 326/472 (69%), Gaps = 6/472 (1%) Query: 5 NQVKRNLKQRHITMIALGGTIGTGLFLTSGATISQAGPWGAVLAYCFIGIMVYFVMTSLG 64 + ++R LK RH+TMIA+GG +GTGLF+ SGA+ISQAGP GA+L YC IG+MVY +MTSLG Sbjct: 16 DDLQRKLKARHLTMIAIGGAVGTGLFVASGASISQAGPGGALLMYCLIGLMVYCLMTSLG 75 Query: 65 EMATYLPTSGSFSDYGGRYVDPAFGFALGWNYWLNGAITIAVDLTTAGLITQFWFPHLPS 124 E+A ++P +GSF Y YV+ FGFALGW+YW + A+TIAV+L A L+ Q+WFPH+ Sbjct: 76 ELAVHMPVAGSFVTYSALYVEEGFGFALGWSYWFSLAVTIAVELAAAQLVMQYWFPHVSG 135 Query: 125 WIFSGIATVLIFIINVMAVGAFGETEYWLSTIKVITIVLFLAIGLLTIFGVLGQGNVDVV 184 ++S +L+F +N +V FGE EYW + IKV TI++FLA GL+ IFG++ G Sbjct: 136 VVWSAGFLLLMFGLNAFSVRGFGEAEYWFALIKVATILIFLAAGLMMIFGIMQGGPQSGW 195 Query: 185 ANLTAGNHGFVGGISGFVGVLLIAGFSFQGTEMLGITAGESEDPGKTIPKAMNSIFWRIL 244 N T G+ FVGGI GV +IAGFSFQGTE +G+ AGE+ DP +TIP+A+ FWRIL Sbjct: 196 HNFTLGDAPFVGGIPAMFGVAMIAGFSFQGTETVGVAAGEAADPARTIPRAIRQTFWRIL 255 Query: 245 LFYIFSIIVIAAIINFKDPRLLNPSSTAV-MSPFTIVFKNIGFAVAASVMNAVILTSVIS 303 LFY+ +I++I +I + DP LL T + +SPF +VF++ G A AA +MNAV+LT+++S Sbjct: 256 LFYVLAILIIGVLIPYTDPSLLRNDVTDIGVSPFALVFRHAGLAFAAGLMNAVVLTALLS 315 Query: 304 SANSVMYASTRILYSLGQEKGAPKFFGRTAKNGIPFYALLATTIICFIAFLTGIFGTQ-I 362 + S MYASTRILY L AP+ R + NG+P+ AL ATT + + FL+ +FG + + Sbjct: 316 AGTSSMYASTRILYGLAVSGRAPRALARLSANGVPYVALFATTAVGALCFLSSLFGDKAV 375 Query: 363 YLFLIDLSSLTGFLAWLGISVSHIRFRRAYIAQGKKLEDLPYKAKWFPFGPIVALLMTGA 422 YL+L++ S +TGF+AWLGI++SH RFRR + QG K DL Y++ +PFGP+ A+++ Sbjct: 376 YLWLLNTSGMTGFIAWLGIAISHYRFRRGLVHQGYKPSDLAYRSPLYPFGPLFAIVLCVV 435 Query: 423 IAINLDPAMLFSE---HWGEGLALYAAIPIFIVLYFGYKWKYNTKIIPLEEV 471 I + + FS+ W E + Y +P+F+VL+ GY+ T++I E++ Sbjct: 436 IVLGQN-YQAFSDVRGRWLEIVGTYIGVPLFLVLWLGYRLVKKTRLIDYEDM 486 Lambda K H 0.327 0.142 0.438 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: 773 Number of extensions: 51 Number of successful extensions: 4 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: 477 Length of database: 509 Length adjustment: 34 Effective length of query: 443 Effective length of database: 475 Effective search space: 210425 Effective search space used: 210425 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