Align histidine permease (characterized)
to candidate BWI76_RS06245 BWI76_RS06245 proline-specific permease ProY
Query= reanno::pseudo3_N2E3:AO353_12275 (468 letters) >FitnessBrowser__Koxy:BWI76_RS06245 Length = 456 Score = 585 bits (1508), Expect = e-171 Identities = 277/441 (62%), Positives = 351/441 (79%), Gaps = 1/441 (0%) Query: 5 ANGLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMRALG 64 +N LKRGLS RHIRFMALGSAIGTGLFYGSA AI+MAGP+VLLAY+IGG A +++MRALG Sbjct: 4 SNKLKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGPSVLLAYIIGGVAAYIIMRALG 63 Query: 65 EMAVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFPEVSR 124 EM+VHNP A SF +YA YLGP+AG+I GWTY FE++IV +ADVTAFGIYMG WFP V Sbjct: 64 EMSVHNPAASSFSRYAQDYLGPLAGYITGWTYCFEILIVAIADVTAFGIYMGVWFPAVPH 123 Query: 125 WIWVLGVVSIVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAPGQVT 184 W+WVL VV I+ +NL +VKVFGE+EFW S KVA I+ MIL GFGI+++GI GQ T Sbjct: 124 WVWVLSVVLIICAVNLMSVKVFGELEFWFSFFKVATIIIMILAGFGIIIWGIGNG-GQPT 182 Query: 185 DISNLWTQGGFMPNGMGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQHVLPRAINAVPLR 244 I NLW+ GGF NG G++ S +VMFA+GGIEIIG+TAGEAKDP+ +PRAIN+VP+R Sbjct: 183 GIHNLWSNGGFFSNGWLGMVMSLQMVMFAYGGIEIIGITAGEAKDPEKSIPRAINSVPMR 242 Query: 245 ILLFYVLTMLVLMSIFPWQQIGSQGSPFVQIFDKLGISSAATILNIVVITAAISAINSDI 304 IL+FYV T+ V+MSI+PW Q+G+ GSPFV F LGI+ AA+ILN VV+TA++SAINSD+ Sbjct: 243 ILVFYVGTLFVIMSIYPWNQVGTNGSPFVLTFQHLGITFAASILNFVVLTASLSAINSDV 302 Query: 305 FGAGRMMFGLAQQGHAPKGFAHLSRNGVPWMTVVVMSVALLLGVLLNYLIPENVFLLIAS 364 FG GRM+ G+A+QG APK FA SR GVPW+TV+VM++ALL V LNY++PENVFL+IAS Sbjct: 303 FGVGRMLHGMAEQGSAPKMFAKTSRRGVPWVTVMVMTIALLFAVYLNYIMPENVFLVIAS 362 Query: 365 IATFATVWVWLMILFTQVAMRRSMTAEQVAQLKFPVPFWPYAPMAAIAFMLFVFGVLGYF 424 +ATFATVWVW+MIL +Q+A RR + E+ LKF VP + + F++F+ G++GY Sbjct: 363 LATFATVWVWIMILLSQIAFRRRLPPEEAKALKFKVPGGVTTTVIGLLFLVFIIGLIGYH 422 Query: 425 PDTQAALIVGVVWIVLLVLAY 445 PDT+ +L VG WI+LL++ + Sbjct: 423 PDTRISLYVGFAWIILLLIGW 443 Lambda K H 0.329 0.142 0.441 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: 774 Number of extensions: 46 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: 468 Length of database: 456 Length adjustment: 33 Effective length of query: 435 Effective length of database: 423 Effective search space: 184005 Effective search space used: 184005 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