Align histidine permease (characterized)
to candidate RR42_RS14635 RR42_RS14635 proline-specific permease
Query= reanno::pseudo3_N2E3:AO353_12275 (468 letters) >FitnessBrowser__Cup4G11:RR42_RS14635 Length = 466 Score = 709 bits (1831), Expect = 0.0 Identities = 349/458 (76%), Positives = 404/458 (88%), Gaps = 1/458 (0%) Query: 1 MQKPANGLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVM 60 MQ+ + GL+RGLSARHIRFMALGSAIGTGLFYGSASAIQ AGPAVLLAY+IGGAAV+MVM Sbjct: 1 MQEQSQGLQRGLSARHIRFMALGSAIGTGLFYGSASAIQTAGPAVLLAYVIGGAAVYMVM 60 Query: 61 RALGEMAVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFP 120 RALGEMAV NPVAGSFGQYAST LGP+AGF+LGWTYAFEM++V +ADVTAFGIYMGFWFP Sbjct: 61 RALGEMAVRNPVAGSFGQYASTGLGPLAGFLLGWTYAFEMIVVCLADVTAFGIYMGFWFP 120 Query: 121 EVSRWIWVLGVVSIVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAP 180 +V RWIWVLG+V ++GGLNL +VKVFGE+EFWLSLLKV AIVAMI GG IMLFG A Sbjct: 121 DVPRWIWVLGIVFLIGGLNLLSVKVFGELEFWLSLLKVGAIVAMIGGGVAIMLFGFGMAD 180 Query: 181 GQV-TDISNLWTQGGFMPNGMGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQHVLPRAIN 239 G V T I NLWT GGFMPNG+ G+IASFAVVMFAFGGIEIIG+TAGEA+DPQ V+PRAIN Sbjct: 181 GGVATGIHNLWTHGGFMPNGIAGVIASFAVVMFAFGGIEIIGITAGEARDPQRVIPRAIN 240 Query: 240 AVPLRILLFYVLTMLVLMSIFPWQQIGSQGSPFVQIFDKLGISSAATILNIVVITAAISA 299 AVPLRILLFYVLT+ VLMS++PW +IGS+GSPFVQIF +LGI SAA +LNIVVI+AA+SA Sbjct: 241 AVPLRILLFYVLTLAVLMSLYPWHRIGSEGSPFVQIFSRLGIGSAAAVLNIVVISAAVSA 300 Query: 300 INSDIFGAGRMMFGLAQQGHAPKGFAHLSRNGVPWMTVVVMSVALLLGVLLNYLIPENVF 359 INSDIFGAGRM++G+A Q AP+ FA +SR GVPWMTVVVM+ ALL GV+LNY++PE+VF Sbjct: 301 INSDIFGAGRMLYGMAVQRQAPRIFASVSRKGVPWMTVVVMAFALLAGVVLNYVMPEDVF 360 Query: 360 LLIASIATFATVWVWLMILFTQVAMRRSMTAEQVAQLKFPVPFWPYAPMAAIAFMLFVFG 419 LIASIATFATVWVWLMIL +QVA+RR M+ +VA LKFPVPFWP AP+AA AFMLF+FG Sbjct: 361 TLIASIATFATVWVWLMILLSQVALRRRMSRAEVAALKFPVPFWPVAPLAATAFMLFIFG 420 Query: 420 VLGYFPDTQAALIVGVVWIVLLVLAYLMWVKPAAGQAA 457 VLG+FP T+AAL+VG VW++LLV+A+ W +P + A Sbjct: 421 VLGWFPQTRAALLVGAVWLLLLVVAWWCWGRPRGQEGA 458 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: 895 Number of extensions: 54 Number of successful extensions: 2 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: 466 Length adjustment: 33 Effective length of query: 435 Effective length of database: 433 Effective search space: 188355 Effective search space used: 188355 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