Align histidine permease (characterized)
to candidate GFF344 PS417_01755 proline-specific permease
Query= reanno::pseudo3_N2E3:AO353_12275 (468 letters) >FitnessBrowser__WCS417:GFF344 Length = 469 Score = 808 bits (2086), Expect = 0.0 Identities = 402/469 (85%), Positives = 434/469 (92%), Gaps = 1/469 (0%) Query: 1 MQKPANGLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVM 60 MQ+ GLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVM Sbjct: 1 MQQQEKGLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVM 60 Query: 61 RALGEMAVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFP 120 RALGEMAVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEM+IV +ADVTAFGIYMGFWFP Sbjct: 61 RALGEMAVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMIIVCLADVTAFGIYMGFWFP 120 Query: 121 EVSRWIWVLGVVSIVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTA- 179 +V+RW+WVLG+V ++GGLNLCNVKVFGEMEFWLSLLKV AIVAMILGGFGIMLFGI +A Sbjct: 121 DVARWVWVLGIVLLIGGLNLCNVKVFGEMEFWLSLLKVGAIVAMILGGFGIMLFGIHSAG 180 Query: 180 PGQVTDISNLWTQGGFMPNGMGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQHVLPRAIN 239 Q + +SNLW GGFMPNG+GGLIASFAVVMFAFGGIEIIG+TAGEAKDPQ V+P+AIN Sbjct: 181 ETQASGLSNLWAHGGFMPNGIGGLIASFAVVMFAFGGIEIIGITAGEAKDPQRVIPKAIN 240 Query: 240 AVPLRILLFYVLTMLVLMSIFPWQQIGSQGSPFVQIFDKLGISSAATILNIVVITAAISA 299 AVPLRILLFYVLT+ VLM+I+PW QIGSQGSPFVQIF LGI SAATILNIVVI+AA+SA Sbjct: 241 AVPLRILLFYVLTLFVLMAIYPWPQIGSQGSPFVQIFSNLGIGSAATILNIVVISAAVSA 300 Query: 300 INSDIFGAGRMMFGLAQQGHAPKGFAHLSRNGVPWMTVVVMSVALLLGVLLNYLIPENVF 359 INSDIFGAGRMM+GLAQQG APKGFA LS+ GVPWMTVVVM ALL GV+LNYLIPENVF Sbjct: 301 INSDIFGAGRMMYGLAQQGQAPKGFAQLSKQGVPWMTVVVMGAALLGGVVLNYLIPENVF 360 Query: 360 LLIASIATFATVWVWLMILFTQVAMRRSMTAEQVAQLKFPVPFWPYAPMAAIAFMLFVFG 419 L+IASIATFATVWVWLMILFTQVAMRRSMT EQVA+LKFPVPFWPYAP AAI FMLFVFG Sbjct: 361 LVIASIATFATVWVWLMILFTQVAMRRSMTKEQVAELKFPVPFWPYAPAAAIVFMLFVFG 420 Query: 420 VLGYFPDTQAALIVGVVWIVLLVLAYLMWVKPAAGQAALVARDPSFSNR 468 VLGYFPDTQAAL+VG VWIVLLV+AYL+WVKP+AGQAA V D + S+R Sbjct: 421 VLGYFPDTQAALLVGAVWIVLLVVAYLLWVKPSAGQAAKVHYDAALSHR 469 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: 1002 Number of extensions: 52 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: 469 Length adjustment: 33 Effective length of query: 435 Effective length of database: 436 Effective search space: 189660 Effective search space used: 189660 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