Align histidinol-phosphatase (EC 3.1.3.15) (characterized)
to candidate 6938111 Sama_2232 cysQ protein (RefSeq)
Query= BRENDA::Q8NS80 (260 letters) >FitnessBrowser__SB2B:6938111 Length = 281 Score = 90.9 bits (224), Expect = 3e-23 Identities = 71/228 (31%), Positives = 110/228 (48%), Gaps = 24/228 (10%) Query: 13 ELAELADSITLDRFEASDLEVSSKPDMTPVSDADLATEEALREKIATARPADSILGEEFG 72 ++A A + + + D+ V+ K D +PV+ ADLA+ + E++A A P +L EE Sbjct: 34 QIARQAGAAIMAVYGQGDVAVTQKSDDSPVTAADLASHTVIIEQLAAAFPFTPVLSEEAV 93 Query: 73 GDVEFSGRQW----IIDPIDGTKNYVRGVPVWATLIALLDNGKPVAGVISAPALARRWWA 128 D E + RQW +IDP+DGTK +++ + IAL+ +G VAGV+ AP L + Sbjct: 94 IDWE-TRRQWQEYFLIDPLDGTKEFIKRNGEFTVNIALVRDGIAVAGVVFAPVLDTCYLG 152 Query: 129 SEGAGAWRTFNG------SSPRKLSVSQVSKLDDASLSFSSLSGWAERDLRDQFVSLTDT 182 +EG GAW G S +K V V + S + ++G+ DL D Sbjct: 153 AEGLGAWLECQGKQQPLQGSAQKRDVPVV--VGSRSHQSAEMAGYL-ADLGDH------- 202 Query: 183 TWRLRGYGDFFSYCLVAEGAVDIAAE-PEVSLWDLAPLSILVTEAGGK 229 L G +C++AEG D+ S WD A ++ AGG+ Sbjct: 203 --ELLSVGSSLKFCMLAEGRADLYPRLGPTSEWDTAAAQAVLESAGGR 248 Lambda K H 0.315 0.133 0.396 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: 181 Number of extensions: 8 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: 260 Length of database: 281 Length adjustment: 25 Effective length of query: 235 Effective length of database: 256 Effective search space: 60160 Effective search space used: 60160 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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