Align Beta-phenylalanine transaminase; Aromatic beta-amino acid aminotransferase; Beta-phenylalanine aminotransferase; VpAT; EC 2.6.1.- (characterized)
to candidate Synpcc7942_0645 Synpcc7942_0645 glutamate-1-semialdehyde aminotransferase
Query= SwissProt::H8WR05 (434 letters) >FitnessBrowser__SynE:Synpcc7942_0645 Length = 453 Score = 218 bits (555), Expect = 3e-61 Identities = 150/417 (35%), Positives = 208/417 (49%), Gaps = 25/417 (5%) Query: 24 SQRQFEAQARYMPGANSRSVLFYAPF---PLTIARGEGAALWDADGHRYADFIAEYTAGV 80 S F A + MPG S V + P+ R + A WD DG+RY D++ + + Sbjct: 32 SDEIFAAAQKLMPGGVSSPVRAFKSVGGQPIVFDRVKDAYAWDVDGNRYIDYVGTWGPAI 91 Query: 81 YGHSAPEIRDAVIEAMQGGINLTGHNLLEGRLARLICERFPQIEQLRFTNSGTEANLMAL 140 GH+ PE+ +A+ AM+ G + LE LA ++ + P IE +RF NSGTEA + L Sbjct: 92 CGHAHPEVIEALKVAMEKGTSFGAPCALENVLAEMVIDAVPSIEMVRFVNSGTEACMAVL 151 Query: 141 TAALHFTGRRKIVVFSGGYHG-----------GVLGFGARPS---PTTVPFDFLVLPYND 186 +TGR KI+ F G YHG GV G S P + + L PYND Sbjct: 152 RLMRAYTGRDKIIKFEGCYHGHADMFLVKAGSGVATLGLPDSPGVPKSTTANTLTAPYND 211 Query: 187 AQTARAQIERHGPEIAVVLVEPMQGASGCIPGQPDFLQALRESATQVGALLVFDEVMTS- 245 + +A + EIA V++EP+ G SG I FL+ LRE + ALLVFDEVMT Sbjct: 212 LEAVKALFAENPGEIAGVILEPIVGNSGFIVPDAGFLEGLREITLEHDALLVFDEVMTGF 271 Query: 246 RLAPHGLANKLGIRSDLTTLGKYIGGGMSFGAFGGRADVMALFDPRTGPLAHSGTFNNNV 305 R+A G+ K G+ DLTTLGK IGGG+ GA+GG+ ++M L P GP+ +GT + N Sbjct: 272 RIAYGGVQEKFGVTPDLTTLGKIIGGGLPVGAYGGKREIMQLVAP-AGPMYQAGTLSGNP 330 Query: 306 MTMAAGYAGLTKLFTPEAAGALAERGEALRARLNALCANEGVAMQFTGIGSLMNAHFVQG 365 + M AG L L P L + + L L A+ G A + + F +G Sbjct: 331 LAMTAGIKTLELLRQPGTYEYLDQITKRLSDGLLAIAQETGHAACGGQVSGMFGFFFTEG 390 Query: 366 DVRSSEDLAAVDGRLRQLLFFH--LLNEDIYSSPRGFVV--LSLPLTDADIDRYVAA 418 V + ED D L++ FH +L + IY +P F SL T+ DID +AA Sbjct: 391 PVHNYEDAKKSD--LQKFSRFHRGMLEQGIYLAPSQFEAGFTSLAHTEEDIDATLAA 445 Lambda K H 0.322 0.138 0.408 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: 454 Number of extensions: 21 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: 434 Length of database: 453 Length adjustment: 32 Effective length of query: 402 Effective length of database: 421 Effective search space: 169242 Effective search space used: 169242 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 51 (24.3 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