Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate BPHYT_RS14615 BPHYT_RS14615 fumarate hydratase
Query= BRENDA::Q9LCC6 (468 letters) >FitnessBrowser__BFirm:BPHYT_RS14615 Length = 466 Score = 387 bits (994), Expect = e-112 Identities = 192/460 (41%), Positives = 289/460 (62%), Gaps = 1/460 (0%) Query: 1 MNTDVRIEKDFLGEKEIPKDAYYGVQTIRATENFPITGYRIHPELIKSLGIVKKSAALAN 60 M DVR+E+D GE +P +G QT R+ +NF I+ + PELI +L ++K++AA N Sbjct: 1 MTEDVRMERDTFGEIAVPNARLWGAQTQRSLQNFRISTEKQSPELIVALAVIKRAAAEVN 60 Query: 61 MEVGLLDKEVGQYIVKAADEVIEGKWNDQFIVDPIQGGAGTSINMNANEVIANRALELMG 120 + +G+LD+ + I++AADE+I+GK D+F + Q G+GT NMN NEVIANRA EL+G Sbjct: 61 LGLGVLDESKAKAIMQAADEIIDGKHPDEFPLAVWQTGSGTQTNMNLNEVIANRASELLG 120 Query: 121 EEKGNYSKISPNSHVNMSQSTNDAFPTATHIAVL-SLLNQLIETTKYMQQEFMKKADEFA 179 +G K+ PN VN QS+ND FPTA H+A +++ L K ++ KA FA Sbjct: 121 GVRGEERKVHPNDDVNRGQSSNDVFPTAMHVAAAYAIVKHLQPALKTLRDTLDGKAKAFA 180 Query: 180 GVIKMGRTHLQDAVPILLGQEFEAYARVIARDIERIANTRNNLYDINMGATAVGTGLNAD 239 ++K+GRTHLQDA P+ LGQEF Y + I + +LY++ G TAVGTGLNA Sbjct: 181 DIVKIGRTHLQDATPLTLGQEFSGYVAQLDHGIRHVETALPHLYELAQGGTAVGTGLNAH 240 Query: 240 PEYISIVTEHLAKFSGHPLRSAQHLVDATQNTDCYTEVSSALKVCMINMSKIANDLRLMA 299 P++ V + K +G P SA + + D ALK +++KIAND+R +A Sbjct: 241 PQFADKVAAAIGKLTGLPFVSAPNKFEVMAAADALVFAHGALKTVAASLNKIANDVRWLA 300 Query: 300 SGPRAGLSEIVLPARQPGSSIMPGKVNPVMPEVMNQVAFQVFGNDLTITSASEAGQFELN 359 SGPR GL E+ +P +PGSSIMPGKVNP E + + QVFGND+ + +G FELN Sbjct: 301 SGPRCGLGELSIPENEPGSSIMPGKVNPTQSEALTMLCAQVFGNDVAVNIGGASGNFELN 360 Query: 360 VMEPVLFFNLIQSISIMTNVFKSFTENCLKGIKANEERMKEYVEKSIGIITAINPHVGYE 419 V P++ N++QS+ ++ + +SF +NC GI+ N ER++ + +S+ ++TA+NPH+GY+ Sbjct: 361 VFRPMIAHNVLQSVRLLADGARSFNDNCAVGIEPNRERIETLLNESLMLVTALNPHIGYD 420 Query: 420 TAAKLAREAYLTGESIRELCIKYGVLTEEQLNEILNPYEM 459 AAK+A++A+ G +++ + G +TE+Q +E + P +M Sbjct: 421 KAAKIAKKAHKEGTTLKAAALALGFVTEQQFDEWVRPKDM 460 Lambda K H 0.316 0.133 0.370 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: 546 Number of extensions: 19 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: 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: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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