Align Histidine ammonia-lyase (EC 4.3.1.3) (characterized)
to candidate BPHYT_RS24020 BPHYT_RS24020 phenylalanine/histidine ammonia-lyase
Query= reanno::pseudo5_N2C3_1:AO356_09605 (507 letters) >FitnessBrowser__BFirm:BPHYT_RS24020 Length = 549 Score = 456 bits (1174), Expect = e-133 Identities = 252/491 (51%), Positives = 330/491 (67%), Gaps = 4/491 (0%) Query: 7 IVITGAPLRWQDVVAVARFGAELELSTQTWARIDNAQAIVQRIVESGERAYGVNTGLGAL 66 ++ + PL W V AVA G LELS ARI A+ +V++IVE G RAYGVNTG+GAL Sbjct: 3 VIRSNRPLDWAQVAAVAA-GEPLELSADARARIAAARVLVEQIVERGIRAYGVNTGVGAL 61 Query: 67 CNVSLKDEQLSQLSRNTLLSHACGVGAPLTDEQTRAILCAAILNYSQGKSGIHRRVVEAL 126 C+V + + LSRN L+SHA GVGAPL +TRA++ AA+ N++ G SGI V + L Sbjct: 62 CDVVVSPGEQRTLSRNILMSHAVGVGAPLGAAETRAVMAAAVNNFAHGHSGIRLEVADQL 121 Query: 127 LALLNRGITPQVPSQGSVGYLTHMAHIGIALLGVGQVSYRGQIVPAQQALVAEGLQPVQL 186 +ALLN P+VP+ GSVGYL+HMAHI + +G G RG+ + + AL GL+P+ L Sbjct: 122 VALLNADCLPEVPAFGSVGYLSHMAHIALVCIGEGYARLRGERITGRAALQRLGLEPLVL 181 Query: 187 GAKDGLCLVNGTPCMTGLSCLALADATRLVQWADVIGAMSFEAQRGQIAAFDAEIIALKP 246 AK+GL LVNGTPC+TGL+ LALA A RL+ W D++ +MSFE RGQ+AAFD + +AL+ Sbjct: 182 EAKEGLSLVNGTPCVTGLAALALARAERLLDWTDMVASMSFENLRGQLAAFDEDSLALRI 241 Query: 247 HPGMQQVGVNLRALLDGSEVIAASRGIRTQDALSIRSIPQVHGAARDQLAHARQQIETEL 306 PG+ VG +RA L S ++AA G RTQD LS+R+IP VHGAARD L + EL Sbjct: 242 SPGLNLVGGRMRAALADSGILAAVVGQRTQDPLSMRTIPHVHGAARDVLTATADVVNREL 301 Query: 307 NAVTDNPLLLGTPENFRVMSQANPHGQSVALAADLLAIAMAEIGSIAERRLDRLINPHVS 366 ++TDNP++ GTPE RV SQA+ G S+ALA D LA A+A++ ++AERRLDRL+NP VS Sbjct: 302 ASITDNPIVAGTPEEPRVYSQAHAVGASIALAMDSLATAIAQVAAMAERRLDRLVNPLVS 361 Query: 367 GLPAFLVANPGVNSGMMIVQYVAASLCAENKQLAQPAVLDNFVTSGLQEDHLSMGTNAAL 426 GLPAFL G SG MI QY AASL A+N++LA PA LD +TS LQEDHL T AAL Sbjct: 362 GLPAFLAEPGGTCSGFMIAQYTAASLVAQNRRLALPASLDGGITSALQEDHLCHATPAAL 421 Query: 427 KLHRALENCTQILAIEYLLAAQAFEF--LKAQRFGAGTDIAWKLLRERVPPYDQDRWLAP 484 K ++N +I+AIE L AAQA++ + A R T W+ +R VP Y DR LA Sbjct: 422 KALEIIDNAGRIVAIELLAAAQAYDLQSIDAPR-APHTGALWQRVRRVVPTYRDDRPLAD 480 Query: 485 DIASAAGLLKD 495 D+++A ++ D Sbjct: 481 DMSAAFRMIAD 491 Lambda K H 0.320 0.133 0.385 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: 718 Number of extensions: 30 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: 507 Length of database: 549 Length adjustment: 35 Effective length of query: 472 Effective length of database: 514 Effective search space: 242608 Effective search space used: 242608 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 (21.8 bits) S2: 52 (24.6 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