Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate 352282 BT2755 aspartate ammonia-lyase (NCBI ptt file)
Query= BRENDA::Q9HTD7 (474 letters) >FitnessBrowser__Btheta:352282 Length = 486 Score = 508 bits (1308), Expect = e-148 Identities = 264/461 (57%), Positives = 330/461 (71%), Gaps = 1/461 (0%) Query: 7 SRIEKDLLGTLEVPADAYYGIQTLRAVNNFRLSGVPLSHYPKLVVALAMVKQAAADANRQ 66 +R E DL+G+ EVP A YG+QTLR + NFR+S L+ YP + ALA+ K AA ANR+ Sbjct: 18 TRTESDLIGSREVPESALYGVQTLRGIENFRISKFHLNEYPLFIQALAITKMGAAVANRE 77 Query: 67 LGHLPEDKHAAISEACARLIRGDFHEQFVVDMIQGGAGTSTNMNANEVIANIALEAMGHT 126 L L E++ AI +AC ++ G H+QF VDMIQGGAGT+TNMNANEVIAN ALE MGH Sbjct: 78 LDLLTEEQTDAILKACKEILEGKHHDQFPVDMIQGGAGTTTNMNANEVIANRALELMGHA 137 Query: 127 KGEYKYLHPNNDVNMAQSTNDAYPTAIRLGLLLGHDTLLASLDSLIQAFAAKGVEFAGVL 186 +GEY Y PN+ VN +QSTNDAYPTAI +GL H L+ +LI+AF KG EFA ++ Sbjct: 138 RGEYHYCSPNDHVNRSQSTNDAYPTAIHIGLYYTHLKLVKHFATLIEAFRKKGAEFAHII 197 Query: 187 KMGRTQLQDAVPMTLGQEFHAFATTLGEDLDRLRRLAPELLTEVNLGGTAIGTGINADPG 246 KMGRTQL+DAVPMTLGQ F+ FA+ L +L L A + LT VN+G TAIGTGI A+P Sbjct: 198 KMGRTQLEDAVPMTLGQTFNGFASILEHELKNLDFAAQDFLT-VNMGATAIGTGITAEPE 256 Query: 247 YQKLAVERLAAISGQPLKPAADLIEATSDMGAFVLFSGMLKRTAVKLSKICNDLRLLSSG 306 Y + + L I+G +K A DLI ATSD V +S ++R AVK++KICNDLRLL+SG Sbjct: 257 YAEKCIAALRKITGLDIKLADDLIGATSDTSCMVGYSSAMRRVAVKMNKICNDLRLLASG 316 Query: 307 PRTGINEINLPPRQPGSSIMPGKVNPVIPEAVNQVAFEVIGNDLALTLAAEGGQLQLNVM 366 PR G+ EINLP QPGSSIMPGKVNPVIPE +NQV+++VIGNDL + ++ E Q++LN M Sbjct: 317 PRCGLGEINLPAMQPGSSIMPGKVNPVIPEVMNQVSYKVIGNDLCVAMSGEAAQMELNAM 376 Query: 367 EPLIAYKIFDSIRLLQRAMDMLREHCITGITANVERCHELVEHSIGLVTALNPYIGYENS 426 EP++A F+S LL D LR CI GITAN E+C V +SIG+VTALNP IGY++S Sbjct: 377 EPVMAQCCFESADLLMNGFDTLRTLCIDGITANEEKCRRDVHNSIGVVTALNPVIGYKHS 436 Query: 427 TRIAKTALESGRGVLELVREEKLLDEATLADILLPENMIAP 467 T+IAK ALE+G+GV ELV E +L + L IL PENMI P Sbjct: 437 TKIAKEALETGKGVYELVLEHNILSKEDLDTILKPENMIKP 477 Lambda K H 0.318 0.135 0.380 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: 609 Number of extensions: 19 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: 474 Length of database: 486 Length adjustment: 34 Effective length of query: 440 Effective length of database: 452 Effective search space: 198880 Effective search space used: 198880 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 (21.7 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