Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate H281DRAFT_02592 H281DRAFT_02592 fumarase, class II
Query= BRENDA::Q9LCC6 (468 letters) >FitnessBrowser__Burk376:H281DRAFT_02592 Length = 462 Score = 332 bits (850), Expect = 2e-95 Identities = 184/462 (39%), Positives = 265/462 (57%), Gaps = 3/462 (0%) Query: 1 MNTDVRIEKDFLGEKEIPKDAYYGVQTIRATENFPITGYRIHPELIKSLGIVKKSAALAN 60 MNT R E D G +IP Y+G QT RA + F R L S G+ K++AA AN Sbjct: 1 MNT--RTESDAFGPVDIPAHRYWGAQTQRALDVFGAAEERFPAALTHSFGLQKRAAARAN 58 Query: 61 MEVGLLDKEVGQYIVKAADEVIEGKWNDQFIVDPIQGGAGTSINMNANEVIANRALELMG 120 G++D + I AA E+ +GKW+D F + Q G+GT NMNANEVIANRA EL+G Sbjct: 59 RGCGVIDPHLADAIEAAATELSDGKWDDHFPLSIWQTGSGTQTNMNANEVIANRANELLG 118 Query: 121 EEKGNYSKISPNSHVNMSQSTNDAFPTATHI-AVLSLLNQLIETTKYMQQEFMKKADEFA 179 + G S + PN HVN SQS+ND+FPT H+ A L L +L MQ ++A FA Sbjct: 119 QPLGTKSPVHPNDHVNASQSSNDSFPTVMHVSAALELTGRLRPALVSMQASLDERARAFA 178 Query: 180 GVIKMGRTHLQDAVPILLGQEFEAYARVIARDIERIANTRNNLYDINMGATAVGTGLNAD 239 V+K+ RTHL DAVP +G+ F AYA +A I RI L + G TA GTGLNA Sbjct: 179 DVVKIARTHLMDAVPTTMGRTFAAYAHQMAAAISRIDAALPQLMVLAQGGTAAGTGLNAP 238 Query: 240 PEYISIVTEHLAKFSGHPLRSAQHLVDATQNTDCYTEVSSALKVCMINMSKIANDLRLMA 299 ++ LA + P R+ H ++ + D +VS L ++ K+AND+RL+ Sbjct: 239 AQFPERFCAELAASTSLPFRTHPHKLEGMASHDALVDVSGVLNTIATSLLKLANDIRLLG 298 Query: 300 SGPRAGLSEIVLPARQPGSSIMPGKVNPVMPEVMNQVAFQVFGNDLTITSASEAGQFELN 359 SGPR GL E+++P SSIMPGK NP + EV+ Q FQ GN T+T A +G FELN Sbjct: 299 SGPRCGLGELIVPDDGLTSSIMPGKRNPTIAEVLVQACFQAMGNHQTVTLAGGSGLFELN 358 Query: 360 VMEPVLFFNLIQSISIMTNVFKSFTENCLKGIKANEERMKEYVEKSIGIITAINPHVGYE 419 V +PVL +N++QSI ++T+ ++F E +KG++ + ++ VE ++ +TA+NP +GY+ Sbjct: 359 VAKPVLIYNVLQSIRVLTDACRNFDERVVKGLQVDTTQLATNVENALLSVTALNPVLGYD 418 Query: 420 TAAKLAREAYLTGESIRELCIKYGVLTEEQLNEILNPYEMTH 461 A++ A G + R + ++ Q + I++P + + Sbjct: 419 AVARITALALREGITPRAAALSLDLIDANQYDRIVDPARLAN 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: 508 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: 468 Length of database: 462 Length adjustment: 33 Effective length of query: 435 Effective length of database: 429 Effective search space: 186615 Effective search space used: 186615 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