Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate AZOBR_RS06120 AZOBR_RS06120 fumarate hydratase
Query= BRENDA::Q9LCC6 (468 letters) >FitnessBrowser__azobra:AZOBR_RS06120 Length = 466 Score = 413 bits (1061), Expect = e-120 Identities = 207/461 (44%), Positives = 299/461 (64%), Gaps = 1/461 (0%) Query: 3 TDVRIEKDFLGEKEIPKDAYYGVQTIRATENFPITGYRIHPELIKSLGIVKKSAALANME 62 T +R E D G E+ D Y+G QT R+ NF I G R+ P L+++LGI KK++ALANM Sbjct: 5 TGMRTETDSFGPIEVAADRYWGAQTQRSLRNFRIGGERMPPALVRALGIQKKASALANMA 64 Query: 63 VGLLDKEVGQYIVKAADEVIEGKWNDQFIVDPIQGGAGTSINMNANEVIANRALELMGEE 122 + +LD +G+ IV+AA+EVI+G D F + Q G+GT NMNANEVI+NRA+E +G E Sbjct: 65 LEVLDPRLGRAIVEAAEEVIDGTLADHFPLVVWQTGSGTQTNMNANEVISNRAIEALGGE 124 Query: 123 KGNYSKISPNSHVNMSQSTNDAFPTATHIAVLSLLN-QLIETTKYMQQEFMKKADEFAGV 181 G+ + PN HVNM QS+ND+FPTA HIA ++ +L+ +++ KA EFA + Sbjct: 125 MGSKKPVHPNDHVNMGQSSNDSFPTAMHIAAAEQIHHELLPALEHLHAALAAKAAEFADI 184 Query: 182 IKMGRTHLQDAVPILLGQEFEAYARVIARDIERIANTRNNLYDINMGATAVGTGLNADPE 241 +K+GRTHLQDA P+ LGQEF YA IA IER+ + LY + G TAVGTGLNA Sbjct: 185 VKIGRTHLQDATPLTLGQEFSGYAAQIAYGIERVKASLPQLYRLAQGGTAVGTGLNAKTG 244 Query: 242 YISIVTEHLAKFSGHPLRSAQHLVDATQNTDCYTEVSSALKVCMINMSKIANDLRLMASG 301 + +A +G P +A++ +A D + +L +++ KIAND+RL+ SG Sbjct: 245 FAEAFAAEVASITGLPFVTAENKFEALATHDALVDAHGSLNTLAVSLMKIANDIRLLGSG 304 Query: 302 PRAGLSEIVLPARQPGSSIMPGKVNPVMPEVMNQVAFQVFGNDLTITSASEAGQFELNVM 361 PR G+ EI LP +PGSSIMPGKVNP E M V QV GN T++ A G FELNV Sbjct: 305 PRCGIGEIALPENEPGSSIMPGKVNPTQSEAMTMVCAQVMGNQTTVSIAGATGHFELNVF 364 Query: 362 EPVLFFNLIQSISIMTNVFKSFTENCLKGIKANEERMKEYVEKSIGIITAINPHVGYETA 421 +PV+ +N++QSI ++ + SFT+N + GI+AN ER+ + + +S+ ++TA+NPH+GY+ A Sbjct: 365 KPVIAYNVLQSIRLLADACNSFTDNAVVGIEANRERIGQLLNESLMLVTALNPHIGYDNA 424 Query: 422 AKLAREAYLTGESIRELCIKYGVLTEEQLNEILNPYEMTHP 462 AK+A++A+ G ++++ + G+LTEEQ ++ + P M P Sbjct: 425 AKIAKKAHKEGTTLKQAGVALGLLTEEQFDQWVKPETMVKP 465 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: 548 Number of extensions: 31 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: 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