Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate GFF2280 PS417_11625 fumarate hydratase
Query= BRENDA::Q9LCC6 (468 letters) >FitnessBrowser__WCS417:GFF2280 Length = 464 Score = 315 bits (806), Expect = 3e-90 Identities = 184/462 (39%), Positives = 263/462 (56%), Gaps = 4/462 (0%) Query: 3 TDVRIEKDFLGEKEIPKDAYYGVQTIRATENFPITGYRIHP-ELIKSLGIVKKSAALANM 61 T +RIE D G IP D Y+G QT RA E F G + P LI++ G K++ A AN Sbjct: 2 TTLRIEHDAFGPVSIPADRYWGAQTQRALEVFG--GKQPFPASLIRAFGQQKRACARANA 59 Query: 62 EVGLLDKEVGQYIVKAADEVIEGKWNDQFIVDPIQGGAGTSINMNANEVIANRALELMGE 121 +G+L + Q I +AA+ + +G + F + Q G+GT NMNANEVIAN A +G Sbjct: 60 RLGVLAPALAQAIEQAAEALAKGDLDQHFPLSIWQTGSGTQTNMNANEVIANCANLTLGG 119 Query: 122 EKGNYSKISPNSHVNMSQSTNDAFPTATHIA-VLSLLNQLIETTKYMQQEFMKKADEFAG 180 E G+ S + PN HVN SQS+ND+FPT H+ VL L +L+ +++ KAD + Sbjct: 120 ELGSKSPVHPNDHVNRSQSSNDSFPTVMHLTTVLELRGRLLPVLGHLRDALGNKADAWQE 179 Query: 181 VIKMGRTHLQDAVPILLGQEFEAYARVIARDIERIANTRNNLYDINMGATAVGTGLNADP 240 V+K+GRTHL DAVP+ GQ F A+A+ I I RI L + G TAVGTGLN Sbjct: 180 VLKIGRTHLMDAVPMSQGQAFGAFAQQIQHGIARIEACMPRLRLLPQGGTAVGTGLNTPA 239 Query: 241 EYISIVTEHLAKFSGHPLRSAQHLVDATQNTDCYTEVSSALKVCMINMSKIANDLRLMAS 300 + E +++ +G + + D E S L V ++++KIAND+RL+ S Sbjct: 240 GFDLAFCEEISRLTGERFETNPCKFEGMGTHDALVEASGTLNVLAVSLTKIANDIRLLGS 299 Query: 301 GPRAGLSEIVLPARQPGSSIMPGKVNPVMPEVMNQVAFQVFGNDLTITSASEAGQFELNV 360 GPR GL E+++P SSIMPGK NP + EV+ Q A QV GN TIT A + FELNV Sbjct: 300 GPRCGLGELIVPDDGLTSSIMPGKRNPTIAEVLVQGAMQVIGNHTTITLAGASSTFELNV 359 Query: 361 MEPVLFFNLIQSISIMTNVFKSFTENCLKGIKANEERMKEYVEKSIGIITAINPHVGYET 420 +PVL NL+ SI ++++ FT L G++ N ++ VE S+ + TA+NP +GY+ Sbjct: 360 AKPVLIHNLLHSIEVLSDCASLFTHKLLGGLEVNRRQLAHNVEHSLLMATALNPVLGYDR 419 Query: 421 AAKLAREAYLTGESIRELCIKYGVLTEEQLNEILNPYEMTHP 462 A++ R+A G S ++ ++ G++T E + P M P Sbjct: 420 VAQITRKAADEGLSPKDAAVQLGLITAEDYERQVRPERMITP 461 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: 484 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: 464 Length adjustment: 33 Effective length of query: 435 Effective length of database: 431 Effective search space: 187485 Effective search space used: 187485 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