Align aspartate transaminase (EC 2.6.1.1); aspartate-prephenate aminotransferase (EC 2.6.1.78); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate CA265_RS07515 CA265_RS07515 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q9SIE1 (475 letters) >FitnessBrowser__Pedo557:CA265_RS07515 Length = 380 Score = 339 bits (869), Expect = 1e-97 Identities = 183/383 (47%), Positives = 241/383 (62%), Gaps = 4/383 (1%) Query: 87 ITDLAATLVQSGVPVIRLAAGEPDFDTPKVVAEAGINAIREGFTRYTLNAGITELREAIC 146 +T L L G+ +I L+ GEPDF+TP V A A+ E +TRY+ G +LR+AI Sbjct: 1 MTKLGRELASKGINIISLSVGEPDFNTPDHVKNAAKKALDENYTRYSPVPGYPDLRQAIV 60 Query: 147 RKLKEENGLSYAPDQILVSNGAKQSLLQAVLAVCSPGDEVIIPAPYWVSYTEQARLADAT 206 KLK EN L Y QI+VS GAKQSL +L + P DEVIIP PYWVSY+E LA+ Sbjct: 61 NKLKTENNLDYDISQIVVSTGAKQSLSNVILTLIDPDDEVIIPTPYWVSYSEMVTLAEGK 120 Query: 207 PVVIPTKISNNFLLDPKDLESKLTEKSRLLILCSPSNPTGSVYPKSLLEEIARIIAKHPR 266 V I T I ++F + P LE+ +T KS+L + SP NPTGSVY K L + + KHP Sbjct: 121 SVFIDTDIESDFKITPAQLEAAITPKSKLFMFSSPCNPTGSVYSKEELAALVAVFEKHPN 180 Query: 267 LLVLSDEIYEHIIYAPATHTSFASLPDMYERTLTVNGFSKAFAMTGWRLGYLAGPKHIVA 326 + +LSDEIYEHI + H S A + +R + VNGFSKAFAMTGWRLGY+A K I A Sbjct: 181 IYILSDEIYEHINFVD-KHESIAQFDSIKDRVIIVNGFSKAFAMTGWRLGYIAANKEIAA 239 Query: 327 ACSKLQGQVSSGASSIAQKAGVAALGLGKAGGETVAEMVKAYRERRDFLVKSLGDIKGVK 386 A KLQGQ +SG SIAQ+AG+ A G A +V EM +A+ RR+ + L +I GVK Sbjct: 240 ANDKLQGQTTSGTCSIAQRAGIVAYEQGLA---SVLEMKEAFLRRRELVYNLLNEIPGVK 296 Query: 387 ISEPQGAFYLFIDFSAYYGSEAEGFGLINDSSSLALYFLDKFQVAMVPGDAFGDDSCIRI 446 + P GAFY F + S+++G + +I DSS LALY L+ VA V GD+FG+++ IR+ Sbjct: 297 TNLPDGAFYFFPEISSFFGKKDADGNVIKDSSDLALYLLNVGHVATVGGDSFGNNNYIRL 356 Query: 447 SYATSLDVLQAAVEKIRKALEPL 469 SYA S + L A+ +I++AL L Sbjct: 357 SYAASDESLVEALRRIKEALGKL 379 Lambda K H 0.317 0.132 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: 404 Number of extensions: 15 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: 475 Length of database: 380 Length adjustment: 32 Effective length of query: 443 Effective length of database: 348 Effective search space: 154164 Effective search space used: 154164 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 Aug 03 2021. The underlying query database was built on Aug 03 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