Align Aspartate aminotransferase; AAT; AspAT; Putative 2-aminoadipate transaminase; Transaminase A; EC 2.6.1.1; EC 2.6.1.39 (characterized)
to candidate CA265_RS07515 CA265_RS07515 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P58350 (410 letters) >FitnessBrowser__Pedo557:CA265_RS07515 Length = 380 Score = 312 bits (800), Expect = 9e-90 Identities = 166/383 (43%), Positives = 238/383 (62%), Gaps = 5/383 (1%) Query: 28 KIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGETKYTALDGTPELKKAI 87 K+G A+ +G +I L GEPDF+TP+HVK AA A+ T+Y+ + G P+L++AI Sbjct: 3 KLGRELAS---KGINIISLSVGEPDFNTPDHVKNAAKKALDENYTRYSPVPGYPDLRQAI 59 Query: 88 REKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPTPYWTSYSDIVHICEG 147 K + EN L Y++ +I V+TGAKQ L N ++ +DP DEVIIPTPYW SYS++V + EG Sbjct: 60 VNKLKTENNLDYDISQIVVSTGAKQSLSNVILTLIDPDDEVIIPTPYWVSYSEMVTLAEG 119 Query: 148 KPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAADYRPLLEVLLRHP 207 K V I D S F++T +LEAAITP+++ + +SP NP+G+ YS + L+ V +HP Sbjct: 120 KSVFIDTDIESDFKITPAQLEAAITPKSKLFMFSSPCNPTGSVYSKEELAALVAVFEKHP 179 Query: 208 HVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAMTGWRIGYAGGPREL 267 ++++L D++YEHI + + + AQ + +K+R + VNG SKA+AMTGWR+GY +E+ Sbjct: 180 NIYILSDEIYEHINFVD-KHESIAQFD-SIKDRVIIVNGFSKAFAMTGWRLGYIAANKEI 237 Query: 268 IKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRRDLVVNGLNAIDGLDC 327 A +Q Q TS SI+Q A + A + E E+F RRR+LV N LN I G+ Sbjct: 238 AAANDKLQGQTTSGTCSIAQRAGIVAYEQGLASVLEMKEAFLRRRELVYNLLNEIPGVKT 297 Query: 328 RVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAVVPGSAFGLSPFFRIS 387 +P+GAFY F + GK G IK +D YLL HVA V G +FG + + R+S Sbjct: 298 NLPDGAFYFFPEISSFFGKKDADGNVIKDSSDLALYLLNVGHVATVGGDSFGNNNYIRLS 357 Query: 388 YATSEAELKEALERIAAACDRLS 410 YA S+ L EAL RI A +L+ Sbjct: 358 YAASDESLVEALRRIKEALGKLA 380 Lambda K H 0.318 0.134 0.393 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: 372 Number of extensions: 16 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: 410 Length of database: 380 Length adjustment: 31 Effective length of query: 379 Effective length of database: 349 Effective search space: 132271 Effective search space used: 132271 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: 50 (23.9 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