Align Aspartate aminotransferase; AAT; AspAT; Putative 2-aminoadipate transaminase; Transaminase A; EC 2.6.1.1; EC 2.6.1.39 (characterized)
to candidate WP_011842075.1 RSPH17029_RS15545 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P58350 (410 letters) >NCBI__GCF_000015985.1:WP_011842075.1 Length = 402 Score = 486 bits (1252), Expect = e-142 Identities = 234/396 (59%), Positives = 302/396 (76%) Query: 15 ASRISSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGETKY 74 +SR+ ++ S + + AA ++REGK +I L GEPDFDTP H++QAA+ AI G+T+Y Sbjct: 7 SSRLQAVQPSPTIAMTRLAAQLRREGKDIIGLSQGEPDFDTPVHIRQAAAAAIEAGQTRY 66 Query: 75 TALDGTPELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPTPY 134 T +DGTPELK AI EKF+RENGL+YE ++I+V TG KQ+L+NA++A+LD GDEVI+P PY Sbjct: 67 TDVDGTPELKAAIVEKFRRENGLSYETNQISVGTGGKQVLYNALLATLDEGDEVIVPAPY 126 Query: 135 WTSYSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAA 194 W SY D+V + G PV ++C F LTA L AAITPRT+WV+LNSPSNP+G YSAA Sbjct: 127 WVSYPDMVRLAGGVPVTVSCPEEDDFLLTASALRAAITPRTKWVILNSPSNPTGMGYSAA 186 Query: 195 DYRPLLEVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAMT 254 R L +VLL PHV ++ DDMYEH+ YDG+ F T AQ+EP L +R LT NGVSKA++MT Sbjct: 187 HLRALADVLLEFPHVLVMTDDMYEHLRYDGWEFATIAQVEPKLMDRVLTCNGVSKAFSMT 246 Query: 255 GWRIGYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRRDL 314 GWRIGYAGGP ++IKAMA +QSQ+TS PSS+SQAA++AAL GP +FL ER E F++RRDL Sbjct: 247 GWRIGYAGGPADIIKAMATLQSQSTSNPSSVSQAAALAALTGPMEFLAERNEIFRQRRDL 306 Query: 315 VVNGLNAIDGLDCRVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAVVP 374 ++ LN I+GL C P GAFY F CAG++G+ P G+RI+TDTD+ YL+E+A VA VP Sbjct: 307 CLSALNQIEGLSCVRPNGAFYLFPSCAGMIGRTRPDGRRIETDTDYVMYLVEEAGVAAVP 366 Query: 375 GSAFGLSPFFRISYATSEAELKEALERIAAACDRLS 410 GSAFGL+P+FRIS+AT L+ A ERI AA RL+ Sbjct: 367 GSAFGLAPYFRISFATDTERLRTACERIRAASARLT 402 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: 517 Number of extensions: 15 Number of successful extensions: 1 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: 402 Length adjustment: 31 Effective length of query: 379 Effective length of database: 371 Effective search space: 140609 Effective search space used: 140609 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 Apr 10 2024. The underlying query database was built on Apr 09 2024.
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