Align Aspartate aminotransferase; AAT; AspAT; Putative 2-aminoadipate transaminase; Transaminase A; EC 2.6.1.1; EC 2.6.1.39 (characterized)
to candidate RR42_RS35305 RR42_RS35305 aspartate aminotransferase
Query= SwissProt::P58350 (410 letters) >FitnessBrowser__Cup4G11:RR42_RS35305 Length = 401 Score = 424 bits (1089), Expect = e-123 Identities = 206/393 (52%), Positives = 274/393 (69%) Query: 17 RISSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGETKYTA 76 R++ I S G R ++ G+ VI L AGEPDF+TP H+++AA A+ G+T+YT Sbjct: 7 RLNRIKPSPSSMAGQRVRELRAAGRDVIGLTAGEPDFETPAHIREAAWRAMQAGKTRYTD 66 Query: 77 LDGTPELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPTPYWT 136 + GT EL+ A +KF+RENGL Y EI V+TGAKQ++FNA+M ++ GDEVI+P PYW Sbjct: 67 VGGTAELRHAAAQKFKRENGLDYAASEIIVSTGAKQVIFNALMCTVQQGDEVIVPAPYWV 126 Query: 137 SYSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAADY 196 SY DI G PV +AC A +GF+LT E+LE AI+ RTRW++LNSP+NPSGAAY+ + Sbjct: 127 SYPDITLFAGGVPVFVACQAENGFKLTPEELERAISARTRWLILNSPNNPSGAAYTRTEL 186 Query: 197 RPLLEVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAMTGW 256 + EVL RHPHVW++ DD+YEH+ YDG FVT AQ P LK RTLT+NGVSKAYAMTGW Sbjct: 187 VAIAEVLERHPHVWVMTDDIYEHLTYDGAAFVTLAQAAPSLKARTLTINGVSKAYAMTGW 246 Query: 257 RIGYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRRDLVV 316 RIGYAG P LIKAM +QSQ+TS ++++QAA++AAL+GPQDF+ FQ RRD VV Sbjct: 247 RIGYAGAPAPLIKAMVKLQSQSTSGANAVAQAAAIAALDGPQDFIAANKAVFQARRDRVV 306 Query: 317 NGLNAIDGLDCRVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAVVPGS 376 L +DG+ C+ P GAFY F+ C ++G TP G I++ D+ ++L+ +AV+ GS Sbjct: 307 AALGQVDGIHCQAPAGAFYVFASCEALIGARTPHGSVIRSSDDWVNWVLDSQDLAVLQGS 366 Query: 377 AFGLSPFFRISYATSEAELKEALERIAAACDRL 409 A+G+ FR+S+A S A+L E RI AA L Sbjct: 367 AYGVDTHFRLSFAASMAQLDEGCRRIEAAAAAL 399 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: 501 Number of extensions: 17 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: 401 Length adjustment: 31 Effective length of query: 379 Effective length of database: 370 Effective search space: 140230 Effective search space used: 140230 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 09 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