Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate HSERO_RS12800 HSERO_RS12800 aspartate aminotransferase
Query= BRENDA::Q9ZEX3 (397 letters) >FitnessBrowser__HerbieS:HSERO_RS12800 Length = 431 Score = 137 bits (346), Expect = 5e-37 Identities = 110/365 (30%), Positives = 166/365 (45%), Gaps = 27/365 (7%) Query: 3 PRLDALHPYPFEKLRALLADAGKPTHDLPPINLSIGEPKHAAPACVGQAIA--ANLAGLS 60 PR++ L PY F L A + D+ I++S+G P A P + + + A Sbjct: 42 PRIERLPPYVFNITAELKMAARRRGEDI--IDMSMGNPDGATPPHIVEKLVEVAQRPDTH 99 Query: 61 VYPSTKGEPALRQAISQWLSRRYSIPAPDPESEVLPVLGSREALFAFAQTVIDPSAGALV 120 Y S+KG P LR+AI+ W RY + DP+SE + +GS+E L +D G V Sbjct: 100 GYSSSKGIPRLRRAIAHWYRSRYEVDF-DPDSEAIVTIGSKEGLAHLMLATLDK--GDTV 156 Query: 121 VCPNPFYQIYEGAALLAGATPYYVNADPARDFGLRTGRVPDEVWRRTQLVFVCSPGNPAG 180 + PNP Y I+ A++AGA V P DF R E + + +++ + P NP Sbjct: 157 LVPNPSYPIHIYGAVIAGANIRSVRMSPGVDFFDELERAVRESYPKPKMMILGFPSNPTA 216 Query: 181 NVMSLEEWRTLFELSDRHGFVIAAYECYSEIYLDE-DTPPLGSLQAARRLGRDRYTNLVA 239 + LE + + +L+ H ++ Y++I D P + + AR + V Sbjct: 217 QCVELEFFERVVKLAREHQILVVHDLAYADITFDGWKAPSIMQVPGAREVA-------VE 269 Query: 240 FSSLSKRSNVPGMRSGFVAGDAALLARFLLYRTYHGSAMSPVVSAASIAAWSMRRMCRKT 299 F +LSK N+ G R GF+ G+A L+A ++YH V A+IAA + C Sbjct: 270 FFTLSKSYNMAGWRIGFMVGNARLVAALARIKSYHDYGSFTPVQVAAIAALEGDQSC--V 327 Query: 300 AQYRAKFEAVLPILQNVLD-----VRAPQASFYLWAGTPG-----SDTAFARELYGRTGV 349 + RA +E +L L V P+AS Y+WA P FAR L + V Sbjct: 328 EEIRANYERRRNVLVKGLHEAGWMVDVPKASMYIWARIPEPYRQFGSLEFARILLEQAKV 387 Query: 350 TVLPG 354 V PG Sbjct: 388 CVSPG 392 Lambda K H 0.321 0.135 0.412 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: 468 Number of extensions: 23 Number of successful extensions: 5 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: 397 Length of database: 431 Length adjustment: 31 Effective length of query: 366 Effective length of database: 400 Effective search space: 146400 Effective search space used: 146400 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 50 (23.9 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