Align Predicted serC by GapMind curators (no experimental data)
to candidate WP_017752398.1 PN53_RS14385 alanine--glyoxylate aminotransferase family protein
Query= predicted:A5I0W7 (357 letters) >NCBI__GCF_000816635.1:WP_017752398.1 Length = 356 Score = 563 bits (1451), Expect = e-165 Identities = 270/356 (75%), Positives = 319/356 (89%) Query: 1 MHKRLFIPGPVEVERDVLEKMSAAMIGHRSKEASVLQKDISDKLRKVFNTKEEILLSTSS 60 MHK+LFIPGPVEV +DVLEKM+ MIGHRSKEAS LQ+ ISDKLRK+F T EEILLSTSS Sbjct: 1 MHKKLFIPGPVEVRKDVLEKMATPMIGHRSKEASQLQRGISDKLRKLFYTNEEILLSTSS 60 Query: 61 GSGLMEGAIRCTTVKRAAVFAIGAFGKRWYDMAVANNVPADLYEVPWGEAIKPELVEEVL 120 G+GL+EGAIRC+TVKRAA+F++GAFGKRWY +A ANNVPADL+E +G+A+ + +++ L Sbjct: 61 GTGLLEGAIRCSTVKRAAIFSVGAFGKRWYQIAEANNVPADLFEEDFGKAVDVDRIDKAL 120 Query: 121 ATGKYDSIFITHNETSTGIMNPVEEISKVIRKYPEVIWSLDCVSSMAGTKIDVDKLGIDV 180 ATGKYD + ITHNETSTG+MNPVEEISKVI+KYPEV+W +D VSSMAGTKI+VDKLGID+ Sbjct: 121 ATGKYDVLCITHNETSTGVMNPVEEISKVIKKYPEVVWCVDTVSSMAGTKIEVDKLGIDI 180 Query: 181 CITSTQKALALPPGMAICSFSQRAVERAEKVTNRGYYLDLLSLYKYIQKKNYQYPSTPSL 240 C+TSTQKA+ LPPGM+ICSFS++AVERA+KV RGYYLDLLSLY YI KK+YQYPSTPSL Sbjct: 181 CLTSTQKAIGLPPGMSICSFSKKAVERAKKVKFRGYYLDLLSLYNYIHKKDYQYPSTPSL 240 Query: 241 SHMFAMDYRLDKILEEGLEERYERHIEMAEYVRDWARKYFKIYGDEKYLSNTLTNIENTR 300 SHMFA+DY+LD+ILEEGLE RY+RH++MAEYVR WARKYF++Y DE+YLSNT+TNI+NTR Sbjct: 241 SHMFALDYQLDRILEEGLENRYKRHLDMAEYVRAWARKYFELYSDERYLSNTVTNIKNTR 300 Query: 301 NIDIKKLNEELGKRGFQISNGYGKLKDKGFRIAHMGQCTLKDIKELLENINNILDL 356 NIDI +LN+ELGKRGFQISNGYG LK K FRIAHM TL DIKEL+ NIN+IL L Sbjct: 301 NIDIGELNKELGKRGFQISNGYGTLKGKAFRIAHMADFTLDDIKELINNINDILKL 356 Lambda K H 0.318 0.135 0.389 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: 496 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: 357 Length of database: 356 Length adjustment: 29 Effective length of query: 328 Effective length of database: 327 Effective search space: 107256 Effective search space used: 107256 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: 49 (23.5 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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