GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serC in Clostridium tyrobutyricum FAM22553

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.

Links

Downloads

Related tools

About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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