GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Cereibacter sphaeroides ATCC 17029

Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_011841935.1 RSPH17029_RS14500 D-amino acid aminotransferase

Query= BRENDA::A0A0A0LJI6
         (555 letters)



>NCBI__GCF_000015985.1:WP_011841935.1
          Length = 299

 Score =  211 bits (536), Expect = 4e-59
 Identities = 120/283 (42%), Positives = 162/283 (57%), Gaps = 2/283 (0%)

Query: 259 NEKLLAWVGDEILPRDSAKVSVFDSVVQGGDSVWEGLRVYRGKIFKLDEHLDRLFDSSKA 318
           NE +  W+   ILPR  A VSV+DS    GD VWEG+R+Y G+   LDEHLDRLF+++ A
Sbjct: 16  NETIRLWLNGRILPRAEALVSVYDSGFMLGDGVWEGIRLYDGRWAFLDEHLDRLFEAALA 75

Query: 319 LAFQNVPSREEVKDAIFRTLIRNGMFDNAHIRLSLTRGKKVTSGMSPQFNLYGCTLIVLA 378
           +       R  ++ AI  T   NGM  +AH RL +TRG K      P  +  G T+ ++ 
Sbjct: 76  IDLDIGMDRAALRQAILDTAAANGMATDAHARLMVTRGVKTRPFQHPSLSRQGPTVAIIM 135

Query: 379 EWKPPVYDNSSGITLVTATTRRNSPNNLDSKIHHNNLLNNILAKIEGNNANAGDAIMLDK 438
           E   P       I L T    R  P + D K++ ++ LN ILA I    A A +A+MLD 
Sbjct: 136 EHSKPKIPRP--IRLATVPHIRGLPMSQDPKLNSHSKLNCILACIAAEKAGADEALMLDV 193

Query: 439 DGFVSETNATNIFLVKKGNVLTPHADYCLPGITRATVMDLVVKEKLILEERRISLSEFHT 498
            GFV+ TNA N F+V+KG V T   DYC+ GITR  V+ +  +  + + E+  SL E ++
Sbjct: 194 HGFVNTTNACNFFIVRKGEVWTSTGDYCMNGITRGKVIRICREAGIPVFEKNFSLVETYS 253

Query: 499 ADEVWTTGTMGELTPVVKIDGRVIGDGQVGPVTRMLQNAYKKL 541
           ADE + TGT G  TPV  IDGR IG G++GP+T  L+  YK L
Sbjct: 254 ADEAFLTGTFGAQTPVGSIDGRRIGTGEMGPMTERLRGLYKAL 296


Lambda     K      H
   0.319    0.137    0.411 

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: 381
Number of extensions: 20
Number of successful extensions: 2
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: 555
Length of database: 299
Length adjustment: 31
Effective length of query: 524
Effective length of database: 268
Effective search space:   140432
Effective search space used:   140432
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 (21.7 bits)
S2: 50 (23.9 bits)

Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_011841934.1 RSPH17029_RS14495 hypothetical protein

Query= BRENDA::A0A0A0LJI6
         (555 letters)



>NCBI__GCF_000015985.1:WP_011841934.1
          Length = 236

 Score =  164 bits (414), Expect = 4e-45
 Identities = 91/230 (39%), Positives = 133/230 (57%), Gaps = 5/230 (2%)

Query: 9   LWSTPRSLSTSLMYSFAQRDDMEVLDEPLYANFLRVTGYDRPYREELLSKMEPDGNKVIK 68
           +WS PR+LST++MYSFA R D  + DEP YA +L+ TG D P R E+L+  E D + +  
Sbjct: 1   MWSGPRNLSTAMMYSFAARGDCGIWDEPFYAAYLKATGIDHPMRAEILAAHETDASVIAD 60

Query: 69  EIIF-APGEKKFRFCKHIAKQKVPGLASDLMKKGRHFILIRNPLDILPSYDKVIPA-SFS 126
                AP  +   + KH+    +P      M+   +  LIR+P  ++ SY K     S +
Sbjct: 61  RCRGEAPLGEPIFYQKHMTLHMIPSFDRGFMRDCENVFLIRHPARVVASYAKKREGPSLA 120

Query: 127 ELGFSELVSIYNELKE-LGRLPPIIDAAELQKNPEATLRGLCEELGIPFQHKMLKWEAGP 185
           ++GF +   +++E+ + LGR P ++D+A+++++PE TL  LC  LG+PF   ML+W AG 
Sbjct: 121 DIGFVQQAELFDEVAQWLGRPPLVVDSADVRQDPEGTLTALCAALGLPFTEAMLRWPAGG 180

Query: 186 KAIDGVWAPWWYKTVHRSTAFEAPRKYPLPFPFNLY-DLLEQTIPLYNFL 234
              DGVWAP WY  VH S+ FE P + PLP     Y DL  Q +P Y  L
Sbjct: 181 HKADGVWAPHWYGAVHLSSGFEDP-EGPLPDLAPHYADLARQALPHYERL 229


Lambda     K      H
   0.319    0.137    0.411 

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: 334
Number of extensions: 17
Number of successful extensions: 4
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: 555
Length of database: 236
Length adjustment: 29
Effective length of query: 526
Effective length of database: 207
Effective search space:   108882
Effective search space used:   108882
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 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Apr 16 2024. The underlying query database was built on Apr 09 2024.

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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