Alignments for a candidate for ilvE in Rhodobacter sphaeroides ATCC 17029

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvE in Rhodobacter sphaeroides ATCC 17029

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

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_043828198.1 RSPH17029_RS14495 hypothetical protein

Query= BRENDA::A0A0A0LJI6
         (555 letters)



>NCBI__GCF_000015985.1:WP_043828198.1
          Length = 240

 Score =  164 bits (416), Expect = 3e-45
 Identities = 92/232 (39%), Positives = 134/232 (57%), Gaps = 5/232 (2%)

Query: 7   IHLWSTPRSLSTSLMYSFAQRDDMEVLDEPLYANFLRVTGYDRPYREELLSKMEPDGNKV 66
           I +WS PR+LST++MYSFA R D  + DEP YA +L+ TG D P R E+L+  E D + +
Sbjct: 3   IAMWSGPRNLSTAMMYSFAARGDCGIWDEPFYAAYLKATGIDHPMRAEILAAHETDASVI 62

Query: 67  IKEIIF-APGEKKFRFCKHIAKQKVPGLASDLMKKGRHFILIRNPLDILPSYDKVIPA-S 124
                  AP  +   + KH+    +P      M+   +  LIR+P  ++ SY K     S
Sbjct: 63  ADRCRGEAPLGEPIFYQKHMTLHMIPSFDRGFMRDCENVFLIRHPARVVASYAKKREGPS 122

Query: 125 FSELGFSELVSIYNELKE-LGRLPPIIDAAELQKNPEATLRGLCEELGIPFQHKMLKWEA 183
            +++GF +   +++E+ + LGR P ++D+A+++++PE TL  LC  LG+PF   ML+W A
Sbjct: 123 LADIGFVQQAELFDEVAQWLGRPPLVVDSADVRQDPEGTLTALCAALGLPFTEAMLRWPA 182

Query: 184 GPKAIDGVWAPWWYKTVHRSTAFEAPRKYPLPFPFNLY-DLLEQTIPLYNFL 234
           G    DGVWAP WY  VH S+ FE P + PLP     Y DL  Q +P Y  L
Sbjct: 183 GGHKADGVWAPHWYGAVHLSSGFEDP-EGPLPDLAPHYADLARQALPHYERL 233


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: 340
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: 240
Length adjustment: 29
Effective length of query: 526
Effective length of database: 211
Effective search space:   110986
Effective search space used:   110986
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 10 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis