Alignments for a candidate for ilvE in Phyllobacterium endophyticum PEPV15

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvE in Phyllobacterium endophyticum PEPV15

Align Branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_106716187.1 CU100_RS08590 PLP-dependent aminotransferase family protein

Query= reanno::azobra:AZOBR_RS06555
         (404 letters)



>NCBI__GCF_003010935.1:WP_106716187.1
          Length = 411

 Score =  405 bits (1040), Expect = e-117
 Identities = 207/400 (51%), Positives = 272/400 (68%), Gaps = 6/400 (1%)

Query: 4   DWGNVFAGRVAGMGASEIRELLKLLERPEIISFAGGIPDPDFFPTAAIARAYEKIFQSNS 63
           DW   ++ R   M ASE+RELLKLL++P+IISFAGGIPDP  FP  AI  AY  +   N+
Sbjct: 3   DWDARYSARTGKMRASEVRELLKLLDQPDIISFAGGIPDPALFPKEAIKEAYSAVLDENA 62

Query: 64  GAGGALQYTISEGFTPLREWICAYLGRRGIQAGLDEVLVTSGSQQALEFVGKLLIGPGEK 123
            A  ALQY++SEG+ PLR+W+  ++   G+   +D +++T+GSQQAL+++GKL I PG+ 
Sbjct: 63  DA--ALQYSVSEGYKPLRQWLVQHMAALGVACTIDNIIITTGSQQALDYLGKLFISPGDT 120

Query: 124 ILVTRPTYLGALQAFSPYEPQY--LSVPGDAEGPDLAAVEA-ALEQKPKFFYLVPDFQNP 180
           IL T PTYLGALQAF+ YEP+Y  L   G    PD     A A   + +  YL  DF NP
Sbjct: 121 ILTTWPTYLGALQAFNAYEPRYDRLIPEGGNTTPDAYRTNAQAAGGRVRLAYLTGDFSNP 180

Query: 181 NGTTISLARREALLDLCAKHGVPIVEDAAYTELRYEGEPIPSMVALDAARNGG-KITNVL 239
            G TI    R  L++L  +  +P++EDAAY  LRYEGE  PSM+ALD  R G    T VL
Sbjct: 181 TGETIGRKERVKLVELAHELDIPLIEDAAYRVLRYEGENAPSMLALDIEREGHIDRTRVL 240

Query: 240 FCGSFSKTMVPALRVGWINGPAEVINRLVLMKQAGDLHTSTINQIVLHDVVSQNFDSHIR 299
           + GSFSK++ P LRVGW+     VI +LVL+KQA DLH+ TINQ+V+H V  ++FD+ + 
Sbjct: 241 YSGSFSKSLTPGLRVGWVCAAQPVIAKLVLIKQAADLHSPTINQMVIHHVAERHFDAQVE 300

Query: 300 RLRAGYKERRDAMLTALSEFAPAGVTWTKPEGGMFVWIELPEGTDGVDLLARAIKDANVA 359
           + R  Y++RRD ML AL+   P GVTWT+PEGGMFVW+ LP+G DG  LLAR+++   VA
Sbjct: 301 KARGHYRQRRDHMLGALARHMPEGVTWTRPEGGMFVWMTLPDGMDGAALLARSVEQIRVA 360

Query: 360 FVPGSAFHADRSGKNTLRLSFSNNNPERIREGIRRLCGLL 399
           FVPG AFHAD +G NT+RL+FS  N E I  G++RL GL+
Sbjct: 361 FVPGVAFHADGTGGNTIRLNFSLPNAEAIETGMQRLGGLI 400


Lambda     K      H
   0.320    0.138    0.410 

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: 507
Number of extensions: 20
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: 404
Length of database: 411
Length adjustment: 31
Effective length of query: 373
Effective length of database: 380
Effective search space:   141740
Effective search space used:   141740
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 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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 2024 update 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 original 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