GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysN in Collimonas arenae Ter10

Align L-2-aminoadipate aminotransferase monomer (EC 2.6.1.39) (characterized)
to candidate WP_061533103.1 CAter10_RS08670 PLP-dependent aminotransferase family protein

Query= metacyc::MONOMER-6727
         (397 letters)



>NCBI__GCF_001584165.1:WP_061533103.1
          Length = 397

 Score =  344 bits (882), Expect = 3e-99
 Identities = 182/396 (45%), Positives = 261/396 (65%), Gaps = 18/396 (4%)

Query: 3   PLSWSEAFGKSAGRIQASTIRELLKLTQRPGILSFAGGLPAPELFPKEEAAEAAARILRE 62
           PL W   F + A ++Q+S IRE+LK+T RP I+SFAGGLP+P  FP E+   A  ++L E
Sbjct: 8   PLEWR--FSERAQKLQSSAIREILKITMRPEIISFAGGLPSPATFPVEQLKVAFDKVLSE 65

Query: 63  KGEVALQYSPTEGYAPLRAFVAEWIG-----VRPEEVLITTGSQQALDLVGKVFLDEGSP 117
           +G+VALQY PT+GY PLR +VA+ +      + P +VL+T+GSQQ LDL+GKV +DEGS 
Sbjct: 66  QGKVALQYGPTDGYGPLREWVADSLSTNGAKILPNQVLMTSGSQQGLDLLGKVLIDEGSK 125

Query: 118 VLLEAPSYMGAIQAFRLQGPRFLTVPAGEEGPDLDALEEVLKR--ERPRFLYLIPSFQNP 175
           VL+E PSY+GA+QAF L GP F++VP+ E G     L E +    +  R LY +P+FQNP
Sbjct: 126 VLVETPSYLGALQAFSLYGPEFVSVPSDEGG----LLPETVATLGQGARMLYALPNFQNP 181

Query: 176 TGGLTPLPARKRLLQMVMERGLVVVEDDAYRELYFGEARLPSLFELAREAGYPGVIYLGS 235
           TG    +  R  L+ +    GL ++EDD Y  L +    LP +  L+   G  GVIY+GS
Sbjct: 182 TGRTLSVERRHALVDICARLGLPLIEDDPYGALSYRTEPLPKM--LSMNPG--GVIYMGS 237

Query: 236 FSKVLSPGLRVAFAVAHPEALQKLVQAKQGADLHTPMLNQMLVHELLKEGF-SERLERVR 294
           FSK+L+PG+R+ + VA    ++KL QAKQ  DLHT  L QM+V+  +K+GF +E +  +R
Sbjct: 238 FSKILTPGIRLGYVVAPRPLIEKLEQAKQATDLHTAQLTQMVVYNTIKDGFLNEHIPTIR 297

Query: 295 RVYREKAQAMLHALDREVPKEVRYTRPKGGMFVWMELPKGLSAEGLFRRALEENVAFVPG 354
           ++Y ++  AML AL    P E  +T+P+GGMF+W+ LPK + +  L   A++++VAFVPG
Sbjct: 298 KLYSDQCDAMLDALKTYFPSECSWTKPEGGMFIWVTLPKHIDSMKLLDEAVQQHVAFVPG 357

Query: 355 GPFFANGGGENTLRLSYATLDREGIAEGVRRLGRAL 390
            PF+ N   ++TLRLS+ T+    I EG+ RLG+ +
Sbjct: 358 APFYGNTPEKHTLRLSFVTVPPAKIREGIERLGKLI 393


Lambda     K      H
   0.320    0.139    0.401 

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: 516
Number of extensions: 26
Number of successful extensions: 5
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: 397
Length of database: 397
Length adjustment: 31
Effective length of query: 366
Effective length of database: 366
Effective search space:   133956
Effective search space used:   133956
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 Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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