GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysN in Williamsia sterculiae CPCC 203464

Align L-2-aminoadipate aminotransferase monomer (EC 2.6.1.39) (characterized)
to candidate WP_076477443.1 BW971_RS04965 PLP-dependent aminotransferase family protein

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



>NCBI__GCF_900156495.1:WP_076477443.1
          Length = 389

 Score =  247 bits (630), Expect = 5e-70
 Identities = 151/389 (38%), Positives = 218/389 (56%), Gaps = 19/389 (4%)

Query: 12  KSAGRIQASTIRELLKLTQRPGILSFAGGLPAPELFPKEEAAEAAARILREKGEVALQYS 71
           ++   I+ S IR+LL++T+RP +LS AGGLPA +L P +  AEAA+R++ E    ALQY+
Sbjct: 10  RALSSIRGSAIRDLLRVTERPDVLSMAGGLPATDLIPSDRIAEAASRVISEAS--ALQYT 67

Query: 72  PTEGYAPLRAFVAEWIGVRPEEVLITTGSQQALDLVGKVFLDEGSPVLLEAPSYMGAIQA 131
            + G  PLR  VA+  G  PE VLIT GSQQAL L  +  LD G  V+++ P Y+GA+Q 
Sbjct: 68  VSAGVRPLREVVADRDGTHPERVLITHGSQQALFLSAQALLDPGDTVIVDDPVYVGALQV 127

Query: 132 FRLQGPRFLTVPAGEEGPDLDALEEVLK-RERPRFLYLIPSFQNPTGGLTPLPARKRLLQ 190
           F+      + +P   EG D+D LE +L    RPR ++ + +F NP G       R+RL +
Sbjct: 128 FQSVRAEIVALPITAEGTDVDRLERLLSDGVRPRIVHTVSNFHNPAGVTASARTRRRLAE 187

Query: 191 MVMERGLVVVEDDAYRELYFGEARLPSLFELAREAGYPG--VIYLGSFSKVLSPGLRVAF 248
           +  + G  ++EDD Y +L F    +  +         PG  VI LGS SK+L+P LRV +
Sbjct: 188 LAADHGFWIIEDDPYGQLRFAGRSMDPI---------PGDRVIRLGSASKILAPALRVGW 238

Query: 249 AVAHPEALQKLVQAKQGADLHTPMLNQMLVHELLKEG--FSERLERVRRVYREKAQAMLH 306
             A P+ ++ +   +QGADL      Q++  +LL +    +  +  +RR Y  +A A+  
Sbjct: 239 LQASPDVVELVELLRQGADLCGSTFAQLMTADLLGDSDFMTAHVSDLRREYARRAAALTG 298

Query: 307 AL--DREVPKEVRYTRPKGGMFVWMELPKGLSAEGLFRRALEENVAFVPGGPFFANGGGE 364
           AL  D      V +  P+GGMF W+ LP GL    L   A+   VAFVPG  F  + G  
Sbjct: 299 ALRTDLGAVCGVEFIEPEGGMFCWLRLP-GLDTAILLDHAVRAGVAFVPGAAFAVDAGLG 357

Query: 365 NTLRLSYATLDREGIAEGVRRLGRALKGL 393
           + LRLS+ATL  + + E VRRL  A+  L
Sbjct: 358 DRLRLSFATLSPDQLTEAVRRLATAVHDL 386


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: 339
Number of extensions: 18
Number of successful extensions: 6
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: 389
Length adjustment: 31
Effective length of query: 366
Effective length of database: 358
Effective search space:   131028
Effective search space used:   131028
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