GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cycA in Corynebacterium deserti GIMN1.010

Align D-serine/D-alanine/glycine transporter (characterized)
to candidate WP_082353324.1 CDES_RS02405 D-serine/D-alanine/glycine transporter

Query= SwissProt::P0AAE0
         (470 letters)



>NCBI__GCF_001277995.1:WP_082353324.1
          Length = 468

 Score =  617 bits (1590), Expect = 0.0
 Identities = 298/459 (64%), Positives = 365/459 (79%)

Query: 11  DQAPAEQSLRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFV 70
           D A  +  L R L+NRH+QLIAIGGAIGTGLFMGSGKTIS+AGPS+I VY IIGFMLFFV
Sbjct: 3   DNAAPDTHLHRGLSNRHLQLIAIGGAIGTGLFMGSGKTISVAGPSVILVYAIIGFMLFFV 62

Query: 71  MRAMGELLLSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWF 130
           MRAMGELLL+NL YKS  D  SD+LGP AG+ TGWTYWFCW+ TGMAD+VAIT Y Q+W+
Sbjct: 63  MRAMGELLLANLNYKSLRDAVSDILGPGAGFVTGWTYWFCWIATGMADIVAITGYTQYWW 122

Query: 131 PDLSDWVASLAVIVLLLTLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHFQSP 190
           P++  W+  +  I++L  LNLA V++FGEMEFWFA+IKIVAIV+LI VG  MV   F +P
Sbjct: 123 PEIPLWLPGVLTIIVLFALNLAAVRLFGEMEFWFAIIKIVAIVALIAVGFFMVITAFGAP 182

Query: 191 TGVEASFAHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAIN 250
            G  ASF +L   GG+FP G++GF AGFQIA+FAFVGIEL GT AAETKDPE +LPRAIN
Sbjct: 183 NGTTASFNNLIEHGGFFPNGITGFLAGFQIAIFAFVGIELAGTAAAETKDPETTLPRAIN 242

Query: 251 SIPIRIIMFYVFALIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSAASS 310
           SIPIRI++FYV AL VIM VTPW+ V P+ SPFV++F L G+PAAA +INFVV+TSAASS
Sbjct: 243 SIPIRIVVFYVLALAVIMMVTPWNEVSPDNSPFVQMFALAGIPAAAGIINFVVITSAASS 302

Query: 311 ANSGVFSTSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVMLYVNPSVIG 370
           ANSG+FSTSRML+GL+ EG APK +  LSKR VPA+GLTFS +CL+  V +LY   +VI 
Sbjct: 303 ANSGIFSTSRMLYGLSLEGAAPKRWGVLSKRQVPARGLTFSVLCLIPAVGLLYAGGTVIE 362

Query: 371 AFTMITTVSAILFMFVWTIILCSYLVYRKQRPHLHEKSIYKMPLGKLMCWVCMAFFVFVV 430
           AFT+ITTVS++LFM VW+ IL +Y+VYR++ P LHEKS++KMP G +M  V + FFV ++
Sbjct: 363 AFTLITTVSSVLFMVVWSYILVAYIVYRRRNPELHEKSVFKMPGGVVMAVVVLVFFVAML 422

Query: 431 VLLTLEDDTRQALLVTPLWFIALGLGWLFIGKKRAAELR 469
            +L+LE DTR ALL TP+WFI LG+GW   G  + A+ R
Sbjct: 423 GVLSLETDTRTALLATPVWFIILGVGWFATGGAKGAQRR 461


Lambda     K      H
   0.329    0.141    0.440 

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: 745
Number of extensions: 12
Number of successful extensions: 1
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: 470
Length of database: 468
Length adjustment: 33
Effective length of query: 437
Effective length of database: 435
Effective search space:   190095
Effective search space used:   190095
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 51 (24.3 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