GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Sphingobium czechense LL01

Align phosphotransacetylase (EC 2.3.1.8) (characterized)
to candidate WP_066607556.1 V473_RS16165 NADP-dependent malic enzyme

Query= metacyc::MONOMER-13062
         (328 letters)



>NCBI__GCF_001046645.1:WP_066607556.1
          Length = 753

 Score =  145 bits (367), Expect = 2e-39
 Identities = 98/306 (32%), Positives = 149/306 (48%), Gaps = 6/306 (1%)

Query: 17  KLVFPEGEDERIISAASRLANDDLAIPVLLGNEAEIKKTADALNVSLDGIEIVDIENVPG 76
           ++VF E E+E ++ AA +       IPVL+G    ++K  +      +  E+ +  N P 
Sbjct: 447 RVVFAEAEEEVVLRAAIQFRELGYGIPVLVGRGDVVEKLKELGVRDPESFELHNSVNSP- 505

Query: 77  EVRQQMVQAIVER--RKGKTTADQAAQWLKDPNYFGTTMVYMDDVDGMVSGAAHPTGDTV 134
            +   MV  +  R  R+G    D      +D N FGT +V M   D M++G   P   T+
Sbjct: 506 -LVPDMVDMLYARLQRRGYLRRDCERMVNRDRNIFGTLLVKMGVADAMITGMTRPYAQTL 564

Query: 135 RPALQIIKTKPGVNLISGSFVMQKGDQRYLFADCAININPNETQLAEIAVESGKTARLFD 194
           R   +++    G     G  VM   D+    AD  +N  P  ++LA+IA  +   AR   
Sbjct: 565 REVKRVMDPAAGRTPF-GIHVMVAKDKTVFLADTTVNERPTASELADIAEGTVAVARRMG 623

Query: 195 IDPRVALLSFSTNGSAKSPEVEKVHNATKLAQEMDPAMPIDGEMQFDAAFVPAVAKAKYS 254
           +DPRVA LS+S  G+     +E V  A KL  E       +GEM  D A  PAV K  Y 
Sbjct: 624 VDPRVAFLSYSNFGNPPGAFLENVRGAVKLLDERAVDFEYEGEMTADVALNPAVMK-NYP 682

Query: 255 DSKVAGHATVFVFPELQSGNIGYKIAQRMGGFEAIGPILQGLNKPVSDLSRGCNAEDVYK 314
            S+++G A + V P LQS NI  K+ + +GG   IGP+L G+ K V   +   NA ++  
Sbjct: 683 FSRLSGPANILVMPGLQSANISAKLLRELGGTSMIGPVLVGMEKSVQIATMSSNASELLT 742

Query: 315 VSIITA 320
           ++++ A
Sbjct: 743 LAVLAA 748


Lambda     K      H
   0.315    0.133    0.369 

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: 23
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: 328
Length of database: 753
Length adjustment: 34
Effective length of query: 294
Effective length of database: 719
Effective search space:   211386
Effective search space used:   211386
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 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