GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Rhizobium etli CFN 42

Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase (uncharacterized)
to candidate WP_011423771.1 RHE_RS01970 NADP-dependent malic enzyme

Query= curated2:Q8CJR5
         (697 letters)



>NCBI__GCF_000092045.1:WP_011423771.1
          Length = 760

 Score =  158 bits (400), Expect = 8e-43
 Identities = 109/316 (34%), Positives = 162/316 (51%), Gaps = 5/316 (1%)

Query: 371 LLEQARSDLRRVVLPEGTEERVLHAAEVLLRRGVCELTLLGPVEQIRKKAADLGIDLG-- 428
           L E+ R   +R+V  E  EE+VL AA     + +    LLG  + IR  A   GIDL   
Sbjct: 443 LYERVRRRPKRIVFAEAEEEQVLRAALSYANQQLGTALLLGREDLIRATAERAGIDLNRP 502

Query: 429 GAELIDPAASELRDSFAEKYAALRAHKGVTVELAYDVV-SDVNYFGTLMVQEGFADGMVS 487
           G E+++   S   +++ +   A    +G     A  ++ +D N+F   MV  G ADGMV+
Sbjct: 503 GLEIVNARISTRVEAYIDYLYARLQRQGYLHRDAQRLIHNDRNHFAATMVALGDADGMVT 562

Query: 488 GSVHSTAATIRPAFEIIKTKPDAAIVSSVFFMCLADKVLVYGDCAVNPDPDAEQLADIAT 547
           G   + +  +      I  KP   ++     +C    V V  D AV+  P AEQLADIA 
Sbjct: 563 GITRNYSTALEDVRRCIDEKPGHRVIGVSLALCRGRTVFV-ADTAVHDMPTAEQLADIAE 621

Query: 548 QSASTAAQFGVEPRIAMLSYSTGTSGSGADVDKVREATELVRSRRPDLSVEGPIQYDAAV 607
           ++A  A + G  PR+AML+YST    SG   ++VREA +++  RR D   +G +  D A+
Sbjct: 622 EAAGLARRMGYPPRVAMLAYSTFGHPSGERSERVREAVKILDRRRVDFEYDGEMAADVAL 681

Query: 608 EPSVAATKLPGSAVAGQASVLIFPDLNTGNNTYKAVQRSAGAIAVGPVLQGLRKPVNDLS 667
              V   + P   ++G A+VL+ P  ++ + + K +Q   G+  +GP+L GL KPV   S
Sbjct: 682 NRKV-MEQYPFCRLSGPANVLVMPAFHSASISTKMLQELGGSTVIGPILVGLDKPVQITS 740

Query: 668 RGALVQDIVNTVAITA 683
            GA   DIVN  AI A
Sbjct: 741 MGAKDSDIVNMAAIAA 756


Lambda     K      H
   0.318    0.134    0.378 

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: 1161
Number of extensions: 60
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: 697
Length of database: 760
Length adjustment: 40
Effective length of query: 657
Effective length of database: 720
Effective search space:   473040
Effective search space used:   473040
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 (21.7 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Apr 09 2024. 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