GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Caulobacter crescentus NA1000

Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase (uncharacterized)
to candidate CCNA_02704 CCNA_02704 NADP-dependent malic enzyme

Query= curated2:P39197
         (318 letters)



>FitnessBrowser__Caulo:CCNA_02704
          Length = 758

 Score =  137 bits (346), Expect = 6e-37
 Identities = 109/327 (33%), Positives = 159/327 (48%), Gaps = 26/327 (7%)

Query: 7   IHEAAKALDRHIILPEGEDPRVAEAARRLLAAGLARVTLMGGPEIPG----------AGR 56
           + E A+     +   E ED RV  A + ++  GLA   L+G  E+            AG+
Sbjct: 433 VFERARKQPVKVAYAEAEDERVLRAVQTVVDEGLAYPVLVGRREVITGKIEELGLRLAGK 492

Query: 57  ---IDPAGGPDL-AELADHWHRMRAARGM---TAERALTEMRDPIRQAAMRVRLGQADGT 109
              IDP    DL A L   + R+   RG+    AER +T  R     A+M +  G  +  
Sbjct: 493 VEIIDPQADKDLFAPLIADYQRLVGRRGVPPIAAERRVTGRRTVA--ASMLLATGYVEAA 550

Query: 110 VGGAVATTADTVRAALQIIGKAPGAGIVSSFFLMLSCGPGAPVRGGMIFADCGLVIQPDA 169
           + G        ++ AL II   P    VS  + M S       +G + F D  + + P A
Sbjct: 551 LVGGSGDWWQHMKYALPII---PRRDNVSRVYAMSSL---ILDKGTLFFCDTHVNVDPTA 604

Query: 170 RELAAIALSAADSCRRILAEEPRVALLSFSTAGSAEHPSLGRIREALALIRAAAPGLEVD 229
            ++A     AA++ RR     P+ ALLS S+ G+++ P+  ++REALAL+R  AP LEVD
Sbjct: 605 EQIAECTQLAAEAVRRF-GLTPKAALLSHSSFGASDSPTARKMREALALLRTQAPDLEVD 663

Query: 230 GEMQFDAALDEAIRARKAPESPLTGRPNVFVFPDLADGNIGYKIAERLAGLTAIGPILQG 289
           GEM  DAAL + +R R   +SPL G  N+ V P L   NIG  +         +GP+L G
Sbjct: 664 GEMHADAALSQHLRDRMVADSPLKGSANLLVMPTLDAANIGLTLLSAATESLLVGPVLLG 723

Query: 290 LAKPANDLSRACSVKDIVNATAITAMQ 316
           +AKP + L  + + + IVN TA+   Q
Sbjct: 724 MAKPLHVLIPSVTARGIVNLTALAVNQ 750


Lambda     K      H
   0.320    0.136    0.391 

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: 440
Number of extensions: 15
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: 318
Length of database: 758
Length adjustment: 34
Effective length of query: 284
Effective length of database: 724
Effective search space:   205616
Effective search space used:   205616
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: 52 (24.6 bits)

This GapMind analysis is from Sep 17 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