GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Magnetospirillum magneticum AMB-1

Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase (uncharacterized)
to candidate WP_043745954.1 AMB_RS03695 NADP-dependent malic enzyme

Query= curated2:P39197
         (318 letters)



>NCBI__GCF_000009985.1:WP_043745954.1
          Length = 760

 Score =  135 bits (340), Expect = 3e-36
 Identities = 99/334 (29%), Positives = 161/334 (48%), Gaps = 26/334 (7%)

Query: 1   MKPLDRIHEAAKALDRHIILPEGEDPRVAEAARRLLAAGLARVTLMGGPEI--------- 51
           MKP   + + A+   R ++  EGE  RV  AA+ ++  GLAR  L+G  E+         
Sbjct: 430 MKP---VFDRARQDMRRVVYCEGEGRRVLHAAQTVVDEGLARPVLIGRREVVEKRIQDLD 486

Query: 52  ------PGAGRIDPAGGPDLAELADHWHRMRAARGMTAERALTEMRDPIRQ-AAMRVRLG 104
                       DP   P   E    +H +   +G++ E A T +R        + ++  
Sbjct: 487 LRLRIDQDFDLCDPEDDPRFNEYWRLYHSIMERQGVSPEYARTVVRTRNTVIGTLMLKRK 546

Query: 105 QADGTVGGAVATTADTVRAALQIIGKAPGAGIVSSFFLMLSCGPGAPVRGGMIFADCGLV 164
           + D  + G +      +   L +IG   G  + ++  L++      P+ G     D  + 
Sbjct: 547 EVDAMICGTIGRYDKHLSHILNVIGTREGVKVPAAMNLLIM-----PI-GTFFICDTYVT 600

Query: 165 IQPDARELAAIALSAADSCRRILAEEPRVALLSFSTAGSAEHPSLGRIREALALIRAAAP 224
            +P   ++  + L A++  RR    EP+VA LS +  G+ +  S  R R+ALAL+R  AP
Sbjct: 601 PEPTPEQICDMTLLASEEVRRF-GIEPKVAFLSHANFGNRQTASAQRQRDALALLREKAP 659

Query: 225 GLEVDGEMQFDAALDEAIRARKAPESPLTGRPNVFVFPDLADGNIGYKIAERLAGLTAIG 284
            LE +GEM  DAAL E IR R  P S L G  N+ V P L   NI + + +      ++G
Sbjct: 660 YLEAEGEMHGDAALSEEIRTRIFPNSKLKGAANLLVMPTLDAANISFNLLKVAGDALSVG 719

Query: 285 PILQGLAKPANDLSRACSVKDIVNATAITAMQTK 318
           PIL G+A+PA+ L+ + +V++I+N TA+ A+  +
Sbjct: 720 PILMGIAQPAHVLTPSATVRNIINITALAAVDAQ 753


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: 423
Number of extensions: 16
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: 760
Length adjustment: 34
Effective length of query: 284
Effective length of database: 726
Effective search space:   206184
Effective search space used:   206184
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